%0 Journal Article %J Nano Letters %D 2024 %T Adaptive and Dissipative Hierarchical Population Crowding of Synthetic Protocells through Click-PISA under Gradient Energy Inputs %A Pearce, Samuel %A Chenyu Lin %A Juan Pérez-Mercader %X The ability of living objects to respond rapidly en masse to various stimuli or stress is an important function in response to externally applied changes in the local environment. This occurs across many length scales, for instance, bacteria swarming in response to different stimuli or stress and macromolecular crowding within cells. Currently there are few mechanisms to induce similar autonomous behaviors within populations of synthetic protocells. Herein, we report a system in which populations of individual objects behave in a coordinated manner in response to changes in the energetic environment by the emergent self-organization of large object swarms. These swarms contain protocell populations of approximately 60 000 individuals. We demonstrate the dissipative nature of the hierarchical constructs, which persist under appropriate UV stimulation. Finally, we identify the ability of the object populations to change behaviors in an adaptive population-wide response to the local energetic environment. %B Nano Letters %V 24 %P 2457–2464 %G eng %U https://doi.org/10.1021/acs.nanolett.3c04035 %N 8 %R 10.1021/acs.nanolett.3c04035 %0 Journal Article %J Nature Ecology & Evolution %D 2024 %T Adaptive tail-length evolution in deer mice is associated with differential Hoxd13 expression in early development %A Kingsley, Evan P. %A Hager, Emily R. %A Lassance, Jean-Marc %A Turner, Kyle M. %A Harringmeyer, Olivia S. %A Kirby, Christopher %A Neugeboren, Beverly I. %A Hoekstra, Hopi E. %K Evolutionary developmental biology %K Evolutionary genetics %X Variation in the size and number of axial segments underlies much of the diversity in animal body plans. Here we investigate the evolutionary, genetic and developmental mechanisms driving tail-length differences between forest and prairie ecotypes of deer mice (Peromyscus maniculatus). We first show that long-tailed forest mice perform better in an arboreal locomotion assay, consistent with tails being important for balance during climbing. We then identify six genomic regions that contribute to differences in tail length, three of which associate with caudal vertebra length and the other three with vertebra number. For all six loci, the forest allele increases tail length, indicative of the cumulative effect of natural selection. Two of the genomic regions associated with variation in vertebra number contain Hox gene clusters. Of those, we find an allele-specific decrease in Hoxd13 expression in the embryonic tail bud of long-tailed forest mice, consistent with its role in axial elongation. Additionally, we find that forest embryos have more presomitic mesoderm than prairie embryos and that this correlates with an increase in the number of neuromesodermal progenitors, which are modulated by Hox13 paralogues. Together, these results suggest a role for Hoxd13 in the development of natural variation in adaptive morphology on a microevolutionary timescale. %B Nature Ecology & Evolution %P 1–15 %8 feb %G eng %U https://www.nature.com/articles/s41559-024-02346-3 %R 10.1038/s41559-024-02346-3 %0 Journal Article %J PNAS Nexus %D 2024 %T Backpack-mediated anti-inflammatory macrophage cell therapy for the treatment of traumatic brain injury %A Kapate, Neha %A Liao, Rick %A Sodemann, Ryan Luke %A Stinson, Tawny %A Prakash, Supriya %A Kumbhojkar, Ninad %A Suja, Vineeth Chandran %A Lily Li-Wen Wang %A Flanz, Mikayla %A Rajeev, Rohan %A Villafuerte, Dania %A Shaha, Suyog %A Janes, Morgan %A Park, Kyung Soo %A Dunne, Michael %A Golemb, Bryan %A Hone, Alexander %A Adebowale, Kolade %A Clegg, John %A Slate, Andrea %A McGuone, Declan %A Costine-Bartell, Beth %A Mitragotri, Samir %X Traumatic brain injury (TBI) is a debilitating disease with no current therapies outside of acute clinical management. While acute, controlled inflammation is important for debris clearance and regeneration after injury, chronic, rampant inflammation plays a significant adverse role in the pathophysiology of secondary brain injury. Immune cell therapies hold unique therapeutic potential for inflammation modulation, due to their active sensing and migration abilities. Macrophages are particularly suited for this task, given the role of macrophages and microglia in the dysregulated inflammatory response after TBI. However, maintaining adoptively transferred macrophages in an anti-inflammatory, wound-healing phenotype against the proinflammatory TBI milieu is essential. To achieve this, we developed discoidal microparticles, termed backpacks, encapsulating anti-inflammatory interleukin-4, and dexamethasone for ex vivo macrophage attachment. Backpacks durably adhered to the surface of macrophages without internalization and maintained an anti-inflammatory phenotype of the carrier macrophage through 7 days in vitro. Backpack–macrophage therapy was scaled up and safely infused into piglets in a cortical impact TBI model. Backpack–macrophages migrated to the brain lesion site and reduced proinflammatory activation of microglia in the lesion penumbra of the rostral gyrus of the cortex and decreased serum concentrations of proinflammatory biomarkers. These immunomodulatory effects elicited a 56% decrease in lesion volume. The results reported here demonstrate, to the best of our knowledge, a potential use of a cell therapy intervention for a large animal model of TBI and highlight the potential of macrophage-based therapy. Further investigation is required to elucidate the neuroprotection mechanisms associated with anti-inflammatory macrophage therapy. %B PNAS Nexus %V 3 %P pgad434 %G eng %U https://doi.org/10.1093/pnasnexus/pgad434 %N 1 %R 10.1093/pnasnexus/pgad434 %0 Journal Article %J Science Advances %D 2023 %T Biochemically functionalized probes for cell-type–specific targeting and recording in the brain %A Anqi Zhang %A Theodore J. Zwang %A Charles M. Lieber %X Selective targeting and modulation of distinct cell types and neuron subtypes is central to understanding complex neural circuitry and could enable electronic treatments that target specific circuits while minimizing off-target effects. However, current brain-implantable electronics have not yet achieved cell-type specificity. We address this challenge by functionalizing flexible mesh electronic probes, which elicit minimal immune response, with antibodies or peptides to target specific cell markers. Histology studies reveal selective association of targeted neurons, astrocytes, and microglia with functionalized probe surfaces without accumulating off-target cells. In vivo chronic electrophysiology further yields recordings consistent with selective targeting of these cell types. Last, probes functionalized to target dopamine receptor 2 expressing neurons show the potential for neuron-subtype–specific targeting and electrophysiology. %B Science Advances %V 9 %P eadk1050 %G eng %U https://www.science.org/doi/full/10.1126/sciadv.adk1050 %N 48 %R 10.1126/sciadv.adk1050 %0 Journal Article %J Acta Neuropathol Commun %D 2023 %T CD8 cytotoxic T-cell infiltrates and cellular damage in the hypothalamus in human obesity %A Ahrendsen, J. T. %A Nong, Y. %A Huo, Y. %A Steele, J. %A Anderson, M. P. %K Animals Humans Mice Arcuate Nucleus of Hypothalamus/metabolism CD8-Positive T-Lymphocytes Hypothalamus/metabolism *Pediatric Obesity/metabolism T-Lymphocytes CD8 T cell Hypothalamus Inflammation Obesity %X Rare cases of paraneoplastic obesity in children suggest sporadic obesity might also arise from an adaptive immune cell-mediated mechanism. Since the hypothalamus is a central regulator of feeding behavior and energy expenditure, we quantified lymphocytic inflammation in this region in a cohort of obese and non-obese human post-mortem brains. We report that CD8-positive cytotoxic T-cells are increased in hypothalamic median eminence/arcuate nucleus (ME/Arc) and bed nucleus of the stria terminalis in 40% of obese compared to non-obese patients, but not in other hypothalamic nuclei or brain regions. CD8 T-cells were most abundant in individuals with concurrent obesity and diabetes. Markers of cytotoxic T-cell induced damage, activated caspase 3 and poly-ADP ribose, were also elevated in the ME/Arc of obese patients. To provoke CD8 cytotoxic T-cell infiltrates in ventromedial region of hypothalamus in mice we performed stereotactic injections of an adeno-associated virus expressing immunogenic green fluorescent protein or saline. AAV but not saline injections triggered hypothalamic CD8 T-cell infiltrates associated with a rapid weight gain in mice recapitulating the findings in human obesity. This is the first description of the neuropathology of human obesity and when combined with its reconstitution in a mouse model suggests adaptive immunity may drive as much as 40% of the human condition. %B Acta Neuropathol Commun %V 11 %P 163 %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/37814324 %N 1 %9 Journal Article %R 10.1186/s40478-023-01659-x %0 Journal Article %J Nat Neurosci %D 2023 %T Dissociating the contributions of sensorimotor striatum to automatic and visually guided motor sequences %A Mizes, K. G. C. %A Lindsey, J. %A Escola, G. S. %A Olveczky, B. P. %K Rats Animals *Corpus Striatum/physiology *Basal Ganglia/physiology Movement/physiology Neostriatum Motor Skills Psychomotor Performance/physiology %X The ability to sequence movements in response to new task demands enables rich and adaptive behavior. However, such flexibility is computationally costly and can result in halting performances. Practicing the same motor sequence repeatedly can render its execution precise, fast and effortless, that is, 'automatic'. The basal ganglia are thought to underlie both types of sequence execution, yet whether and how their contributions differ is unclear. We parse this in rats trained to perform the same motor sequence instructed by cues and in a self-initiated overtrained, or 'automatic,' condition. Neural recordings in the sensorimotor striatum revealed a kinematic code independent of the execution mode. Although lesions reduced the movement speed and affected detailed kinematics similarly, they disrupted high-level sequence structure for automatic, but not visually guided, behaviors. These results suggest that the basal ganglia are essential for 'automatic' motor skills that are defined in terms of continuous kinematics, but can be dispensable for discrete motor sequences guided by sensory cues. %B Nat Neurosci %V 26 %P 1791-1804 %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/37667040 %N 10 %9 Journal Article %R 10.1038/s41593-023-01431-3 %0 Journal Article %J Applied Physics Reviews %D 2023 %T Dynamics of macrophage tumor infiltration %A Adebowale, K. %A Guerriero, J. L. %A Mitragotri, S. %K monocyte-derived macrophages in-vivo adoptive immunotherapy 3d culture migration tumorigenesis mechanisms plasticity cells %X Long-term remission in cancer patients treated with ex vivo bona fide M1-induced macrophages has been poor, and the reasons behind this are not understood. Injected M1 macrophages must physically migrate to tumors to execute their role that leads to a therapeutic benefit. However, the trafficking of macrophages to tumors has not been rigorously studied. We hypothesized that trafficking capabilities of macrophages are impacted when naive M0 macrophages are converted into an M1 phenotype for macrophage therapy. To test this, we developed a three-dimensional assay comprising a tumor spheroid and macrophages to quantify macrophage tumor transport. Cell migration, permeability, and kinetics of tumor entry were quantitatively defined and compared between macrophage phenotypes. Our results demonstrate that compared to M0 macrophages, M1 macrophages migrate less efficiently toward the tumor spheroid and exhibit a fivefold lower tumor permeability. Live imaging data combined with unsupervised machine learning algorithms reveal that macrophage migration correlates with their shape transitions. Our studies highlight the importance of transport considerations in determining the efficacy of cell therapies. This study quantitatively demonstrates that the transport properties of macrophages in tumors depend on their phenotype. %B Applied Physics Reviews %V 10 %G eng %U ://WOS:001081926500001 %N 4 %9 Journal Article %R Artn 041402 10.1063/5.0160924 %0 Journal Article %J Nat Biomed Eng %D 2023 %T Laminin-coated electronic scaffolds with vascular topography for tracking and promoting the migration of brain cells after injury %A Yang, X. %A Qi, Y. %A Wang, C. %A Zwang, T. J. %A Rommelfanger, N. J. %A G. Hong %A Lieber, C. M. %X In the adult brain, neural stem cells are largely restricted into spatially discrete neurogenic niches, and hence areas of neuron loss during neurodegenerative disease or following a stroke or traumatic brain injury do not typically repopulate spontaneously. Moreover, understanding neural activity accompanying the neural repair process is hindered by a lack of minimally invasive devices for the chronic measurement of the electrophysiological dynamics in damaged brain tissue. Here we show that 32 individually addressable platinum microelectrodes integrated into laminin-coated branched polymer scaffolds stereotaxically injected to span a hydrogel-filled cortical lesion and deeper regions in the brains of mice promote neural regeneration while allowing for the tracking of migrating host brain cells into the lesion. Chronic measurements of single-unit activity and neural-circuit analyses revealed the establishment of spiking activity in new neurons in the lesion and their functional connections with neurons deeper in the brain. Electronic implants mimicking the topographical and surface properties of brain vasculature may aid the stimulation and tracking of neural-circuit restoration following injury. %B Nat Biomed Eng %V 7 %P 1282-1292 %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/37814007 %N 10 %9 Journal Article %R 10.1038/s41551-023-01101-6 %0 Journal Article %J Proc Natl Acad Sci U S A %D 2023 %T Molecular mechanisms controlling the biogenesis of the TGF-beta signal Vg1 %A Dingal, Pcdp %A Carte, A. N. %A Montague, T. G. %A Lim Suan, M. B., Jr. %A Schier, A. F. %K Nodal Vg1 processing retention zebrafish %X The TGF-beta signals Vg1 (Dvr1/Gdf3) and Nodal form heterodimers to induce vertebrate mesendoderm. The Vg1 proprotein is a monomer retained in the endoplasmic reticulum (ER) and is processed and secreted upon heterodimerization with Nodal, but the mechanisms underlying Vg1 biogenesis are largely elusive. Here, we clarify the mechanisms underlying Vg1 retention, processing, secretion, and signaling and introduce a Synthetic Processing (SynPro) system that enables the programmed cleavage of ER-resident and extracellular proteins. First, we find that Vg1 can be processed by intra- or extracellular proteases. Second, Vg1 can be processed without Nodal but requires Nodal for secretion and signaling. Third, Vg1-Nodal signaling activity requires Vg1 processing, whereas Nodal can remain unprocessed. Fourth, Vg1 employs exposed cysteines, glycosylated asparagines, and BiP chaperone-binding motifs for monomer retention in the ER. These observations suggest two mechanisms for rapid mesendoderm induction: Chaperone-binding motifs help store Vg1 as an inactive but ready-to-heterodimerize monomer in the ER, and the flexibility of Vg1 processing location allows efficient generation of active heterodimers both intra- and extracellularly. These results establish SynPro as an in vivo processing system and define molecular mechanisms and motifs that facilitate the generation of active TGF-beta heterodimers. %B Proc Natl Acad Sci U S A %V 120 %P e2307203120 %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/37844219 %N 43 %9 Journal Article %R 10.1073/pnas.2307203120 %0 Journal Article %J Mater Today Bio %D 2023 %T Multifunctional magnetic nanoparticles elicit anti-tumor immunity in a mouse melanoma model %A Lafuente-Gomez, N. %A de Lazaro, I. %A Dhanjani, M. %A Garcia-Soriano, D. %A Sobral, M. C. %A Salas, G. %A D. J. Mooney %A Somoza, A. %K Cancer immunotherapy Cancer vaccine Magnetic nanoparticles Nanomedicine %X Immunotherapy has emerged as a promising strategy to eradicate cancer cells. Particularly, the development of cancer vaccines to induce a potent and sustained antigen-specific T cell response has become a center of attention. Herein, we describe a novel immunotherapy based on magnetic nanoparticles (MNP) covalently modified with the OVA(254-267) antigen and a CpG oligonucleotide via disulfide bonds. The MNP-CpG-COVA significantly enhances dendritic cell activation and CD8(+) T cell antitumoral response against B16-OVA melanoma cells in vitro. Notably, the immune response induced by the covalently modified MNP is more potent and sustained over time than that triggered by the free components, highlighting the advantage of nanoformulations in immunotherapies. What is more, the nanoparticles are stable in the blood after in vivo administration and induce potent levels of systemic tumor-specific effector CD8 + T cells. Overall, our findings highlight the potential of covalently functionalized MNP to induce robust immune responses against mouse melanoma. %B Mater Today Bio %V 23 %P 100817 %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/37822453 %9 Journal Article %R 10.1016/j.mtbio.2023.100817 %0 Journal Article %J Proc Natl Acad Sci U S A %D 2023 %T A polygenic explanation for Haldane's rule in butterflies %A Xiong, T. %A Tarikere, S. %A Rosser, N. %A Li, X. %A Yago, M. %A Mallet, J. %K Animals Female *Butterflies/genetics Hybridization %K Genetic Models %K Genetic Sex Chromosomes Haldane's rule Lepidoptera Qtl hybrid incompatibility polygenic trait %X Two robust rules have been discovered about animal hybrids: Heterogametic hybrids are more unfit (Haldane's rule), and sex chromosomes are disproportionately involved in hybrid incompatibility (the large-X/Z effect). The exact mechanisms causing these rules in female heterogametic taxa such as butterflies are unknown but are suggested by theory to involve dominance on the sex chromosome. We investigate hybrid incompatibilities adhering to both rules in Papilio and Heliconius butterflies and show that dominance theory cannot explain our data. Instead, many defects coincide with unbalanced multilocus introgression between the Z chromosome and all autosomes. Our polygenic explanation predicts both rules because the imbalance is likely greater in heterogametic females, and the proportion of introgressed ancestry is more variable on the Z chromosome. We also show that mapping traits polygenic on a single chromosome in backcrosses can generate spurious large-effect QTLs. This mirage is caused by statistical linkage among polygenes that inflates estimated effect sizes. By controlling for statistical linkage, most incompatibility QTLs in our hybrid crosses are consistent with a polygenic basis. Since the two genera are very distantly related, polygenic hybrid incompatibilities are likely common in butterflies. %B Proc Natl Acad Sci U S A %V 120 %P e2300959120 %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/37856563 %N 44 %9 Journal Article %R 10.1073/pnas.2300959120 %0 Journal Article %J Elife %D 2023 %T Molecular tuning of sea anemone stinging %A He, L. S. %A Qi, Y. %A Allard, C.A.H. %A Valencia-Montoya, W.A. %A Krueger, S. P. %A Weir, K. %A A. Seminara %A Bellono, N.W. %K Animals *Sea Anemones/genetics Biological Evolution Venoms Nematostella vectensis cassiopea xamachana clytia hemisphaerica cyanea capillata exaiptasia diaphana molecular biophysics neuroscience physalia physalis structural biology %X Jellyfish and sea anemones fire single-use, venom-covered barbs to immobilize prey or predators. We previously showed that the anemone Nematostella vectensis uses a specialized voltage-gated calcium (Ca(V)) channel to trigger stinging in response to synergistic prey-derived chemicals and touch (Weir et al., 2020). Here, we use experiments and theory to find that stinging behavior is suited to distinct ecological niches. We find that the burrowing anemone Nematostella uses uniquely strong Ca(V) inactivation for precise control of predatory stinging. In contrast, the related anemone Exaiptasia diaphana inhabits exposed environments to support photosynthetic endosymbionts. Consistent with its niche, Exaiptasia indiscriminately stings for defense and expresses a Ca(V) splice variant that confers weak inactivation. Chimeric analyses reveal that Ca(V)beta subunit adaptations regulate inactivation, suggesting an evolutionary tuning mechanism for stinging behavior. These findings demonstrate how functional specialization of ion channel structure contributes to distinct organismal behavior. %B Elife %V 12 %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/37906220 %9 Journal Article %R 10.7554/eLife.88900 %0 Journal Article %J Proc Natl Acad Sci U S A %D 2023 %T A backpack-based myeloid cell therapy for multiple sclerosis %A Kapate, N. %A Dunne, M. %A Kumbhojkar, N. %A Prakash, S. %A Wang, L. L. %A Graveline, A. %A Park, K.S. %A Chandran Suja, V. %A Goyal, J. %A Clegg, J. R. %A Mitragotri, S. %K Autoimmune %K Experimental Central Nervous System Monocytes Mice %K Inbred C57BL Cns Immunoengineering macrophages myeloid phenotype %K Mice Animals *Multiple Sclerosis/therapy Myeloid Cells *Encephalomyelitis %X Multiple sclerosis (MS) is an incurable autoimmune disease and is currently treated by systemic immunosuppressants with off-target side effects. Although aberrant myeloid function is often observed in MS plaques in the central nervous system (CNS), the role of myeloid cells in therapeutic intervention is currently overlooked. Here, we developed a myeloid cell-based strategy to reduce the disease burden in experimental autoimmune encephalomyelitis (EAE), a mouse model of progressive MS. We developed monocyte-adhered microparticles ("backpacks") for activating myeloid cell phenotype to an anti-inflammatory state through localized interleukin-4 and dexamethasone signals. We demonstrate that backpack-laden monocytes infiltrated into the inflamed CNS and modulated both the local and systemic immune responses. Within the CNS, backpack-carrying monocytes regulated both the infiltrating and tissue-resident myeloid cell compartments in the spinal cord for functions related to antigen presentation and reactive species production. Treatment with backpack-monocytes also decreased the level of systemic pro-inflammatory cytokines. Additionally, backpack-laden monocytes induced modulatory effects on T(H)1 and T(H)17 populations in the spinal cord and blood, demonstrating cross talk between the myeloid and lymphoid arms of disease. Backpack-carrying monocytes conferred therapeutic benefit in EAE mice, as quantified by improved motor function. The use of backpack-laden monocytes offers an antigen-free, biomaterial-based approach to precisely tune cell phenotype in vivo, demonstrating the utility of myeloid cells as a therapeutic modality and target. %B Proc Natl Acad Sci U S A %V 120 %P e2221535120 %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/37075071 %N 17 %9 Journal Article %R 10.1073/pnas.2221535120 %0 Journal Article %J Commun Biol %D 2023 %T Complex hemolymph circulation patterns in grasshopper wings %A Salcedo, M. K. %A Jun, B. H. %A Socha, J. J. %A Pierce, N. E. %A Vlachos, P. P. %A Combes, S. A. %K Animal/physiology %K Animal/physiology Insecta/physiology Wings %K Animals *Grasshoppers Biomechanical Phenomena Hemolymph Flight %X An insect's living systems-circulation, respiration, and a branching nervous system-extend from the body into the wing. Wing hemolymph circulation is critical for hydrating tissues and supplying nutrients to living systems such as sensory organs across the wing. Despite the critical role of hemolymph circulation in maintaining healthy wing function, wings are often considered "lifeless" cuticle, and flows remain largely unquantified. High-speed fluorescent microscopy and particle tracking of hemolymph in the wings and body of the grasshopper Schistocerca americana revealed dynamic flow in every vein of the fore- and hindwings. The global system forms a circuit, but local flow behavior is complex, exhibiting three distinct types: pulsatile, aperiodic, and "leaky" flow. Thoracic wing hearts pull hemolymph from the wing at slower frequencies than the dorsal vessel; however, the velocity of returning hemolymph (in the hindwing) is faster than in that of the dorsal vessel. To characterize the wing's internal flow mechanics, we mapped dimensionless flow parameters across the wings, revealing viscous flow regimes. Wings sustain ecologically important insect behaviors such as pollination and migration. Analysis of the wing circulatory system provides a template for future studies investigating the critical hemodynamics necessary to sustaining wing health and insect flight. %B Commun Biol %V 6 %P 313 %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/36959465 %N 1 %9 Journal Article %R 10.1038/s42003-023-04651-2 %0 Journal Article %J Integr Comp Biol %D 2023 %T Formation and Replacement of Bone And Tooth Mineralized Tissues in Green Iguanas (Iguana Iguana) Revealed by In-Vivo Fluorescence Marking %A Green, D. R. %A Winkler, D. E. %A Leichliter, J. %A Harms, G. S. %A Hatt, J. M. %A Clauss, M. %A Tutken, T. %X Hard tissue formation patterns and rates reveal details of animal physiology, life history, and environment, but are understudied in reptiles. Here, we use fluorescence labels delivered in vivo and laser confocal scanning microscopy to study tooth and bone formation in a managed group of green iguanas (Iguana iguana, Linne 1758) kept for 1.5 years under experimentally controlled conditions and undergoing several dietary switches. We constrain rates of tooth elongation, which we observe to be slow when enamel is initially deposited (c. 9 microm/day), but then increases exponentially in the dentin root, reaching c. 55 microm/day or more after crown completion. We further constrain the total timing of tooth formation to approximately 40-60 days, and observe highly variable timings of tooth resorption onset and replacement. Fluorescent labels clearly indicate cohorts of teeth recruited within Zahnreihen replacement waves, with faster sequential tooth recruitment and greater wave sizes posteriorly, where each wave initiates. Rates of hard tissue formation in long bones range from 0.4-3.4 microm/day, correlating with animal weight gain, and cortical bone recording the entire history of the experiment. We suggest additional labeling experiments to study hard tissue formation patterns in other reptiles, and propose strategies for chemical analyses of hard tissues in order to extract temporal information about past environments, behaviors and diets from reptilian fossils throughout the Phanerozoic. %B Integr Comp Biol %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/37475667 %9 Journal Article %R 10.1093/icb/icad089 %0 Journal Article %J Commun Biol %D 2023 %T Hominoid SVA-lncRNA AK057321 targets human-specific SVA retrotransposons in SCN8A and CDK5RAP2 to initiate neuronal maturation %A Nadler, M. J. S. %A W. Chang %A Ozkaynak, E. %A Huo, Y. %A Nong, Y. %A Boillot, M. %A Johnson, M. %A Moreno, A. %A Matthew, P. Anderson %K Animals Humans *Retroelements/genetics *RNA %K Long Noncoding/genetics Minisatellite Repeats Short Interspersed Nucleotide Elements Primates/genetics Chromatin Assembly Factor-1/genetics NAV1.6 Voltage-Gated Sodium Channel/genetics Nerve Tissue Proteins/genetics Cell Cycle Proteins/genetics %X SINE-VNTR-Alu (SVA) retrotransposons arose and expanded in the genome of hominoid primates concurrent with the slowing of brain maturation. We report genes with intronic SVA transposons are enriched for neurodevelopmental disease and transcribed into long non-coding SVA-lncRNAs. Human-specific SVAs in microcephaly CDK5RAP2 and epilepsy SCN8A gene introns repress their expression via transcription factor ZNF91 to delay neuronal maturation. Deleting the SVA in CDK5RAP2 initiates multi-dimensional and in SCN8A selective sodium current neuronal maturation by upregulating these genes. SVA-lncRNA AK057321 forms RNA:DNA heteroduplexes with the genomic SVAs and upregulates these genes to initiate neuronal maturation. SVA-lncRNA AK057321 also promotes species-specific cortex and cerebellum-enriched expression upregulating human genes with intronic SVAs (e.g., HTT, CHAF1B and KCNJ6) but not mouse orthologs. The diversity of neuronal genes with intronic SVAs suggest this hominoid-specific SVA transposon-based gene regulatory mechanism may act at multiple steps to specialize and achieve neoteny of the human brain. %B Commun Biol %V 6 %P 347 %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/36997626 %N 1 %9 Journal Article %R 10.1038/s42003-023-04683-8 %0 Journal Article %J Cell Rep %D 2023 %T Inter-axonal molecular crosstalk via Lumican proteoglycan sculpts murine cervical corticospinal innervation by distinct subpopulations %A Itoh, Y. %A Sahni, V. %A Shnider, S. J. %A McKee, H. %A Macklis, J. D. %K Animals Mice *Spinal Cord/physiology Lumican *Axons/physiology Neurons/physiology Movement Pyramidal Tracts CP: Neuroscience Lumican proteoglycan axon collateralization axon development circuit refinement corticospinal neurons corticospinal segmental spec %X How CNS circuits sculpt their axonal arbors into spatially and functionally organized domains is not well understood. Segmental specificity of corticospinal connectivity is an exemplar for such regional specificity of many axon projections. Corticospinal neurons (CSN) innervate spinal and brainstem targets with segmental precision, controlling voluntary movement. Multiple molecularly distinct CSN subpopulations innervate the cervical cord for evolutionarily enhanced precision of forelimb movement. Evolutionarily newer CSN(BC-lat) exclusively innervate bulbar-cervical targets, while CSN(medial) are heterogeneous; distinct subpopulations extend axons to either bulbar-cervical or thoraco-lumbar segments. We identify that Lumican controls balance of cervical innervation between CSN(BC-lat) and CSN(medial) axons during development, which is maintained into maturity. Lumican, an extracellular proteoglycan expressed by CSN(BC-lat), non-cell-autonomously suppresses cervical collateralization by multiple CSN(medial) subpopulations. This inter-axonal molecular crosstalk between CSN subpopulations controls murine corticospinal circuitry refinement and forelimb dexterity. Such crosstalk is generalizable beyond the corticospinal system for evolutionary incorporation of new neuron populations into preexisting circuitry. %B Cell Rep %V 42 %P 112182 %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/36934325 %N 3 %9 Journal Article %R 10.1016/j.celrep.2023.112182 %0 Journal Article %J Blood Adv %D 2023 %T Membrane curvature and PS localize coagulation proteins to filopodia and retraction fibers of endothelial cells %A Carman, C. V. %A Nikova, D. N. %A Sakurai, Y. %A Shi, J. %A Novakovic, V. A. %A J. T. Rasmussen %A Lam, W. A. %A Gilbert, G. E. %K *Thromboplastin/metabolism *Phosphatidylserines/metabolism Endothelial Cells/metabolism Factor Va/chemistry/metabolism Pseudopodia/metabolism Fibrin %X Prior reports indicate that the convex membrane curvature of phosphatidylserine (PS)-containing vesicles enhances formation of binding sites for factor Va and lactadherin. Yet, the relationship of convex curvature to localization of these proteins on cells remains unknown. We developed a membrane topology model, using phospholipid bilayers supported by nano-etched silica substrates, to further explore the relationship between curvature and localization of coagulation proteins. Ridge convexity corresponded to maximal curvature of physiologic membranes (radii of 10 or 30 nm) and the troughs had a variable concave curvature. The benchmark PS probe lactadherin exhibited strong differential binding to the ridges, on membranes with 4% to 15% PS. Factor Va, with a PS-binding motif homologous to lactadherin, also bound selectively to the ridges. Bound factor Va supported coincident binding of factor Xa, localizing prothrombinase complexes to the ridges. Endothelial cells responded to prothrombotic stressors and stimuli (staurosporine, tumor necrosis factor-alpha [TNF- alpha]) by retracting cell margins and forming filaments and filopodia. These had a high positive curvature similar to supported membrane ridges and selectively bound lactadherin. Likewise, the retraction filaments and filopodia bound factor Va and supported assembly of prothrombinase, whereas the cell body did not. The perfusion of plasma over TNF-alpha-stimulated endothelia in culture dishes and engineered 3-dimensional microvessels led to fibrin deposition at cell margins, inhibited by lactadherin, without clotting of bulk plasma. Our results indicate that stressed or stimulated endothelial cells support prothrombinase activity localized to convex topological features at cell margins. These findings may relate to perivascular fibrin deposition in sepsis and inflammation. %B Blood Adv %V 7 %P 60-72 %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/35849711 %N 1 %9 Journal Article %R 10.1182/bloodadvances.2021006870 %0 Journal Article %J Adv Mater %D 2023 %T Microporogen-Structured Collagen Matrices for Embedded Bioprinting of Tumor Models for Immuno-Oncology %A Reynolds, D. S. %A de Lazaro, I. %A Blache, M. L. %A Liu, Y. %A Jeffreys, N. C. %A Doolittle, R. M. %A Grandidier, E. %A Olszewski, J. %A Dacus, M. T. %A D. J. Mooney %A Lewis, J. A. %K cancer collagen embedded bioprinting immunotherapy microporogens %X Embedded bioprinting enables the rapid design and fabrication of complex tissues that recapitulate in vivo microenvironments. However, few biological matrices enable good print fidelity, while simultaneously facilitate cell viability, proliferation, and migration. Here, a new microporogen-structured (microPOROS) matrix for embedded bioprinting is introduced, in which matrix rheology, printing behavior, and porosity are tailored by adding sacrificial microparticles composed of a gelatin-chitosan complex to a prepolymer collagen solution. To demonstrate its utility, a 3D tumor model is created via embedded printing of a murine melanoma cell ink within the microPOROS collagen matrix at 4 degrees C. The collagen matrix is subsequently crosslinked around the microparticles upon warming to 21 degrees C, followed by their melting and removal at 37 degrees C. This process results in a microPOROS matrix with a fibrillar collagen type-I network akin to that observed in vivo. Printed tumor cells remain viable and proliferate, while antigen-specific cytotoxic T cells incorporated in the matrix migrate to the tumor site, where they induce cell death. The integration of the microPOROS matrix with embedded bioprinting opens new avenues for creating complex tissue microenvironments in vitro that may find widespread use in drug discovery, disease modeling, and tissue engineering for therapeutic use. %B Adv Mater %P e2210748 %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/37163476 %9 Journal Article %R 10.1002/adma.202210748 %0 Journal Article %J Nat Commun %D 2023 %T Multiplexed analysis of EV reveals specific biomarker composition with diagnostic impact %A Spitzberg, J. D. %A Ferguson, S. %A Yang, K. S. %A Peterson, H. M. %A Carlson, J. C. T. %A Weissleder, R. %K *Extracellular Vesicles *Exosomes Biomarkers Chromatography %K Affinity Staining and Labeling %X Exosomes and extracellular vesicles (EV) are increasingly being explored as circulating biomarkers, but their heterogenous composition will likely mandate the development of multiplexed EV technologies. Iteratively multiplexed analyses of near single EVs have been challenging to implement beyond a few colors during spectral sensing. Here we developed a multiplexed analysis of EV technique (MASEV) to interrogate thousands of individual EVs during 5 cycles of multi-channel fluorescence staining for 15 EV biomarkers. Contrary to the common belief, we show that: several markers proposed to be ubiquitous are less prevalent than believed; multiple biomarkers concur in single vesicles but only in small fractions; affinity purification can lead to loss of rare EV subtypes; and deep profiling allows detailed analysis of EV, potentially improving the diagnostic content. These findings establish the potential of MASEV for uncovering fundamental EV biology and heterogeneity and increasing diagnostic specificity. %B Nat Commun %V 14 %P 1239 %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/36870999 %N 1 %9 Journal Article %R 10.1038/s41467-023-36932-z %0 Journal Article %J Elife %D 2023 %T Neural mechanisms of parasite-induced summiting behavior in 'zombie' Drosophila %A Elya, C. %A Lavrentovich, D. %A Lee, E. %A Pasadyn, C. %A Duval, J. %A Basak, M. %A Saykina, V. %A B. de Bivort %K Animals *Drosophila Drosophila melanogaster/physiology *Parasites Corpora Allata/metabolism Juvenile Hormones/metabolism D. melanogaster Entomophthora muscae behavior circadian rhythm genetics genomics juvenile hormone neuroscience parasitic mind-control %X For at least two centuries, scientists have been enthralled by the "zombie" behaviors induced by mind-controlling parasites. Despite this interest, the mechanistic bases of these uncanny processes have remained mostly a mystery. Here, we leverage the Entomophthora muscae-Drosophila melanogaster "zombie fly" system to reveal the mechanistic underpinnings of summit disease, a manipulated behavior evoked by many fungal parasites. Using a high-throughput approach to measure summiting, we discovered that summiting behavior is characterized by a burst of locomotion and requires the host circadian and neurosecretory systems, specifically DN1p circadian neurons, pars intercerebralis to corpora allata projecting (PI-CA) neurons and corpora allata (CA), the latter being solely responsible for juvenile hormone (JH) synthesis and release. Using a machine learning classifier to identify summiting animals in real time, we observed that PI-CA neurons and CA appeared intact in summiting animals, despite invasion of adjacent regions of the "zombie fly" brain by E. muscae cells and extensive host tissue damage in the body cavity. The blood-brain barrier of flies late in their infection was significantly permeabilized, suggesting that factors in the hemolymph may have greater access to the central nervous system during summiting. Metabolomic analysis of hemolymph from summiting flies revealed differential abundance of several compounds compared to non-summiting flies. Transfusing the hemolymph of summiting flies into non-summiting recipients induced a burst of locomotion, demonstrating that factor(s) in the hemolymph likely cause summiting behavior. Altogether, our work reveals a neuro-mechanistic model for summiting wherein fungal cells perturb the fly's hemolymph, activating a neurohormonal pathway linking clock neurons to juvenile hormone production in the CA, ultimately inducing locomotor activity in their host. %B Elife %V 12 %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/37184212 %9 Journal Article %R 10.7554/eLife.85410 %0 Journal Article %J ACS Nano %D 2023 %T Polymer Micropatches as Natural Killer Cell Engagers for Tumor Therapy %A Prakash, S. %A Kumbhojkar, N. %A Lu, A. %A Kapate, N. %A Suja, V. C. %A Park, K.S. %A Wang, L. L. %A Mitragotri, S. %K NK cell NK cell activation NK engager adoptive cell transfer cross-linking lung metastasis microparticle %X Natural killer (NK) cell therapies have emerged as a potential therapeutic approach to various cancers. Their efficacy, however, is limited by their low persistence and anergy. Current approaches to sustain NK cell persistence in vivo include genetic modification, activation via pretreatment, or coadministration of supporting cytokines or antibodies. Such supporting therapies exhibit limited efficacy in vivo, in part due to the reversal of their effect within the immunosuppressive tumor microenvironment and off-target toxicity. Here, we report a material-based approach to address this challenge. Specifically, we describe the use of polymeric micropatches as a platform for sustained, targeted activation of NK cells, an approach referred to as microparticles as cell engagers (MACE). Poly(lactide-co-glycolic) acid (PLGA) micropatches, 4-8 mum in diameter and surface-modified with NK cell receptor targeting antibodies, exhibited strong adhesion to NK cells and induced their activation without the need of coadministered cytokines. The activation induced by MACE was greater than that induced by nanoparticles, attesting to the crucial role of MACE geometry in the activation of NK cells. MACE-bound NK cells remained viable and exhibited trans-endothelial migration and antitumor activity in vitro. MACE-bound NK cells activated T cells, macrophages, and dendritic cells in vitro. Adoptive transfer of NK-MACE also demonstrated superior antitumor efficacy in a mouse melanoma lung metastasis model compared to unmodified NK cells. Overall, MACE offers a simple, scalable, and effective way of activating NK cells and represents an attractive platform to improve the efficacy of NK cell therapy. %B ACS Nano %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/37565806 %9 Journal Article %R 10.1021/acsnano.3c03980 %0 Journal Article %J Genome Res %D 2023 %T A single-cell transcriptome atlas of the maturing zebrafish telencephalon %A Pandey, S. %A Moyer, A. J. %A Thyme, S. B. %K Animals Mice *Zebrafish/metabolism *Transcriptome Zebrafish Proteins/genetics Neurons/metabolism Telencephalon/metabolism %X The zebrafish telencephalon is composed of highly specialized subregions that regulate complex behaviors such as learning, memory, and social interactions. The transcriptional signatures of the neuronal cell types in the telencephalon and the timeline of their emergence from larva to adult remain largely undescribed. Using an integrated analysis of single-cell transcriptomes of approximately 64,000 cells obtained from 6-day-postfertilization (dpf), 15-dpf, and adult telencephalon, we delineated nine main neuronal cell types in the pallium and eight in the subpallium and nominated novel marker genes. Comparing zebrafish and mouse neuronal cell types revealed both conserved and absent types and marker genes. Mapping of cell types onto a spatial larval reference atlas created a resource for anatomical and functional studies. Using this multiage approach, we discovered that although most neuronal subtypes are established early in the 6-dpf fish, some emerge or expand in number later in development. Analyzing the samples from each age separately revealed further complexity in the data, including several cell types that expand substantially in the adult forebrain and do not form clusters at the larval stages. Together, our work provides a comprehensive transcriptional analysis of the cell types in the zebrafish telencephalon and a resource for dissecting its development and function. %B Genome Res %V 33 %P 658-671 %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/37072188 %N 4 %9 Journal Article %R 10.1101/gr.277278.122 %0 Journal Article %J Brain Commun %D 2023 %T Spatial characterization of tangle-bearing neurons and ghost tangles in the human inferior temporal gyrus with three-dimensional imaging %A Zwang, T. J. %A Woost, B. %A Bailey, J. %A Hoglund, Z. %A Richardson, D.S. %A Bennett, R. E. %A Hyman, B. T. %K ghost tangles inferior temporal gyrus spatial mapping tau tissue clearing %X Studies of post-mortem human tissue provide insight into pathological processes, but are inherently limited by practical considerations that limit the scale at which tissue can be examined, and the obvious issue that the tissue reflects only one time point in a continuous disease process. We approached this problem by adapting new tissue clearance techniques to an entire cortical area of human brain, which allows surveillance of hundreds of thousands of neurons throughout the depth of the entire cortical thickness. This approach allows detection of 'rare' events that may be difficult to detect in standard 5 micrometre-thick paraffin sections. For example, it is well established that neurofibrillary tangles begin within a neuron, and ultimately, in at least some instances, persist in the brain even after the neuron has died. These are referred to as 'ghost tangles', a term that appropriately implies their 'difficult to see' ephemeral qualities. We set out to find ghost tangles as one example of the power of the tissue clearance/image analysis techniques to detect rare events, and to learn what happens at the end-point of a tangle's life history. We were able to identify 8103 tau tangles, 132 465 neurons and 299 640 nuclei in tissue samples from three subjects with severe Alzheimer's disease (Braak V-VI) and 4 tau tangles, 200 447 neurons and 462 715 nuclei in tissue samples from three subjects with no significant tau pathology (Braak 0-I). Among these data, we located 57 ghost tangles, which makes them only 0.7% of the total tau tangles observed. We found that ghost tangles are more likely to be found in cortical layers 3 and 5 (49/57), with a select few scattered across other layers 1, 2, 4 and 6. This ability to find rare events, such as ghost tangles, in large enough quantities to statistically test their distribution exemplifies how tissue clearing can be used as a powerful tool for studying selective vulnerability or resilience to pathology across brain regions. %B Brain Commun %V 5 %P fcad130 %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/37324243 %N 3 %9 Journal Article %R 10.1093/braincomms/fcad130 %0 Journal Article %J Cell Rep %D 2023 %T Tle4 controls both developmental acquisition and early post-natal maturation of corticothalamic projection neuron identity %A Galazo, M. J. %A Sweetser, D. A. %A Macklis, J. D. %K CP: Developmental biology CP: Neuroscience Fezf2 Tle4 corticospinal neurons corticothalamic neurons epigenetic regulation neuron identity acquisition neuron identity stability subcerebral projection neurons %X Identities of distinct neuron subtypes are specified during embryonic development, then maintained during post-natal maturation. In cerebral cortex, mechanisms controlling early acquisition of neuron-subtype identities have become increasingly understood. However, mechanisms controlling neuron-subtype identity stability during post-natal maturation are largely unexplored. We identify that Tle4 is required for both early acquisition and post-natal stability of corticothalamic neuron-subtype identity. Embryonically, Tle4 promotes acquisition of corticothalamic identity and blocks emergence of core characteristics of subcerebral/corticospinal projection neuron identity, including gene expression and connectivity. During the first post-natal week, when corticothalamic innervation is ongoing, Tle4 is required to stabilize corticothalamic neuron identity, limiting interference from differentiation programs of developmentally related neuron classes. We identify a deacetylation-based epigenetic mechanism by which TLE4 controls Fezf2 expression level by corticothalamic neurons. This contributes to distinction of cortical output subtypes and ensures identity stability for appropriate maturation of corticothalamic neurons. %B Cell Rep %V 42 %P 112957 %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/37561632 %N 8 %9 Journal Article %R 10.1016/j.celrep.2023.112957 %0 Journal Article %J Cell Rep %D 2023 %T Transplantation-based screen identifies inducers of muscle progenitor cell engraftment across vertebrate species %A Tavakoli, S. %A Garcia, V. %A Gahwiler, E. %A Adatto, I. %A Rangan, A. %A Messemer, K. A. %A Kakhki, S. A. %A Yang, S. %A Chan, V. S. %A Manning, M. E. %A Fotowat, H. %A Zhou, Y. %A Wagers, A.J. %A Zon, L. I. %K CP: Developmental biology cell therapy engraftment lysophosphatidic acid muscular dystrophy niflumic acid satellite cell %X Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle, but this approach is limited by the deleterious effects of cell expansion in vitro and consequent poor engraftment efficiency. In an effort to overcome this limitation, we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here, we report the development and application of a cross-species small-molecule screening platform employing zebrafish and mice, which enables rapid, direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system, we screened a library of bioactive lipids to discriminate those that could increase myogenic engraftment in vivo in zebrafish and mice. This effort identified two lipids, lysophosphatidic acid and niflumic acid, both linked to the activation of intracellular calcium-ion flux, which showed conserved, dose-dependent, and synergistic effects in promoting muscle engraftment across these vertebrate species. %B Cell Rep %V 42 %P 112365 %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/37018075 %N 4 %9 Journal Article %R 10.1016/j.celrep.2023.112365 %0 Journal Article %J Nat Methods %D 2023 %T Video-based pooled screening yields improved far-red genetically encoded voltage indicators %A H. Tian %A Davis, H. C. %A Wong-Campos, J. D. %A Park, P. %A Fan, L. Z. %A Gmeiner, B. %A Begum, S. %A Werley, C. A. %A Borja, G. B. %A Upadhyay, H. %A Shah, H. %A Jacques, J. %A Qi, Y. %A Parot, V. %A K. Deisseroth %A Cohen, A. E. %K Cultured Neurons/physiology Interneurons %K Mice Animals *Hippocampus/physiology *Electrophysiological Phenomena Cells %X Video-based screening of pooled libraries is a powerful approach for directed evolution of biosensors because it enables selection along multiple dimensions simultaneously from large libraries. Here we develop a screening platform, Photopick, which achieves precise phenotype-activated photoselection over a large field of view (2.3 x 2.3 mm, containing >10(3) cells, per shot). We used the Photopick platform to evolve archaerhodopsin-derived genetically encoded voltage indicators (GEVIs) with improved signal-to-noise ratio (QuasAr6a) and kinetics (QuasAr6b). These GEVIs gave improved signals in cultured neurons and in live mouse brains. By combining targeted in vivo optogenetic stimulation with high-precision voltage imaging, we characterized inhibitory synaptic coupling between individual cortical NDNF (neuron-derived neurotrophic factor) interneurons, and excitatory electrical synapses between individual hippocampal parvalbumin neurons. The QuasAr6 GEVIs are powerful tools for all-optical electrophysiology and the Photopick approach could be adapted to evolve a broad range of biosensors. %B Nat Methods %V 20 %P 1082-1094 %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/36624211 %N 7 %9 Journal Article %R 10.1038/s41592-022-01743-5 %0 Journal Article %J Sci Robot %D 2023 %T Anti-inflammatory therapy enables robot-actuated regeneration of aged muscle %A S. L. MCNAMARA %A B. R. Seo %A B. R. Freedman %A E. B. Roloson %A Alvarez, J.T. %A O'Neill, C. T. %A H. H. Vandenburgh %A C. J. Walsh %A D. J. Mooney %K Animals Mice *Regeneration/physiology *Robotics Muscle %K Skeletal/physiology Anti-Inflammatory Agents %X Robot-actuated mechanical loading (ML)-based therapies ("mechanotherapies") can promote regeneration after severe skeletal muscle injury, but the effectiveness of such approaches during aging is unknown and may be influenced by age-associated decline in the healing capacity of skeletal muscle. To address this knowledge gap, this work used a noninvasive, load-controlled robotic device to impose highly defined tissue stresses to evaluate the age dependence of ML on muscle repair after injury. The response of injured muscle to robot-actuated cyclic compressive loading was found to be age sensitive, revealing not only a lack of reparative benefit of ML on injured aged muscles but also exacerbation of tissue inflammation. ML alone also disrupted the normal regenerative processes of aged muscle stem cells. However, these negative effects could be reversed by introducing anti-inflammatory therapy alongside ML application, leading to enhanced skeletal muscle regeneration even in aged mice. %B Sci Robot %V 8 %P eadd9369 %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/36947599 %N 76 %9 Journal Article %R 10.1126/scirobotics.add9369 %0 Journal Article %J Cell %D 2023 %T Controlling human organoid symmetry breaking reveals signaling gradients drive segmentation clock waves %A Yusuf Ilker Yaman %A Ramanathan, Sharad %B Cell %V 186 %G eng %U https://www.cell.com/cell/fulltext/S0092-8674(22)01585-9#secsectitle0085 %0 Journal Article %J Cell %D 2023 %T Controlling organoid symmetry breaking uncovers an excitable system underlying human axial elongation %A Anand, Giridhar M. %A Megale, Heitor C. %A Murphy, Sean H. %A Weis, Theresa %A Zuwan Lin %A Yichun He %A Wang, Xiao %A Jia Liu %A Ramanathan, Sharad %B Cell %V 186 %G eng %U https://www.cell.com/cell/fulltext/S0092-8674(22)01586-0 %0 Journal Article %J eLife %D 2023 %T Tissue libraries enable rapid determination of conditions that preserve antibody labeling in cleared mouse and human tissue. %A Theodore J Zwang %A Bennett, Rachel E %A Maria Lysandrou %A Benjamin Woost %A Anqi Zhang %A Charles m Lieber %A Richardson, Douglas S %A Hyman, Bradley T %B eLife %V 84122 %G eng %U https://elifesciences.org/articles/84112 %0 Journal Article %J Nature Biotechnology %D 2023 %T Time-tagged ticker tapes for intracellular recordings %A Lin, Dingchang %A Li, Xiuyuan %A Moult, Eric %A Park, Pojeong %A Tang, Benjamin %A Shen, Hao %A Grimm, Jonathan B. %A Falco, Natalie %A Jia, Bill Z. %A Baker, David %A Lavis, Luke D. %A Adam E. Cohen %B Nature Biotechnology %G eng %U https://dx.doi.org/10.1038/s41587-022-01524-7 %9 Journal Article %R 10.1038/s41587-022-01524-7 %0 Journal Article %J American Journal of Botany %D 2022 %T A bump in the node: The hydraulic implications of rhizomatousgrowth %A Jacob S. Suissa %A Andrews A. Agbleke %A William E. Friedman %B American Journal of Botany %V e16105 %G eng %U https://bsapubs.onlinelibrary.wiley.com/doi/10.1002/ajb2.16105 %0 Journal Article %J Neuron %D 2022 %T Striatal dopamine explains novelty-induced behavioral dynamics and individual variability in threat prediction %A Korleki Akiti %A Iku Tsutsui-Kimura %A Yudi Xie %A Mathis, Alexander %A Jeffrey E. Markowitz %A Rockwell Anyoha %A Datta, Sandeep Robert %A Mathis, Mackenzie Weygandt %A Uchida, Naoshige %A Watabe-Uchida, Mitsuko %B Neuron %V 110 %P 3789-3804.e9 %G eng %U https://dx.doi.org/10.1016/j.neuron.2022.08.022 %N 22 %9 Journal Article %R 10.1016/j.neuron.2022.08.022 %0 Journal Article %J Proceedings of the National Academy of Sciences %D 2022 %T A deep eutectic-based, self-emulsifying subcutaneous depot system for apomorphine therapy in Parkinson’s disease %A Kim, Jayoung %A Gao, Yongsheng %A Zhao, Zongmin %A Rodrigues, Danika %A Tanner, Eden E L %A Ibsen, Kelly %A Sasmal, Pradip K %A Jaladi, Rajasekhar %A Alikunju, Shanavas %A Mitragotri, Samir %B Proceedings of the National Academy of Sciences %V 119 %P e2110450119 %G eng %N 9 %9 Journal Article %0 Journal Article %J Journal of Cellular Physiology %D 2022 %T Deletion of TrkB in parvalbumin interneurons alters cortical neural dynamics %A Lau, Chunyue Geoffrey %A Zhang, Huiqi %A Murthy, Venkatesh N %B Journal of Cellular Physiology %V 237 %P 949-964 %G eng %N 1 %9 Journal Article %0 Journal Article %J Journal of the American Society of Nephrology %D 2022 %T DGAT2 Inhibition Potentiates Lipid Droplet Formation To Reduce Cytotoxicity in APOL1 Kidney Risk Variants %A Justin Chun %A Riella, Cristian V. %A Chung, Hyunjae %A Shah, Shrijal S. %A Wang, Minxian %A Jose M. Magraner %A Ribas, Guilherme T. %A Ribas, Hennrique T. %A Jia-Yue Zhang %A Seth L. Alper %A David J. Friedman %A Pollak, Martin R. %B Journal of the American Society of Nephrology %V 33 %P 889-907 %G eng %U https://dx.doi.org/10.1681/asn.2021050723 %N 5 %9 Journal Article %R 10.1681/asn.2021050723 %0 Journal Article %J Genes & development %D 2022 %T A distinct core regulatory module enforces oncogene expression in KMT2A-rearranged leukemia %A Harada, Taku %A Heshmati, Yaser %A Kalfon, Jérémie %A Perez, Monika W %A Ferrucio, Juliana Xavier %A Ewers, Jazmin %A Engler, Benjamin Hubbell %A Kossenkov, Andrew %A Ellegast, Jana M %A Joanna, S Yi %B Genes & development %V 36 %P 368-389 %G eng %N 5-6 %9 Journal Article %0 Journal Article %J Elife %D 2022 %T Distinct representation of cue-outcome association by D1 and D2 neurons in the ventral striatum’s olfactory tubercle %A Martiros, Nuné %A Kapoor, Vikrant %A Kim, Spencer E %A Murthy, Venkatesh N %B Elife %V 11 %P e75463 %G eng %9 Journal Article %0 Journal Article %J Science advances %D 2022 %T Distinct roles for motor cortical and thalamic inputs to striatum during motor skill learning and execution %A Steffen B E Wolff %A Ko, Raymond %A Ölveczky, Bence P %B Science advances %V 8 %P eabk0231 %G eng %N 8 %9 Journal Article %0 Journal Article %J Journal of Experimental Botany %D 2022 %T Genetic architecture underlying variation in floral meristem termination in Aquilegia %A Min, Ya %A Ballerini, Evangeline S %A Edwards, Molly B %A Hodges, Scott A %A Kramer, Elena M %X Floral organs are produced by floral meristems (FMs), which harbor stem cells in their centers. Since each flower only has a finite number of organs, the stem cell activity of an FM will always terminate at a specific time point, a process termed floral meristem termination (FMT). Variation in the timing of FMT can give rise to floral morphological diversity, but how this process is fine-tuned at a developmental and evolutionary level is poorly understood. Flowers from the genus Aquilegia share identical floral organ arrangement except for stamen whorl number (SWN), making Aquilegia a well-suited system for investigation of this process: differences in SWN between species represent differences in the timing of FMT. By crossing A. canadensis and A. brevistyla, quantitative trait locus (QTL) mapping has revealed a complex genetic architecture with seven QTL. We explored potential candidate genes under each QTL and characterized novel expression patterns of select loci of interest using in situ hybridization. To our knowledge, this is the first attempt to dissect the genetic basis of how natural variation in the timing of FMT is regulated, and our results provide insight into how floral morphological diversity can be generated at the meristematic level. %B Journal of Experimental Botany %G eng %U https://doi.org/10.1093/jxb/erac277 %9 Journal Article %R 10.1093/jxb/erac277 %0 Journal Article %J bioRxiv %D 2022 %T Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types %A Methodios Ximerakis %A Holton, Kristina M %A Giadone, Richard M %A Ceren Ozek %A Saxena, Monika %A Santiago, Samara %A Adiconis, Xian %A Dionne, Danielle %A Lan Nguyen %A Shah, Kavya M %B bioRxiv %G eng %9 Journal Article %0 Journal Article %J Proceedings of the National Academy of Sciences %D 2022 %T Identification of basal complex protein that is essential for maturation of transmission-stage malaria parasites %A Clements, Rebecca L. %A Morano, Alexander A. %A Navarro, Francesca M. %A McGee, James P. %A Du, Esrah W. %A Streva, Vincent A. %A Lindner, Scott E. %A Jeffrey D. Dvorin %X Malaria remains a global driver of morbidity and mortality. To generate new antimalarials, one must elucidate the fundamental cell biology of Plasmodium falciparum, the parasite responsible for the deadliest cases of malaria. A membranous and proteinaceous scaffold called the inner membrane complex (IMC) supports the parasite during morphological changes, including segmentation of daughter cells during asexual replication and formation of transmission-stage gametocytes. The basal complex lines the edge of the IMC during segmentation and likely facilitates IMC expansion. It is unknown, however, what drives IMC expansion during gametocytogenesis. We describe the discovery of a basal complex protein, PfBLEB, which we find to be essential for gametocytogenesis. Parasites lacking PfBLEB harbor defects in IMC expansion and are unable to form mature gametocytes. This article demonstrates a role for a basal complex protein outside of asexual division, and, importantly, highlights a potential molecular target for the ablation of malaria transmission. %B Proceedings of the National Academy of Sciences %V 119 %P e2204167119 %G eng %U https://doi.org/10.1073/pnas.2204167119 %N 34 %9 Journal Article %R 10.1073/pnas.2204167119 %0 Journal Article %J Neuron %D 2022 %T Loss of mouse Stmn2 function causes motor neuropathy %A Guerra San Juan, Irune %A Nash, Leslie A %A Smith, Kevin S %A Leyton-Jaimes, Marcel F %A Menglu Qian %A Klim, Joseph R %A Limone, Francesco %A Dorr, Alexander B %A Alexander Couto %A Pintacuda, Greta %B Neuron %V 110 %P 1671-1688. e6 %G eng %N 10 %9 Journal Article %0 Unpublished Work %D 2022 %T Machine learning directed organoid morphogenesis uncovers an excitable system driving human axial elongation %A Anand, Giridhar M. %A Megale, Heitor C. %A Murphy, Sean H. %A Weis, Theresa %A Zuwan Lin %A Yichun He %A Wang, Xiao %A Jia Liu %A Ramanathan, Sharad %I Cold Spring Harbor Laboratory %G eng %U https://dx.doi.org/10.1101/2022.05.10.491358 %9 Unpublished Work %R 10.1101/2022.05.10.491358 %0 Journal Article %J Blood Advances %D 2022 %T Membrane curvature and PS localize coagulation proteins to filopodia and retraction fibers of endothelial cells %A Carman, Christopher V %A Nikova, Dessislava N %A Sakurai, Yumiko %A Shi, Jialan %A Novakovic, Valerie A %A Rasmussen, Jan T %A Lam, Wilbur %A Gilbert, Gary E %B Blood Advances %G eng %9 Journal Article %0 Journal Article %J Nature communications %D 2022 %T Nuclear speed and cycle length co-vary with local density during syncytial blastoderm formation in a cricket %A Seth Donoughe %A Jordan Hoffmann %A Nakamura, Taro %A Chris H Rycroft %A Cassandra G. Extavour %B Nature communications %V 13 %P 1-14 %G eng %N 1 %9 Journal Article %0 Journal Article %J Nature Biomedical Engineering %D 2022 %T Orthogonally induced differentiation of stem cells for the programmatic patterning of vascularized organoids and bioprinted tissues %A Skylar-Scott, Mark A %A Huang, Jeremy Y %A Lu, Aric %A Ng, Alex H M %A Duenki, Tomoya %A Liu, Songlei %A Nam, Lucy L %A Damaraju, Sarita %A Church, George M %A Lewis, Jennifer A. %B Nature Biomedical Engineering %V 6 %P 449-462 %G eng %N 4 %9 Journal Article %0 Journal Article %J Biosensors and Bioelectronics %D 2022 %T Simultaneous multiparameter whole blood hemostasis assessment using a carbon nanotube-paper composite capacitance sensor %A Sekar, Praveen K %A Liang, Xin M %A Kahng, Seong-Joong %A Shu, Zhiquan %A Dichiara, Anthony B %A Chung, Jae-Hyun %A Wu, Yanyun %A Gao, Dayong %B Biosensors and Bioelectronics %V 197 %P 113786 %G eng %9 Journal Article %0 Journal Article %J Nature communications %D 2022 %T Social isolation modulates appetite and avoidance behavior via a common oxytocinergic circuit in larval zebrafish %A Caroline L Wee %A Song, Erin %A Maxim Nikitchenko %A Herrera, Kristian J %A Wong, Sandy %A Engert, Florian %A Kunes, Samuel %B Nature communications %V 13 %P 1-17 %G eng %N 1 %9 Journal Article %0 Journal Article %J Cell reports %D 2022 %T Structural basis for acyl chain control over glycosphingolipid sorting and vesicular trafficking %A Schmieder, Stefanie S %A Tatituri, Raju %A Anderson, Michael %A Kelly, Kate %A Lencer, Wayne I %B Cell reports %V 40 %P 111063 %G eng %N 2 %9 Journal Article %0 Journal Article %J Science advances %D 2022 %T Transplanted organoids empower human preclinical assessment of drug candidate for the clinic %A Westerling-Bui, Amy D %A Fast, Eva Maria %A Soare, Thomas W %A Venkatachalan, Srinivasan %A DeRan, Michael %A Fanelli, Alyssa B %A Kyrychenko, Sergii %A Hoang, Hien %A Corriea, Grinal M %A Zhang, Wei %B Science advances %V 8 %P eabj5633 %G eng %N 27 %9 Journal Article %0 Journal Article %J JoVE (Journal of Visualized Experiments) %D 2021 %T 3D Imaging of PDL Collagen Fibers during Orthodontic Tooth Movement in Mandibular Murine Model %A Xu, Han %A Lee, Andy %A Sun, Lu %A Naveh, Gili RS %B JoVE (Journal of Visualized Experiments) %P e62149 %G eng %N 170 %9 Journal Article %0 Journal Article %J bioRxiv %D 2021 %T Adaptive tail-length evolution in deer mice is associated with differential Hoxd13 expression in early development %A Kingsley, Evan P %A Hager, Emily R %A Lassance, Jean Marc %A Turner, Kyle M %A Harringmeyer, Olivia S %A Kirby, Christopher %A Neugeboren, Beverly I %A Hoekstra, Hopi E %B bioRxiv %G eng %9 Journal Article %0 Journal Article %J bioRxiv %D 2021 %T Axis formation in annual killifish: Nodal coordinates morphogenesis in absence of Huluwa prepatterning %A Abitua, Philip B %A Deniz C Aksel %A Schier, Alexander F %B bioRxiv %G eng %9 Journal Article %0 Journal Article %J Nature Communications %D 2021 %T Aβ receptors specifically recognize molecular features displayed by fibril ends and neurotoxic oligomers %A Amin, Ladan %A Harris, David A %B Nature Communications %V 12 %P 1-16 %G eng %N 1 %9 Journal Article %0 Journal Article %J Proceedings of the National Academy of Sciences %D 2021 %T Carbonate-hosted microbial communities are prolific and pervasive methane oxidizers at geologically diverse marine methane seep sites %A Marlow, Jeffrey J. %A Hoer, Daniel %A Jungbluth, Sean P. %A Reynard, Linda M. %A Gartman, Amy %A Chavez, Marko S. %A El-Naggar, Mohamed Y. %A Tuross, Noreen %A Orphan, Victoria J. %A Peter R. Girguis %B Proceedings of the National Academy of Sciences %V 118 %P e2006857118 %G eng %U https://dx.doi.org/10.1073/pnas.2006857118 %N 25 %9 Journal Article %R 10.1073/pnas.2006857118 %0 Journal Article %J Nanoscale %D 2021 %T Controlled delivery of gold nanoparticle-coupled miRNA therapeutics via an injectable self-healing hydrogel %A van der Ven, Casper F T %A Tibbitt, Mark W %A Conde, João %A van Mil, Alain %A Hjortnaes, Jesper %A Doevendans, Pieter A %A Sluijter, Joost P G %A Elena Aikawa %A Langer, Robert S %B Nanoscale %V 13 %P 20451-20461 %G eng %N 48 %9 Journal Article %0 Journal Article %J Cell reports %D 2021 %T Corticospinal neuron subpopulation-specific developmental genes prospectively indicate mature segmentally specific axon projection targeting %A Sahni, Vibhu %A Shnider, Sara J %A Jabaudon, Denis %A Song, Janet HT %A Itoh, Yasuhiro %A Greig, Luciano C %A Jeffrey D Macklis %B Cell reports %V 37 %P 109843 %G eng %N 3 %9 Journal Article %0 Journal Article %J Cellular microbiology %D 2021 %T Depletion of the mini‐chromosome maintenance complex binding protein allows the progression of cytokinesis despite abnormal karyokinesis during the asexual development of Plasmodium falciparum %A Sabrina Absalon %A Dvorin, Jeffrey D %B Cellular microbiology %V 23 %P e13284 %G eng %N 3 %9 Journal Article %0 Journal Article %J Frontiers in Cardiovascular Medicine %D 2021 %T Elastogenesis correlates with pigment production in murine aortic valve leaflets %A Joshua D Hutcheson %A Schlotter, Florian %A Creager, Michael D %A Li, Xiaoshuang %A Tan Pham %A Vyas, Payal %A Higashi, Hideyuki %A Body, Simon C %A Aikawa, Masanori %A Sasha A Singh %B Frontiers in Cardiovascular Medicine %V 8 %P 533 %G eng %9 Journal Article %0 Journal Article %J Molecular brain %D 2021 %T GDF11 expressed in the adult brain negatively regulates hippocampal neurogenesis %A Mayweather, Brittany A %A Buchanan, Sean M %A Rubin, Lee L %B Molecular brain %V 14 %P 1-13 %G eng %N 1 %9 Journal Article %0 Journal Article %J Mol Cancer Ther %D 2021 %T Lipidome-based Targeting of STAT3-driven Breast Cancer Cells Using Poly-l-glutamic Acid-coated Layer-by-Layer Nanoparticles %A Tosic, I. %A Heppler, L. N. %A Egusquiaguirre, S. P. %A Boehnke, N. %A Correa, S. %A Costa, D. F. %A Moore, E. A. G. %A Pal, S. %A Richardson, D.S. %A Ivanov, A. R. %A Haas-Kogan, D. A. %A Nomura, D. K. %A Hammond, P. T. %A Frank, D. A. %K Drug Delivery Systems/*methods Glutamic Acid/pharmacology/*therapeutic use Humans Lipidomics/*methods Nanoparticles/*metabolism STAT3 Transcription Factor/*metabolism Triple Negative Breast Neoplasms/*genetics/pathology %X The oncogenic transcription factor STAT3 is aberrantly activated in 70% of breast cancers, including nearly all triple-negative breast cancers (TNBCs). Because STAT3 is difficult to target directly, we considered whether metabolic changes driven by activated STAT3 could provide a therapeutic opportunity. We found that STAT3 prominently modulated several lipid classes, with most profound effects on N-acyl taurine and arachidonic acid, both of which are involved in plasma membrane remodeling. To exploit these metabolic changes therapeutically, we screened a library of layer-by-layer (LbL) nanoparticles (NPs) differing in the surface layer that modulates interactivity with the cell membrane. We found that poly-l-glutamic acid (PLE)-coated NPs bind to STAT3-transformed breast cancer cells with 50% greater efficiency than to nontransformed cells, and the heightened PLE-NP binding to TNBC cells was attenuated by STAT3 inhibition. This effect was also observed in densely packed three-dimensional breast cancer organoids. As STAT3-transformed cells show greater resistance to cytotoxic agents, we evaluated whether enhanced targeted delivery via PLE-NPs would provide a therapeutic advantage. We found that cisplatin-loaded PLE-NPs induced apoptosis of STAT3-driven cells at lower doses compared with both unencapsulated cisplatin and cisplatin-loaded nontargeted NPs. In addition, because radiation is commonly used in breast cancer treatment, and may alter cellular lipid distribution, we analyzed its effect on PLE-NP-cell binding. Irradiation of cells enhanced the STAT3-targeting properties of PLE-NPs in a dose-dependent manner, suggesting potential synergies between these therapeutic modalities. These findings suggest that cellular lipid changes driven by activated STAT3 may be exploited therapeutically using unique LbL NPs. %B Mol Cancer Ther %V 20 %P 726-738 %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/33536189 %N 4 %9 Journal Article %R 10.1158/1535-7163.MCT-20-0505 %0 Journal Article %J bioRxiv %D 2021 %T Loss of TBK1 activity leads to TDP-43 proteinopathy through lysosomal dysfunction in human motor neurons %A Hao, Jin %A Wells, Michael F %A Niu, Gengle %A Guerra San Juan, Irune %A Limone, Francesco %A Fukuda, Atsushi %A Leyton-Jaimes, Marcel F %A Joseph, Brian %A Menglu Qian %A Mordes, Daniel A %B bioRxiv %G eng %9 Journal Article %0 Journal Article %J BioRxiv %D 2021 %T Lumican regulates cervical corticospinal axon collateralization via non-autonomous crosstalk between distinct corticospinal neuron subpopulations %A Itoh, Yasuhiro %A Sahni, Vibhu %A Shnider, Sara J %A Jeffrey D Macklis %B BioRxiv %G eng %9 Journal Article %0 Journal Article %J Zootaxa %D 2021 %T Martensopsalis, a new genus of Neopilionidae from New Caledonia (Opiliones: Eupnoi) %A Giribet, Gonzalo %A Baker, Caitlin M. %A Brouste, Damien %B Zootaxa %V 4984 %P 98-107 %G eng %U https://dx.doi.org/10.11646/zootaxa.4984.1.9 %N 1 %9 Journal Article %R 10.11646/zootaxa.4984.1.9 %0 Journal Article %J Cell reports %D 2021 %T Modulating mesendoderm competence during human germ layer differentiation %A Valcourt, James R %A Huang, Roya E %A Kundu, Sharmistha %A Venkatasubramanian, Divya %A Kingston, Robert E %A Ramanathan, Sharad %B Cell reports %V 37 %P 109990 %G eng %N 6 %9 Journal Article %0 Journal Article %J bioRxiv %D 2021 %T Neural correlates of individual odor preference in Drosophila %A Churgin, Matthew %A Lavrentovich, Danylo %A Smith, Matthew AY %A Gao, Ruixuan %A Edward S Boyden %A de Bivort, Benjamin L %B bioRxiv %G eng %9 Journal Article %0 Journal Article %J STAR Protocols %D 2021 %T Optogenetic axon guidance in embryonic zebrafish %A James M. Harris %A Andy Yu-Der Wang %A Arlotta, Paola %K Developmental biology Microscopy Model Organisms Molecular Biology Neuroscience %X Summary Axons form the long-range connections of biological neuronal networks, which are built through the developmental process of axon guidance. Here, we describe a protocol to precisely and non-invasively control axonal growth trajectories in live zebrafish embryos using focal light activation of a photoactivatable Rac1. We outline techniques for photostimulation, time-lapse imaging, and immunohistochemistry. These approaches enable engineering of long-range axonal circuitry or repair of defective circuits in living zebrafish, despite a milieu of competing endogenous signals and repulsive barriers. For complete details on the use and execution of this protocol, please refer to Harris et al. (2020). %B STAR Protocols %V 2 %P 100947 %G eng %U https://www.sciencedirect.com/science/article/pii/S2666166721006535 %N 4 %9 Journal Article %R https://doi.org/10.1016/j.xpro.2021.100947 %0 Journal Article %J eLife %D 2021 %T The pattern of nodal morphogen signaling is shaped by co-receptor expression %A Lord, Nathan D. %A Carte, Adam N. %A Abitua, Philip B. %A Alexander F. Schier %B eLife %V 10 %G eng %U https://dx.doi.org/10.7554/elife.54894 %9 Journal Article %R 10.7554/elife.54894 %0 Journal Article %J Elife %D 2021 %T Phenotypic and molecular evolution across 10,000 generations in laboratory budding yeast populations %A Johnson, Milo S %A Gopalakrishnan, Shreyas %A Goyal, Juhee %A Dillingham, Megan E %A Bakerlee, Christopher W %A Humphrey, Parris T %A Jagdish, Tanush %A Jerison, Elizabeth R %A Kosheleva, Katya %A Lawrence, Katherine R %B Elife %V 10 %P e63910 %G eng %9 Journal Article %0 Journal Article %J Disease Models & Mechanisms %D 2021 %T Recessive, gain-of-function toxicity in an APOL1 BAC transgenic mouse model mirrors human APOL1 kidney disease %A McCarthy, Gizelle M %A Blasio, Angelo %A Donovan, Olivia G %A Schaller, Lena B %A Bock-Hughes, Althea %A Magraner, Jose M %A Suh, Jung Hee %A Tattersfield, Calum F %A Stillman, Isaac E %A Shah, Shrijal S %B Disease Models & Mechanisms %V 14 %P dmm048952 %G eng %N 8 %9 Journal Article %0 Journal Article %J Science translational medicine %D 2021 %T Skeletal muscle regeneration with robotic actuation–mediated clearance of neutrophils %A Seo, Bo Ri %A Payne, Christopher J %A McNamara, Stephanie L %A Freedman, Benjamin R %A Kwee, Brian J %A Nam, Sungmin %A de Lázaro, Irene %A Darnell, Max %A Alvarez, Jonathan T %A Dellacherie, Maxence O %B Science translational medicine %V 13 %P eabe8868 %G eng %N 614 %9 Journal Article %0 Journal Article %J Environmental microbiology %D 2021 %T Spatially resolved correlative microscopy and microbial identification reveal dynamic depth‐and mineral‐dependent anabolic activity in salt marsh sediment %A Marlow, Jeffrey %A Spietz, Rachel %A Kim, Keun‐Young %A Mark Ellisman %A Girguis, Peter %A Hatzenpichler, Roland %B Environmental microbiology %V 23 %P 4756-4777 %G eng %N 8 %9 Journal Article %0 Journal Article %J Nat Rev Methods Primers %D 2021 %T Tissue Clearing %A Richardson, D.S. %A Guan, W. %A Matsumoto, K. %A Pan, C. %A Chung, K. %A Erturk, A. %A Ueda, H. R. %A Lichtman, J. W. %X Tissue clearing of gross anatomical samples was first described over a century ago and has only recently found widespread use in the field of microscopy. This renaissance has been driven by the application of modern knowledge of optical physics and chemical engineering to the development of robust and reproducible clearing techniques, the arrival of new microscopes that can image large samples at cellular resolution and computing infrastructure able to store and analyze large data volumes. Many biological relationships between structure and function require investigation in three dimensions and tissue clearing therefore has the potential to enable broad discoveries in the biological sciences. Unfortunately, the current literature is complex and could confuse researchers looking to begin a clearing project. The goal of this Primer is to outline a modular approach to tissue clearing that allows a novice researcher to develop a customized clearing pipeline tailored to their tissue of interest. Further, the Primer outlines the required imaging and computational infrastructure needed to perform tissue clearing at scale, gives an overview of current applications, discusses limitations and provides an outlook on future advances in the field. %B Nat Rev Methods Primers %V 1 %G eng %U https://www.ncbi.nlm.nih.gov/pubmed/35128463 %N 1 %9 Journal Article %R 10.1038/s43586-021-00080-9 %0 Journal Article %J PLOS Pathogens %D 2021 %T The type 3 secretion system requires actin polymerization to open translocon pores %A Russo, Brian C. %A Duncan-Lowey, Jeffrey K. %A Chen, Poyin %A Goldberg, Marcia B. %B PLOS Pathogens %V 17 %P e1009932 %G eng %U https://dx.doi.org/10.1371/journal.ppat.1009932 %N 9 %9 Journal Article %R 10.1371/journal.ppat.1009932 %0 Journal Article %J Nature metabolism %D 2021 %T UCP1 governs liver extracellular succinate and inflammatory pathogenesis %A Mills, Evanna L %A Harmon, Cathal %A Jedrychowski, Mark P %A Xiao, Haopeng %A Garrity, Ryan %A Tran, Nhien V %A Bradshaw, Gary A %A Fu, Accalia %A Szpyt, John %A Reddy, Anita %B Nature metabolism %V 3 %P 604-617 %G eng %N 5 %9 Journal Article %0 Unpublished Work %D 2021 %T Viscous effects and complex local flow behaviors dominate hemolymph circulation in the living wings of locusts %A Mary K. Salcedo %A Jun, Brian %A Vlachos, Pavlos %A Mahadevan, Lakshminarayanan %A Combes, Stacey A. %I Cold Spring Harbor Laboratory %G eng %U https://dx.doi.org/10.1101/2021.09.15.460448 %9 Unpublished Work %R 10.1101/2021.09.15.460448 %0 Journal Article %J Cell reports %D 2021 %T Crim1 and Kelch-like 14 exert complementary dual-directional developmental control over segmentally specific corticospinal axon projection targeting %A Sahni, Vibhu %A Itoh, Yasuhiro %A Shnider, Sara J %A Jeffrey D Macklis %B Cell reports %I Elsevier %V 37 %P 109842 %@ 2211-1247 %G eng %N 3 %0 Journal Article %J ACS central science %D 2021 %T Storing and reading information in mixtures of fluorescent molecules %A Nagarkar, Amit A %A Root, Samuel E %A Fink, Michael J %A Ten, Alexei S %A Cafferty, Brian J %A Richardson, Douglas S %A Mrksich, Milan %A Whitesides, George M. %B ACS central science %I ACS Publications %V 7 %P 1728-1735 %@ 2374-7943 %G eng %N 10 %0 Journal Article %J Neuron %D 2020 %T Absence of survival and motor deficits in 500 repeat C9ORF72 BAC mice %A Mordes, Daniel A %A Morrison, Brett M %A Ament, Xanthe H %A Christopher Cantrell %A Joanie Mok %A Pierce Eggan %A Xue, Carolyn %A Jin-Yuan Wang %A Eggan, Kevin %A Rothstein, Jeffrey D %B Neuron %V 108 %P 775-783. e4 %G eng %N 4 %9 Journal Article %0 Journal Article %J Science Advances %D 2020 %T Annexin A1–dependent tethering promotes extracellular vesicle aggregation revealed with single–extracellular vesicle analysis %A Rogers, Maximillian A. %A Buffolo, Fabrizio %A Schlotter, Florian %A Atkins, Samantha K. %A Lang H. Lee %A Halu, Arda %A Mark C. Blaser %A Tsolaki, Elena %A Higashi, Hideyuki %A Luther, Kristin %A Daaboul, George %A Carlijn V. C. Bouten %A Simon C. Body %A Singh, Sasha A. %A Sergio Bertazzo %A Libby, Peter %A Aikawa, Masanori %A Elena Aikawa %X Protein-mediated tethering of vesicles in the extracellular matrix contributes to microcalcification formation. Extracellular vesicles (EVs) including plasma membrane–derived microvesicles and endosomal-derived exosomes aggregate by unknown mechanisms, forming microcalcifications that promote cardiovascular disease, the leading cause of death worldwide. Here, we show a framework for assessing cell-independent EV mechanisms in disease by suggesting that annexin A1 (ANXA1)–dependent tethering induces EV aggregation and microcalcification. We present single-EV microarray, a method to distinguish microvesicles from exosomes and assess heterogeneity at a single-EV level. Single-EV microarray and proteomics revealed increased ANXA1 primarily on aggregating and calcifying microvesicles. ANXA1 vesicle aggregation was suppressed by calcium chelation, altering pH, or ANXA1 neutralizing antibody. ANXA1 knockdown attenuated EV aggregation and microcalcification formation in human cardiovascular cells and acellular three-dimensional collagen hydrogels. Our findings explain why microcalcifications are more prone to form in vulnerable regions of plaque, regulating critical cardiovascular pathology, and likely extend to other EV-associated diseases, including autoimmune and neurodegenerative diseases and cancer. %B Science Advances %V 6 %P eabb1244 %G eng %U https://www.science.org/doi/abs/10.1126/sciadv.abb1244 %N 38 %9 Journal Article %R doi:10.1126/sciadv.abb1244 %0 Journal Article %J Neuroscience %D 2020 %T Automated quantification of immunohistochemical staining of large animal brain tissue using QuPath software %A Morriss, Nicholas J %A Conley, Grace M %A Ospina, Sara M %A Meehan III, William P %A Qiu, Jianhua %A Mannix, Rebekah %B Neuroscience %V 429 %P 235-244 %G eng %9 Journal Article %0 Journal Article %J Advanced Materials Interfaces %D 2020 %T Capturing bubbles and preventing foam using aerophilic surfaces %A Rapoport, Leonid %A Emmerich, Theo %A Varanasi, Kripa K %B Advanced Materials Interfaces %V 7 %P 1901599 %G eng %N 6 %9 Journal Article %0 Journal Article %J bioRxiv %D 2020 %T Changing the Waddington landscape to control mesendoderm competence %A Valcourt, James R %A Huang, Roya %A Kundu, Sharmistha %A Venkatasubramanian, Divya %A Kingston, Robert E %A Ramanathan, Sharad %B bioRxiv %P 867010 %G eng %9 Journal Article %0 Journal Article %J bioRxiv %D 2020 %T CUB and Sushi Multiple Domains 1 (CSMD1) opposes the complement cascade in neural tissues %A Baum, Matthew L %A Daniel K Wilton %A Muthukumar, Allie %A Fox, Rachel G %A Carey, Alanna %A Crotty, William %A Scott-Hewitt, Nicole %A Bien, Elizabeth %A Sabatini, David A %A Lanser, Toby %B bioRxiv %G eng %9 Journal Article %0 Journal Article %J Nature biomedical engineering %D 2020 %T Cytosine and adenine base editing of the brain, liver, retina, heart and skeletal muscle of mice via adeno-associated viruses %A Levy, Jonathan M %A Yeh, Wei-Hsi %A Pendse, Nachiket %A Davis, Jessie R %A Hennessey, Erin %A Butcher, Rossano %A Koblan, Luke W %A Comander, Jason %A Liu, Qin %A Liu, David R %B Nature biomedical engineering %V 4 %P 97-110 %G eng %N 1 %9 Journal Article %0 Journal Article %J Neuron %D 2020 %T Encoding of 3D head orienting movements in the primary visual cortex %A Grigori Guitchounts %A Masis, Javier %A Steffen B E Wolff %A David Cox %B Neuron %V 108 %P 512-525. e4 %G eng %N 3 %9 Journal Article %0 Journal Article %J Proceedings of the National Academy of Sciences %D 2020 %T Extracellular matrix plasticity as a driver of cell spreading %A Grolman, Joshua M %A Weinand, Philipp %A Mooney, David J %B Proceedings of the National Academy of Sciences %V 117 %P 25999-26007 %G eng %N 42 %9 Journal Article %0 Journal Article %J Nucleic Acids Research %D 2020 %T FIN-Seq: transcriptional profiling of specific cell types from frozen archived tissue of the human central nervous system %A Ryoji Amamoto %A Zuccaro, Emanuela %A Curry, Nathan C %A Khurana, Sonia %A Chen, Hsu-Hsin %A Cepko, Constance L %A Arlotta, Paola %B Nucleic Acids Research %V 48 %P e4-e4 %G eng %N 1 %9 Journal Article %0 Journal Article %J Journal of the American Society of Nephrology %D 2020 %T FSGS-causing INF2 mutation impairs cleaved INF2 N-fragment functions in podocytes %A Balajikarthick Subramanian %A Justin Chun %A Perez-Gill, Chandra %A Yan, Paul %A Stillman, Isaac E %A Higgs, Henry N %A Alper, Seth L %A Schlöndorff, Johannes S %A Pollak, Martin R. %B Journal of the American Society of Nephrology %V 31 %P 374-391 %G eng %N 2 %9 Journal Article %0 Journal Article %J Cell reports %D 2020 %T Glucose response by stem cell-derived β cells in vitro is inhibited by a bottleneck in glycolysis %A Davis, Jeffrey C %A Alves, Tiago C %A Helman, Aharon %A Chen, Jonathan C %A Kenty, Jennifer H %A Cardone, Rebecca L %A Liu, David R %A Kibbey, Richard G %A Douglas A Melton %B Cell reports %V 31 %P 107623 %G eng %N 6 %9 Journal Article %0 Journal Article %J bioRxiv %D 2020 %T The importomer is a peroxisomal membrane protein translocase %A Martenson, James S %A Tam, Hanson %A McQuown, Alexander J %A Reif, Dvir %A Zhou, Jing %A Denic, Vladimir %B bioRxiv %G eng %9 Journal Article %0 Journal Article %J Cell metabolism %D 2020 %T Induction of a timed metabolic collapse to overcome cancer chemoresistance %A van Gastel, Nick %A Spinelli, Jessica B %A Sharda, Azeem %A Schajnovitz, Amir %A Baryawno, Ninib %A Rhee, Catherine %A Oki, Toshihiko %A Grace, Eliane %A Soled, Heather J %A Milosevic, Jelena %B Cell metabolism %V 32 %P 391-403. e6 %G eng %N 3 %9 Journal Article %0 Journal Article %J Circulation %D 2020 %T Inhibition of mTOR signaling enhances maturation of cardiomyocytes derived from human-induced pluripotent stem cells via p53-induced quiescence %A Garbern, Jessica C %A Helman, Aharon %A Sereda, Rebecca %A Sarikhani, Mohsen %A Ahmed, Aishah %A Escalante, Gabriela O %A Ogurlu, Roza %A Kim, Sean L %A Zimmerman, John F %A Cho, Alexander %B Circulation %V 141 %P 285-300 %G eng %N 4 %9 Journal Article %0 Journal Article %J Neuroscience %D 2020 %T Internal jugular vein compression collar mitigates histopathological alterations after closed head rotational head impact in swine: A pilot study %A Mannix, Rebekah %A Morriss, Nicholas J %A Conley, Grace M %A Meehan III, William P %A Nedder, Arthur %A Qiu, Jianhua %A Float, Jamison %A DiCesare, Christopher A %A Myer, Gregory D %B Neuroscience %V 437 %P 132-144 %G eng %9 Journal Article %0 Journal Article %J Nature %D 2020 %T Lipid availability determines fate of skeletal progenitor cells via SOX9 %A van Gastel, Nick %A Stegen, Steve %A Eelen, Guy %A Schoors, Sandra %A Carlier, Aurélie %A Daniëls, Veerle W %A Baryawno, Ninib %A Przybylski, Dariusz %A Depypere, Maarten %A Stiers, Pieter-Jan %B Nature %V 579 %P 111-117 %G eng %N 7797 %9 Journal Article %0 Journal Article %J Advanced Therapeutics %D 2020 %T Macrophage‐Mediated Delivery of Hypoxia‐Activated Prodrug Nanoparticles %A Evans, Michael A %A Shields IV, C Wyatt %A Krishnan, Vinu %A Wang, Lily Li‐Wen %A Zhao, Zhongmin %A Ukidve, Anvay %A Lewandowski, Michael %A Gao, Yongsheng %A Mitragotri, Samir %B Advanced Therapeutics %V 3 %P 1900162 %G eng %N 2 %9 Journal Article %0 Journal Article %J NanoImpact %D 2020 %T Mapping 2D-and 3D-distributions of metal/metal oxide nanoparticles within cleared human ex vivo skin tissues %A Touloumes, George J %A Ardoña, Herdeline Ann M %A Casalino, Evan K %A Zimmerman, John F %A Chantre, Christophe O %A Dimitrios Bitounis %A Philip Demokritou %A Kevin Kit Parker %B NanoImpact %V 17 %P 100208 %G eng %9 Journal Article %0 Journal Article %J FEMS Microbiology Letters %D 2020 %T Mapping metabolic activity at single cell resolution in intact volcanic fumarole sediment %A Marlow, Jeffrey J %A Colocci, Isabella %A Jungbluth, Sean P %A Weber, Nils Moritz %A Gartman, Amy %A Kallmeyer, Jens %B FEMS Microbiology Letters %V 367 %P fnaa031 %G eng %N 1 %9 Journal Article %0 Journal Article %J eLife %D 2020 %T Mouse retinal cell behaviour in space and time using light sheet fluorescence microscopy %A Prahst, Claudia %A Ashrafzadeh, Parham %A Mead, Thomas %A Figueiredo, Ana %A Chang, Karen %A Douglas Richardson %A Venkaraman, Lakshmi %A Richards, Mark %A Russo, Ana Martins %A Harrington, Kyle %A Ouarné, Marie %A Pena, Andreia %A Chen, Dong Feng %A Claesson-Welsh, Lena %A Cho, Kin-Sang %A Franco, Claudio A. %A Bentley, Katie %B eLife %V 9 %G eng %U https://dx.doi.org/10.7554/elife.49779 %9 Journal Article %R 10.7554/elife.49779 %0 Journal Article %J Journal of Neuroscience %D 2020 %T Ocular dominance plasticity in binocular primary visual cortex does not require C1q %A Welsh, Christina A %A Stephany, Céleste-Élise %A Sapp, Richard W %A Beth Stevens %B Journal of Neuroscience %V 40 %P 769-783 %G eng %N 4 %9 Journal Article %0 Journal Article %J Cell %D 2020 %T pH-gated succinate secretion regulates muscle remodeling in response to exercise %A Reddy, Anita %A Bozi, Luiz HM %A Yaghi, Omar K %A Mills, Evanna L %A Xiao, Haopeng %A Nicholson, Hilary E %A Paschini, Margherita %A Paulo, Joao A %A Garrity, Ryan %A Laznik-Bogoslavski, Dina %B Cell %V 183 %P 62-75. e17 %G eng %N 1 %9 Journal Article %0 Journal Article %J Advanced Science %D 2020 %T Photo‐disassembly of membrane microdomains revives conventional antibiotics against MRSA %A Hui, Jie %A Dong, Pu‐Ting %A Liang, Lijia %A Mandal, Taraknath %A Li, Junjie %A Ulloa, Erlinda R %A Zhan, Yuewei %A Jusuf, Sebastian %A Zong, Cheng %A Seleem, Mohamed N %B Advanced Science %V 7 %P 1903117 %G eng %N 6 %9 Journal Article %0 Journal Article %J Chemical senses %D 2020 %T Renewal and differentiation of GCD necklace olfactory sensory neurons %A Bloom, Maria Lissitsyna %A Johnston, Lucille B %A Datta, Sandeep Robert %B Chemical senses %V 45 %P 333-346 %G eng %N 5 %9 Journal Article %0 Journal Article %J The EMBO Journal %D 2020 %T A splicing isoform of GPR56 mediates microglial synaptic refinement via phosphatidylserine binding %A Li, Tao %A Chiou, Brian %A Gilman, Casey K. %A Luo, Rong %A Koshi, Tatsuhiro %A Yu, Diankun %A Oak, Hayeon C. %A Stefanie Giera %A Johnson‐Venkatesh, Erin %A Muthukumar, Allie K. %A Beth Stevens %A Hisashi Umemori %A Xianhua Piao %B The EMBO Journal %V 39 %G eng %U https://dx.doi.org/10.15252/embj.2019104136 %N 16 %9 Journal Article %R 10.15252/embj.2019104136 %0 Journal Article %J Stem cell reports %D 2020 %T Sustained activation of AMPK enhances differentiation of human iPSC-derived cardiomyocytes via sirtuin activation %A Sarikhani, Mohsen %A Garbern, Jessica C %A Sai Ma %A Sereda, Rebecca %A Conde, Jeffrey %A Krähenbühl, Guido %A Escalante, Gabriela O %A Ahmed, Aishah %A Buenrostro, Jason D %A Lee, Richard T %B Stem cell reports %V 15 %P 498-514 %G eng %N 2 %9 Journal Article %0 Journal Article %J IScience %D 2020 %T Thioredoxin interacting protein is required for a chronic energy-rich diet to promote intestinal fructose absorption %A Shah, Anu %A Dagdeviren, Sezin %A Lewandowski, Jordan P %A Schmider, Angela B %A Ricci-Blair, Elisabeth M %A Niranjana Natarajan %A Hundal, Henna %A Noh, Hye Lim %A Friedline, Randall H %A Vidoudez, Charles %B IScience %V 23 %P 101521 %G eng %N 9 %9 Journal Article %0 Journal Article %J Advanced Science %D 2020 %T Photo‐disassembly of membrane microdomains revives conventional antibiotics against MRSA %A Hui, Jie %A Dong, Pu‐Ting %A Liang, Lijia %A Mandal, Taraknath %A Li, Junjie %A Ulloa, Erlinda R %A Zhan, Yuewei %A Jusuf, Sebastian %A Zong, Cheng %A Seleem, Mohamed N %B Advanced Science %I Wiley Online Library %V 7 %P 1903117 %@ 2198-3844 %G eng %N 6 %0 Journal Article %J Cerebral Cortex %D 2020 %T Increase in seizure susceptibility after repetitive concussion results from oxidative stress, parvalbumin-positive interneuron dysfunction and biphasic increases in glutamate/GABA ratio %A MacMullin, Paul %A Hodgson, Nathaniel %A Damar, Ugur %A Lee, Henry Hing Cheong %A Hameed, Mustafa Q %A Dhamne, Sameer C %A Hyde, Damon %A Conley, Grace M %A Morriss, Nicholas %A Qiu, Jianhua %B Cerebral Cortex %I Oxford University Press %V 30 %P 6108-6120 %@ 1047-3211 %G eng %N 12 %0 Journal Article %J Science %D 2020 %T Neuron class–specific responses govern adaptive myelin remodeling in the neocortex %A Sung Min Yang %A Katrin Michel %A Vahbiz Jokhi %A Nedivi, Elly %A Arlotta, Paola %B Science %V 370 %G eng %U https://science.sciencemag.org/content/370/6523/eabd2109.long %N 6523 %0 Journal Article %J eLife %D 2020 %T Distinct temporal difference error signals in dopamine axons in three regions of the striatum in a decision-making task %A Iku Tsutsui-Kimura %A Hideyuki Matsumo %A Korleki Akiti %A Melissa M Yamada %A Uchida, Naoshige %A Watabe-Uchida, Mitsuko %B eLife %V 9 %P e62390 %G eng %U https://elifesciences.org/articles/62390#s4 %0 Journal Article %J Cell %D 2020 %T Molecular Basis of Chemotactile Sensation in Octopus %A Lena van Giesen %A Peter B Kilian %A Corey A.H. Allard %A Nicholas W. Bellono %B Cell %V 183 %P 587-588 %G eng %U https://www-sciencedirect-com.ezp-prod1.hul.harvard.edu/science/article/pii/S0092867420311491 %N 3 %0 Journal Article %J Nature Protocols %D 2020 %T Tutorial: avoiding and correcting sample-induced spherical aberration artifacts in 3D fluorescence microscopy %A Erin E Diel %A Lichtman, Jeff W %A Richardson, Douglas S %B Nature Protocols %V epub %G eng %U https://www.nature.com/articles/s41596-020-0360-2?utm_source=other&utm_medium=other&utm_content=null&utm_campaign=JRCN_2_DD01_CN_NatureRJ_article_paid_XMOL#Abs1 %0 Journal Article %J Molecular Cell %D 2020 %T The 3D Topography of Mitotic Chromosomes %A Lingluo Chu %A Liang, Zhangyi %A Maria Mukhina %A Fisher, Jay %A Nadine Vincenten %A Zhang, Zheng %A Hutchinson, John %A Zickler, Denise %A Kleckner, Nancy %B Molecular Cell %V 79 %P 1-15 %G eng %U https://www.sciencedirect.com/science/article/pii/S1097276520304688 %0 Journal Article %J Developmental Cell %D 2020 %T Long-Range Optogenetic Control of Axon Guidance Overcomes Developmental Boundaries and Defects %A James M. Harris %A Andy Yu-Der Wang %A Jonathan Boulanger-Weill %A Cristina Santoriello %A Stephan Foianini %A Jeff W. Lichtman %A Leonard I. Zon %A Arlotta, Paola %B Developmental Cell %V 53 %P 577-588 %G eng %U https://www.sciencedirect.com/science/article/pii/S1534580720303981?via%3Dihub %0 Journal Article %J Cell %D 2020 %T Cell Types Promoting Goosebumps Forma Niche to Regulate Hair Follicle Stem Cells %A Shwartz, Yulia %A Meryem Gonzalez-Celeiro %A Chih-Lung Chen %A H. Amalia Pasolli %A Sheu, Shu-Hsien %A Sabrina Mai-Yi Fan %A Shamsi, Farnaz %A Steven Assaad %A Edrick Tai-Yu Lin %A Zhang, Bing %A Pai-Chi Tsai %A Megan He %A Tseng, Yu-Hua %A Sung-Jan Lin %A Ya-Chieh Hsu %B Cell %G eng %U https://reader.elsevier.com/reader/sd/pii/S0092867420308084?token=B34EF1B6440173F4A332B30E4D5644ADBB415C0CEE5278AB0CE282B314EF92E5B8275F02EFB05F0FFC19CC48FB57E55E %0 Journal Article %J Nature %D 2020 %T MeCP2 links heterochromatin condensates and neurodevelopmental disease %A Charles H Li %A Eliot L Coffey %A Alessandra Dall'Agnese %A Nancy M Hannett %A Xin Tang %A Jonathan E Henninger %A Jesse M Platt %A Ozgur Oksuz %A Alicia V Zamudio %A Lena K Afeyan %A Jurian Schuijers %A X Shawn Liu %A Styliani Markoulaki %A Tenzin Lungjangwa %A Gary LeRoy %A Devon S Svoboda %A Emile Wogram %A Tong Ihn Lee %A Jaenisch, Rudolf %A Young, Richard A %B Nature %G eng %U https://www.nature.com/articles/s41586-020-2574-4 %0 Journal Article %J Nature %D 2020 %T C9orf72 suppresses systemic and neural inflammation induced by gut bacteria %A Burberry, Aaron %A Michael F. Wells %A Limone, Francesco %A Alexander Couto %A Kevin S. Smith %A James Keaney %A Gaëlle Gillet %A van Gastel, Nick %A Jin-Yuan Wang %A Olli Pietilainen %A Menglu Qian %A Pierce Eggan %A Christopher Cantrell %A Joanie Mok %A Irena Kadiu %A David T. Scadden %A Eggan, Kevin %B Nature %V 582 %P 89-94 %G eng %U https://www.nature.com/articles/s41586-020-2288-7 %0 Journal Article %J Science %D 2020 %T Partitioning of cancer therapeutics in nuclear condensates %A Isaac A. Klein %A Boija, Ann %A Lena K. Afeyan %A Susana Wilson Hawken %A Mengyang Fan %A Alessandra Dall'Agnese %A Ozgur Oksuz %A Jonathan E. Henninger %A Krishna Shrinivas %A Benjamin R. Sabari %A Ido Sagi %A Victoria E. Clark %A Jesse M. Platt %A Mrityunjoy Kar %A Patrick M. McCall %A Alicia V. Zamudio %A John C. Manteiga %A Eliot L. Coffey %A Charles H. Li %A Nancy M. Hannett %A Yang Eric Guo %A Tim-Michael Decker %A Tong Ihn Lee %A Zhang, Tinghu %A Jing-Ke Weng %A Dylan J. Taatjes %A Arup Chakraborty %A Phillip A. Sharp %A Young Tae Chang %A Anthony A. Hyman %A Nathanael S. Gray %A Richard A. Young %B Science %V 368 %P 1386-1392 %G eng %U https://science.sciencemag.org/content/sci/368/6497/1386.full.pdf %0 Journal Article %J EMBO Reports %D 2020 %T To Buy or to Lease: The Advantages and Costs of Leasing Versus Buying Scientific Instruments for Academic Core Facilities %A Yupeng Wang %A Richardson, Douglas S %B EMBO Reports %V 21 %P e49971 %G eng %U https://www.embopress.org/doi/abs/10.15252/embr.202049971 %0 Journal Article %J eLife %D 2020 %T Mouse retinal cell behaviour in space and time using light sheet fluorescencemicroscopy %A Prahst, Claudia %A Ashrafzadeh, Parham %A Mead, Thomas %A Figueiredo, Ana %A Chang, Karen %A Douglas Richardson %A Lakshmi Venkatraman %A Richards, Mark %A Russo, Ana Martins %A Harrington, Kyle %A Marie Ouarne %A Pena, Andreia %A Chen, Dong Feng %A Lena 7 Claesson-Welsh %A Cho, Kin-Sang %A Claudio Franco %A Bentley, Katie %B eLife %V 9 %P e49779 %G eng %U https://elifesciences.org/articles/49779 %0 Journal Article %J Nature %D 2020 %T Hyperactivation of sympathetic nerves drives depletion of melanocyte stem cells %A Zhang, Bing %A Sai Ma %A Inbal Rachmin %A Megan He %A Baral, Pankaj %A Sekyu Choi %A William A. Gonçalves %A Shwartz, Yulia %A Eva M. Fast %A Yiqun Su %A Leonard I. Zon %A Regev, Aviv %A Buenrostro, Jason D. %A Thiago M. Cunha %A Isaac M. Chiu %A David E. Fisher %A Ya-Chieh Hsu %B Nature %V 577 %P 676-681 %G eng %U https://www.nature.com/articles/s41586-020-1935-3.pdf %0 Journal Article %J Nature Neuroscience %D 2019 %T Single-cell transcriptomic profiling of the aging mouse brain %A Methodios Ximerakis %A Scott L. Lipnick %A Brendan T. Innes %A Sean K. Simmons %A Adiconis, Xian %A Dionne, Danielle %A Brittany A. Mayweather %A Lan Nguyen %A Zachary Niziolek %A Ceren Ozek %A Vincent L. Butty  %A Ruth Isserlin %A Sean M. Buchanan %A Stuart S. Levine %A Regev, Aviv %A Gary D. Bader %A Joshua Z. Levin %A Lee L. Rubin %B Nature Neuroscience %V 22 %P 1696-1708 %G eng %U https://www.nature.com/articles/s41593-019-0491-3.pdf %0 Journal Article %J Nature Neuroscience %D 2019 %T Single-cell transcriptomic profiling of the aging mouse brain %A Methodios Ximerakis %A Scott L. Lipnick %A Brendan T. Innes %A Sean K. Simmons %A Adiconis, Xian %A Dionne, Danielle %A Brittany A. Mayweather %A Lan Nguyen %A Zachary Niziolek %A Ceren Ozek %A Vincent L. Butty %A Ruth Isserlin %A Sean M. Buchanan %A Stuart S. Levine %A Regev, Aviv %A Gary D. Bader %A Joshua Z. Levin %A Lee L. Rubin %B Nature Neuroscience %V 22 %P 1696-1708 %G eng %U https://www.nature.com/articles/s41593-019-0491-3.pdf %0 Journal Article %J Cell Reports %D 2019 %T In Situ Modification of Tissue Stem and Progenitor Cell Genomes %A Jill M. Goldstein %A Tabebordbar, Mohammadsharif %A Zhu, Kexian %A Leo D. Wang %A Kathleen A. Messemer %A Peacker, Bryan %A Ashrafi Kakhki, Sara %A Meryem Gonzalez-Celeiro %A Shwartz, Yulia %A Jason K.W. Cheng %A Xiao, Ru %A Barungi, Trisha %A Albright, Charles %A Ya-Chieh Hsu %A Luk H. Vandenberghe %A Amy J. Wagers %B Cell Reports %V 27 %P 1254-1264 %G eng %U https://www.cell.com/action/showPdf?pii=S2211-1247%2819%2930452-8 %0 Journal Article %J JCI Insight %D 2019 %T Effect of dietary fat and sucrose consumption on cardiac fibrosis in mice and rhesus monkeys %A Niranjana Natarajan %A Ana Vujic %A Das, Jishnu %A Annie C. Wang %A Krystal K. Phu %A Spencer H. Kiehm %A Elisabeth M. Ricci-Blair %A Anthony Y. Zhu %A Kelli L. Vaughan %A Kicki J. Colman %A Julie A. Mattison %A Lee, Richard T. %B JCI Insight %V 4 %P e128685 %G eng %U https://insight.jci.org/articles/view/128685/pdf %N 18 %0 Journal Article %J eLife %D 2019 %T A bidirectional network for appetite control in larval zebrafish %A Caroline Lei Wee %A Erin Yue Song %A Robert Evan Johnson %A Deepak Ailani %A Randlett, Owen %A Ji-Yoon Kim %A Maxim Nikitchenko %A Armin Bahl %A Chao-Tsung Yang %A Ahrens, Misha B %A Koichi Kawakami %A Engert, Florian %A Kunes, Sam %B eLife %V 8 %G eng %U https://elifesciences.org/articles/43775 %N e43775 %0 Journal Article %J Nature Communications %D 2019 %T Mouse embryo geometry drives formation of robust signaling gradients through receptor localization %A Zhenchun Zhang %A Steven Zwick %A Ethan Loew %A Joshua S Grimley %A Ramanathan, Sharad %B Nature Communications %V 10 %G eng %U https://www.nature.com/articles/s41467-019-12533-7.pdf %N 4516 %0 Journal Article %J Nano Letters %D 2019 %T Cyborg Organoids: Implantation of Nanoelectronics via Organogenesis for Tissue-Wide Electrophysiology %A Li, Qiang %A Kewang Nan %A Paul Le Floch %A Zuwan Lin %A Hao Sheng %A Thomas S Blum %A Jia Liu %B Nano Letters %V 19 %P 5781-5789 %G eng %U https://pubs.acs.org/doi/10.1021/acs.nanolett.9b02512 %N 8 %0 Journal Article %J Nature %D 2019 %T Individual brain organoids reproducibly form cell diversity of the human cerebral cortex %A Silvia Velasco %A Amanda J. Kedaigle %A Sean K. Simmons %A Allison Nash %A Marina Rocha %A Giorgia Quadrato %A Bruna Paulsen %A Lan Nguyen %A Adiconis, Xian %A Regev, Aviv %A Joshua Z. Levin %A Arlotta, Paola %B Nature %G eng %U https://www.nature.com/articles/s41586-019-1289-x.pdf %0 Journal Article %J Nature %D 2019 %T Charting cellular identity during human in vitro β-cell differentiation %A Veres, Adrian %A Aubrey L. Faust %A Henry L. Bushnell %A Elise N. Engquist %A Jennifer Hyoje-Ryu Kenty %A George Harb %A Yeh-Chuin Poh %A Elad Sintov %A Mads Gürtler %A Felicia W. Pagliuca %A Quinn P. Peterson %A Douglas A. Melton %B Nature %G eng %U https://www.nature.com/articles/s41586-019-1168-5.pdf %0 Journal Article %J Science %D 2019 %T Acoel genome reveals the regulatory landscape of whole-body regeneration %A Andrew R. Gehrke %A Emily Neverett %A Yi-Jyun Luo %A Alexander Brandt %A Lorenzo Ricci %A Ryan E. Hulett %A Annika Gompers %A J. Graham Ruby %A Daniel S. Rokhsar %A Peter W. Reddien %A Mansi Srivastava %B Science %V 363 %G eng %U http://science.sciencemag.org/content/363/6432/eaau6173 %0 Journal Article %J Nature %D 2019 %T Subcellular transcriptomes and proteomes of developing axon projections in the cerebral cortex %A Poulopoulos, Alexandros %A Alexander J. Murphy %A Abdulkadir Ozkan %A Patrick Davis %A John Hatch %A Rory Kirchner %A Jeffrey D. Macklis %B Nature %V 565 %P 356-360 %G eng %U https://www.nature.com/articles/s41586-018-0847-y.pdf %0 Journal Article %J Cell %D 2019 %T Phenotypic Landscape of Schizophrenia-Associated Genes Defines Candidates and Their Shared Functions %A Summer B. Thyme %A Lindsey M. Pieper %A Eric H. Li %A Shristi Pandey %A Wang, Yiqun %A Nathan S. Morris %A Carrie Sha %A Joo Won Choi %A Kristian J. Herrera %A Edward R. Soucy %A Zimmerman, Steve %A Randlett, Owen %A Greenwood, Joel %A Steven A. McCarroll %A Alexander F. Schier %B Cell %G eng %U https://dmg5c1valy4me.cloudfront.net/wp-content/uploads/2019/03/28094049/1-s2.0-S0092867419301114-main.pdf %0 Journal Article %J The Journal of Molecular Diagnostics %D 2019 %T Highly Multiplexed FISH for in Situ Genomics %A Maristela L. Onozato %A Yapp, Clarence %A Douglas Richardson %A Tilak Sundaresan %A Varun Chahal %A Jesse Lee %A James P. Sullivan %A Marisa W. Madden %A Hyo Sup Shim %A Mathew Liebers %A Quan Ho %A Maheswaran,Shyamala %A Haber, Daniel A. %A Zongli Zheng %A Brian Clancy %A Hunter L. Elliott %A Jochen K. Lennerz %A A. John Iafrate %B The Journal of Molecular Diagnostics %G eng %U https://www.sciencedirect.com/science/article/pii/S1525157818300229?via%3Dihub %0 Journal Article %J Nature Materials %D 2019 %T Bioinspired neuron-like electronics %A Xiao Yang %A Zhou, Tao %A Theodore J. Zwang %A Guosong Hong %A Yunlong Zhao %A Robert D. Viveros %A Tian-Ming Fu %A Teng Gao %A Charles m Lieber %B Nature Materials %G eng %U https://www.nature.com/articles/s41563-019-0292-9.pdf %0 Journal Article %J PNAS %D 2019 %T Recruitment of APOL1 kidney disease risk variants tolipid droplets attenuates cell toxicity %A Justin Chun %A Jia-Yue Zhang %A Maris S. Wilkins %A Balajikarthick Subramanian %A Cristian Riella %A Jose M. Magraner %A Seth L. Alper %A David J. Friedman %A Pollak, Martin R. %B PNAS %G eng %U https://www.pnas.org/content/early/2019/02/06/1820414116 %0 Journal Article %J Cell %D 2019 %T A Peninsular Structure Coordinates AsynchronousDifferentiation with Morphogenesis to GeneratePancreatic Islets %A Nadav Sharon %A Raghav Chawla %A Jonas Mueller %A Jordan Vanderhooft %A Luke James Whitehorn %A Benjamin Rosenthal %A Mads Gurtler %A Ralph R. Estanboulieh %A Shvartsman, Dmitry %A David K. Gifford %A Cole Trapnell %A Doug Melton %B Cell %V 176 %G eng %U https://www.sciencedirect.com/science/article/pii/S0092867418315861 %0 Journal Article %J Development %D 2019 %T Blastemal progenitors modulate immune signaling during early limb regeneration %A Stephanie L. Tsai %A Clara Baselga-Garriga %A Douglas A. Melton1 %B Development %V 146 %G eng %U http://dev.biologists.org/content/develop/146/1/dev169128.full.pdf %0 Journal Article %J PNAS %D 2018 %T A simple developmental model recapitulates complex insect wing venation patterns %A Jordan Hoffmann %A Seth Donoughe %A Kathy Li %A Mary K. Salcedo %A Chris H. Rycroft %B PNAS %V 115 %P 9905-9910 %G eng %U https://www.pnas.org/content/pnas/115/40/9905.full.pdf %N 40 %0 Journal Article %J PNAS %D 2018 %T Nonuniformity in ligaments is a structural strategy for optimizing functionality %A Gili R. S. Naveh %A Jonathan E. Foster %A Tomas M. Silva Santisteban %A Xianrui Yang %A Bjorn R. Olsen %B PNAS %V 115 %P 9008-9013 %G eng %U https://www.pnas.org/content/pnas/115/36/9008.full.pdf %N 36 %0 Journal Article %J Circulation %D 2018 %T Complement Receptor C5aR1 Plays an Evolutionarily Conserved Role in Successful Cardiac Regeneration %A Niranjana Natarajan %A Yamen Abbas %A Donald M. Bryant %A Juan Manuel GonzalezRosa %A Michka Sharpe %A Aysu Uygur %A Lucas H. Cocco-Delgado %A Nhi Ngoc Ho %A Norma P. Gerard %A Craig J. Gerard %A Calum A. MacRae %A Caroline E. Burns %A C. Geoffrey Burns %A Jessica L. Whited %A Lee, Richard T. %B Circulation %V 137 %P 2152-2165 %G eng %U https://www.ahajournals.org/doi/pdf/10.1161/CIRCULATIONAHA.117.030801 %0 Journal Article %J Development %D 2018 %T Conserved regulation of Nodal-mediated left-right patterning in zebrafish and mouse %A Tessa G. Montague %A James A. Gagnon %A Alexander F. Schier %B Development %G eng %U http://dev.biologists.org/content/develop/early/2018/11/15/dev.171090.full.pdf %0 Journal Article %J Neuron %D 2018 %T CD47 Protects Synapses from Excess Microglia-Mediated Pruning during Development %A Emily K. Lehrman %A Daniel K. Wilton %A Elizabeth Y. Litvina %A Christina A. Welsh %A Stephen T. Chang %A Arnaud Frouin %A Alec J. Walker %A Molly D. Heller %A Hisashi Umemori %A Chinfei Chen %A Beth Stevens %B Neuron %V 100 %G eng %U https://reader.elsevier.com/reader/sd/pii/S0896627318307906?token=F33EAE513E37FF3E747C37DF5C3743BDAE4A28CECB5DC4F1118719FCFAD7AB9F8597DF955F7F2D91697D9C4C1AE5F2A4 %0 Journal Article %J Immunity %D 2018 %T Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes %A Timothy R. Hammond %A Connor Dufort %A Lasse Dissing-Olesen %A Stefanie Giera %A Young, Adam %A Wysoker, Alec %A Alec J. Walker %A Frederick Gergits %A Michael Segel %A James Nemesh %A Samuel E. Marsh %A Saunders, Arpiar %A Macosko, Evan %A Ginhoux, Florent %A Jinmiao Chen %A Robin J.M. Franklin %A Xianhua Piao %A Steven A. McCarroll %A Beth Stevens %B Immunity %V 50 %G eng %U https://ac.els-cdn.com/S1074761318304850/1-s2.0-S1074761318304850-main.pdf?_tid=4889bc20-6168-4eb8-ac19-fd9392791e9b&acdnat=1543941514_87158b42afd2359de7657f581e4393ed %0 Journal Article %J Science %D 2018 %T Molecular, spatial and functional single-cell profiling of the hypothalamic preoptic region %A Jeffrey R. Moffitt %A Dhananjay Bambah-Mukku %A Stephen W. Eichhorn %A Eric Vaughn %A Karthik Shekhar %A Julio D. Perez %A Nimrod D. Rubinstein %A Junjie Hao %A Regev, Aviv %A Dulac, Catherine %A Zhuang, Xiaowei %B Science %G eng %U http://science.sciencemag.org.ezp-prod1.hul.harvard.edu/content/early/2018/10/31/science.aau5324 %0 Journal Article %J Nature Methods %D 2018 %T Nanobody immunostaining for correlated light and electron microscopy with preservation of ultrastructure %A Tao Fang %A Xiaotang Lu %A Daniel Berger %A Christina Gmeiner %A Julia Cho %A Schalek, Richard %A Ploegh, Hidde %A Jeff Lichtman %B Nature Methods %G eng %0 Journal Article %J Nanomaterials %D 2018 %T Engineering a 3D-Bioprinted Model of Human Heart Valve Disease Using Nanoindentation-Based Biomechanics %A Dewy C. van der Valk %A Casper F. T. van der Ven %A Mark C. Blaser %A Joshua M. Grolman %A Wu, Pin-Jou %A Owen S. Fenton %A Lang H. Lee %A Mark W. Tibbitt %A Jason L. Andresen %A Jennifer R. Wen %A Anna H. Ha %A Buffolo, Fabrizio %A van Mil, Alain %A Carlijn V. C. Bouten %A Simon C. Body %A Mooney, David J. %A Joost P. G. Sluijter %A Aikawa, Masanori %A Hjortnaes, Jesper %A Langer, Robert %A Elena Aikawa %B Nanomaterials %V 8 %G eng %U https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5977310/pdf/nanomaterials-08-00296.pdf %N 296 %0 Journal Article %J Science %D 2018 %T Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis %A Jeffrey A. Farrell %A Wang, Yiqun %A Samantha J. Riesenfeld %A Karthik Shekhar %A Regev, Aviv %A Alexander F. Schier %B Science %V 360 %G eng %U http://science.sciencemag.org/content/360/6392/eaar3131/tab-pdf %0 Journal Article %J Science Advances %D 2018 %T Regulated nuclear accumulation of a histone methyltransferase times the onset of heterochromatin formation in C. elegans embryos %A Beste Mutlu %A Huei-Mei Chen %A James J. Moresco %A Barbara D. Orelo %A Bing Yang %A John M. Gaspar %A Sabine Keppler-Ross %A John R. Yates III %A David H. Hall %A Eleanor M. Maine %A Susan E. Mango %B Science Advances %V 4 %G eng %U https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6105299/pdf/aat6224.pdf %0 Journal Article %J Journal of Bacteriology %D 2018 %T Swarmer Cell Development of the Bacterium Proteus mirabilis Requires the Conserved Enterobacterial Common Antigen Biosynthesis Gene rffG %A Kristin Little %A Murray J. Tipping %A Karine A. Gibbs %B Journal of Bacteriology %V 200 %G eng %U https://jb.asm.org/content/jb/200/18/e00230-18.full.pdf %N 18 %0 Journal Article %J Nature Neuroscience %D 2018 %T Dopamine neurons projecting to the posterior striatum reinforce avoidance of threatening stimuli %A Menegas, William %A Korleki Akiti %A Ryunosuke Amo %A Uchida, Naoshige %A Watabe-Uchida, Mitsuko %B Nature Neuroscience %G eng %U http://www.nature.com.ezp-prod1.hul.harvard.edu/articles/s41593-018-0222-1.pdf %0 Journal Article %J The Journal of Clinical Investigation %D 2018 %T Blocking p62-dependent SMN degradation ameliorates spinal muscular atrophy disease phenotypes %A Rodriguez-Muela, Natalia %A Parkhitko, Andrey %A Grass, Tobias %A Rebecca M. Gibbs %A Erika M. Norabuena %A Perrimon, Norbert %A Singh, Rajat %A Lee L. Rubin %B The Journal of Clinical Investigation %V 128 %P 3008-3023 %G eng %U https://www.jci.org/articles/view/95231/pdf %N 7 %0 Journal Article %J Biology Open %D 2018 %T High-throughput live-imaging of embryos in microwell arrays using a modular specimen mounting system %A Seth Donoughe %A Chiyoung Kim %A Cassandra G. Extavour %B Biology Open %V 7 %G eng %U http://bio.biologists.org/content/biolopen/7/7/bio031260.full.pdf %0 Journal Article %J Science %D 2018 %T A method for single-neuron chronic recording from the retina in awake mice %A Guosong Hong %A Tian-Ming Fu %A Tian-Ming Fu %A Robert D. Viveros %A Xiao Yang %A Zhou, Tao %A Jung Min Lee %A Park, Hong-Gyu %A Joshua R. Sanes %A Charles M. Lieber %B Science %V 360 %P 1447-1451 %G eng %U http://science.sciencemag.org/content/sci/360/6396/1447.full.pdf %0 Journal Article %J Nature %D 2018 %T Protection from UV light is an evolutionarily conserved feature of the haematopoietic niche %A Friedrich G. Kapp %A Julie R. Perlin %A Elliott J. Hagedorn %A John M. Gansner %A Daniel E. Schwarz %A Lauren A. O’Connell %A Nicholas S. Johnson %A Chris Amemiya %A David E. Fisher %A Ute Wölfle %A Trompouki, Eirini %A Charlotte M. Niemeyer %A Wolfgang Driever %A Leonard I. Zon %B Nature %V 558 %P 445-448 %G eng %U https://www.nature.com/articles/s41586-018-0213-0.pdf %0 Journal Article %J Science %D 2018 %T Coactivator condensation at super-enhancers links phase separation and gene control %A Benjamin R. Sabari %A Alessandra Dall'Agnese %A Boija, Ann %A Isaac A. Klein %A Eliot L. Coffey %A Krishna Shrinivas %A Brian J. Abraham %A Nancy M. Hannett %A Alicia V. Zamudio %A John C. Manteiga %A Charles H. Li %A Yang E. Guo %A Day, Daniel S. %A Jurian Schuijers %A Vasile, Eliza %A Sohail Malik %A Denes Hnisz %A Tong Ihn Lee %A Ibrahim I. Cisse %A Robert G. Roeder %A Phillip A. Sharp %A Arup K. Chakraborty %A Richard A. Young %B Science %G eng %U http://science.sciencemag.org/content/early/2018/06/20/science.aar3958/tab-pdf %0 Journal Article %J PNAS %D 2018 %T Cargo transport shapes the spatial organization of a microbial community %A Abhishek Shrivastava %A Visha K. Patel %A Yisha Tang %A Susan Connolly Yost %A Floyd E. Dewhirst %A Howard C. Berg %B PNAS %G eng %0 Journal Article %J Nature Communications %D 2018 %T A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus %A A. Rasim Barutcu %A Philipp G. Maass %A Jordan P. Lewandowski %A Catherine L. Weiner %A John L. Rinn %B Nature Communications %V 9 %G eng %U https://www.nature.com/articles/s41467-018-03614-0.pdf %N 1444 %0 Journal Article %J Nature %D 2018 %T Functional circuit architecture underlying parental behaviour %A Johannes Kohl %A Benedicte M. Babayan %A Nimrod D. Rubinstein %A Anita E. Autry %A Brenda Marin-Rodriguez %A Kapoor, Vikrant %A Kazunari Miyamishi %A Larry S. Zweifel %A Liqun Luo %A Uchida, Naoshige %A Dulac, Catherine %B Nature %V 556 %P 326-331 %G eng %U https://www.nature.com/articles/s41586-018-0027-0#Ack1 %0 Journal Article %J Nature Neuroscience %D 2018 %T Developmentally primed cortical neurons maintain fidelity of differentiation and establish appropriate functional connectivity after transplantation %A Thomas V. Wuttke %A Foivos Markopoulos %A Hari Padmanabhan %A Aaron P. Wheeler %A Venkatesh N. Murthy %A Jeffrey D. Macklis %B Nature Neuroscience %V 21 %P 517-529 %G eng %U https://www.nature.com/articles/s41593-018-0098-0.pdf %0 Journal Article %J Scientific Reports %D 2018 %T A micro-CT-based method for quantitative brain lesion characterization and electrode localization %A Javier Masís %A David Mankus %A Steffen B. E. Wolff %A Grigori Guitchounts %A Maximilian Joesch %A David D. Cox %B Scientific Reports %V 8 %G eng %U https://www.nature.com/articles/s41598-018-23247-z.pdf %N 5184 %0 Journal Article %J Nature Communications %D 2018 %T Dynamic air/liquid pockets for guiding microscale flow %A Hou, Xu %A Li, Jianyu %A Alexander B. Tesler %A Yuxing Yao %A Miao Wang %A Lingli Min %A Zhizhi Sheng %A Aizenberg, Joanna %B Nature Communications %V 9 %G eng %U https://www.nature.com/articles/s41467-018-03194-z.pdf %N 733 %0 Journal Article %J Molecular Cell %D 2018 %T Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C %A Philipp G. Maass %A A. Rasim Barutcu %A Catherine L. Weiner %A John L. Rinn %B Molecular Cell %V 69 %P 1039-1045 %G eng %U http://www.cell.com/molecular-cell/pdf/S1097-2765(18)30105-9.pdf %0 Journal Article %J Current Biology %D 2018 %T Comprehensive Identification and Spatial Mapping of Habenular Neuronal Types Using Single-Cell RNA-Seq %A Shristi Pandey %A Karthik Shekhar %A Regev, Aviv %A Schier, Alexander F %B Current Biology %G eng %U http://www.cell.com/action/showMethods?pii=S0960-9822%2818%2930225-2 %0 Journal Article %J EMBO %D 2018 %T High‐throughput identification of RNA nuclear enrichment sequences %A Chinmay J Shukla %A Alexandra L McCorkindale %A Chiara Gerhardinger %A Keegan D Korthauer %A Moran N Cabili %A David M Shechner %A Irizarry, Rafael A %A Philipp G Maass %A Rinn, John L %B EMBO %G eng %U http://emboj.embopress.org/content/embojnl/early/2018/01/15/embj.201798452.full.pdf %0 Journal Article %J Nature Structural and Molecular Biology %D 2018 %T Spatiotemporal allele organization by allele-specific CRISPR live-cell imaging (SNP-CLING) %A Philipp G. Maass %A A. Rasim Barutcu %A David M. Shechner %A Catherine L. Weiner %A Marta Melé %A John L. Rinn %B Nature Structural and Molecular Biology %G eng %U https://www.nature.com/articles/s41594-017-0015-3 %0 Journal Article %J Cell %D 2017 %T Organism-Level Analysis of Vaccination Reveals Networks of Protection across Tissues %A Kadoki, Motohiko %A Patil, Ashwini %A Cornelius C. Thaiss %A Donald J. Brooks %A Pandey, Surya %A Deep, Deeksha %A Alvarez, David %A Ulrich H. von Andrian %A Amy J. Wagers %A Nakai, Kenta %A Tarjei S. Mikkelsen %A Soumillon, Magali %A Chevrier, Nicolas %B Cell %V 171 %P 398-413 %G eng %U https://reader.elsevier.com/reader/sd/7D99DBD39003B2D9B5A9417A799B70CE15A91C7BE0999EF8CE9CC58116936CF4BB6CEDC43A3131F4D6AC06EFC76697C3 %0 Journal Article %J Nature %D 2017 %T Kctd13 deletion reduces synaptic transmission via increased RhoA %A Christine Ochoa Escamilla %A Irina Filonova %A Angela K. Walker %A Zhong X. Xuan %A Roopashri Holehonnur %A Felipe espinosa %A Shunan Liu %A Summer B. Thyme %A Isabel A. López-García %A Dorian B. mendoza %A Noriyoshi Usui %A Jacob Ellegood %A Amelia J. Eisch %A Genevieve Konopka %A Jason P. Lerch %A Alexander F. Schier %A Haley E. Speed %A Craig M. Powell %B Nature %V 551 %P 227-231 %G eng %U https://www.nature.com/articles/nature24470#supplementary-information %0 Journal Article %J eLIFE %D 2017 %T Toddler signaling regulates mesodermal cell migration downstream of Nodal signaling %A Norris, Megan L %A Pauli, Andrea %A Gagnon, James A %A Lord, Nathan D %A Rogers, Katherine W %A Christian Mosimann %A Zon, Leonard I %A Schier, Alexander F %B eLIFE %V 6 %G eng %U https://elifesciences.org/articles/22626 %N e22626 %0 Journal Article %J Development %D 2017 %T Zebrafish nanog is primarily required in extraembryonic tissue %A James A. Gagnon %A Kamal Obbad %A Alexander F. Schier %B Development %G eng %U http://dev.biologists.org/content/early/2017/11/25/dev.147793.article-info %0 Journal Article %J eLIFE %D 2017 %T Vg1-1 Nodal heterodimers are the endogenous inducers of mesendoderm %A Tessa G. Montague %A Alexander F. Schier %B eLIFE %V 6 %G eng %U https://elifesciences.org/articles/28183 %N e28183 %0 Journal Article %J eLIFE %D 2017 %T Nodal patterning without Lefty inhibitory feedback is functional but fragile %A Rogers, Katherine W %A Gagnon, James A %A Pauli, Andrea %A Zimmerman, Steven %A Deniz C Aksel %A Reyon, Deepak %A Tsai, Shengdar Q %A Joung, J Keith %A Schier, Alexander F %B eLIFE %V 6 %G eng %U https://elifesciences.org/articles/28785 %N e28785 %0 Journal Article %J Scientific Reports %D 2017 %T Transit and integration of extracellular mitochondria in human heart cells %A Douglas B. Cowan %A Rouan Yao %A Jerusha K. Thedsanamoorthy %A Zurakowski, David %A Pedro J. del Nido %A James D. McCully %B Scientific Reports %V 7 %G eng %U https://www.nature.com/articles/s41598-017-17813-0 %N 17450 %0 Journal Article %J Cell %D 2017 %T Neuronal Representation of Social Information in theMedial Amygdala of Awake Behaving Mice %A Li, Ying %A Mathis, Alexander %A Benjamin F. Grewe %A Jessica A. Osterhout %A Biafra Ahanonu %A Mark J. Schnitzer %A Venkatesh N. Murthy %A Dulac, Catherine %B Cell %V 171 %P 1-15 %G eng %U https://dmg5c1valy4me.cloudfront.net/wp-content/uploads/2017/10/26111031/PIIS0092867417312047.pdf %0 Journal Article %J Neuron %D 2017 %T Development and Refinement of FunctionalProperties of Adult-Born Neurons %A Jenelle L. Wallace %A Martin Wienisch %A Venkatesh N. Murthy %B Neuron %V 96 %P 1-14 %G eng %U https://dmg5c1valy4me.cloudfront.net/wp-content/uploads/2017/10/19165950/PIIS089662731730908X.pdf %0 Journal Article %J Cell %D 2017 %T Snapshot: Tissue Clearing %A Richardson, Douglas S %A Jeff W. Lichtman %B Cell %V 171 %P 496-496 %G eng %U http://www.cell.com/cell/abstract/S0092-8674(17)31119-4 %N 2 %0 Journal Article %J SLAS Technology %D 2017 %T Development of MAST: A Microscopy-Based Antimicrobial Susceptibility Testing Platform %A Kenneth P. Smith %A David L. Richmond %A Thea Brennan-Krohn %A Hunter L. Elliot %A James E. Kirby %B SLAS Technology %G eng %U http://journals.sagepub.com/doi/pdf/10.1177/2472630317727721 %0 Journal Article %J The Journal of Neuroscience %D 2017 %T Gaze-stabilizing central vestibular neurons project asymmetrically toextraocular motoneuron pools %A Schoppik, David %A Isaac H. Bianco %A David A. Prober %A Adam D. Douglass %A Drew N. Robson %A Jennifer M.B. Li %A Joel S.F. Greenwood %A Edward Soucy %A Engert, Florian %A Alexander F. Schier %B The Journal of Neuroscience %G eng %U http://www.jneurosci.org/content/jneuro/early/2017/09/29/JNEUROSCI.1711-17.2017.full.pdf %0 Journal Article %J Genetics %D 2017 %T SID-1 Functions in Multiple Roles To Support Parental RNAi in Caenorhabditis elegans %A Eddie Wang %A Hunter, Craig P %B Genetics %G eng %U http://www.genetics.org/content/early/2017/07/26/genetics.117.300067 %0 Journal Article %J Nature %D 2017 %T A novel mechanism for mechanosensory-based rheotaxis in larval zebrafish %A Pablo Oteiza %A Iris Odstrcil %A George Lauder %A Portugues, Ruben %A Engert, Florian %B Nature %V 547 %P 445-448 %G eng %U http://www.nature.com/nature/journal/v547/n7664/full/nature23014.html#affil-auth %0 Journal Article %J Molecular Biology of the Cell %D 2017 %T Temporal regulation of epithelium formation mediated by FoxA, MKLP1, MgcRacGAP and PAR-6. %A Von Stetina, Stephen E %A J Liang %A G Marnellos %A Mango, S E %B Molecular Biology of the Cell %G eng %U http://www.molbiolcell.org/content/early/2017/05/22/mbc.E16-09-0644.abstract %0 Journal Article %J Nature %D 2017 %T Cell diversity and network dynamics in photosensitive human brain organoids %A Giorgia Quadrato %A Tuan Nguyen %A Evan Z. Macosko %A John L. Sherwood %A Sung Min Yang %A Daniel R. Berger %A Natalie Maria %A Jorg Scholvin %A Melissa Goldman %A Justin P. Kinney %A Edward S. Boyden %A Jeff W. Lichtman %A Ziv M. Williams %A Steven A. McCarroll %A Arlotta, Paola %B Nature %G eng %U http://www.nature.com/nature/journal/vaop/ncurrent/full/nature22047.html %0 Journal Article %J ACS Nano %D 2017 %T Intracellular Delivery Using Nanosecond-Laser Excitation of Large-Area Plasmonic Substrates %A Nabiha Saklayen %A Marinus Huber %A Marinna Madrid %A Valeria Nuzzo %A Daryl I. Vulis %A Weilu Shen %A Jeffery Nelson %A Arthur A. McClelland %A Alexander Heisterkamp %A Mazur, Eric %B ACS Nano %G eng %U http://pubs.acs.org/doi/full/10.1021/acsnano.6b08162 %0 Journal Article %J eLIFE %D 2017 %T Opposite initialization to novel cues in dopamine signaling in ventral and posterior striatum in mice %A Menegas, William %A Babayan, Benedicte M %A Uchida, Naoshige %A Watabe-Uchida, Mitsuko %B eLIFE %V 6 %P e21886 %G eng %U https://elifesciences.org/content/6/e21886 %0 Journal Article %J PNAS %D 2016 %T O-fucosylated glycoproteins form assemblies in close proximity to the nuclear pore complexes of Toxoplasma gondii %A Giulia Bandini %A John R. Haserick %A Edwin Motari %A Dinkorma T. Ouologuem %A Sebastian Lourido %A David S. Roos %A Catherine E. Costello %A Phillips W. Robbins %A John Samuelson %B PNAS %V 113 %P 11567-11572 %G eng %U https://www.pnas.org/content/pnas/113/41/11567.full.pdf %N 41 %0 Journal Article %J Mycologia %D 2016 %T Fireworks under the microscope: a spectacular new species of Zodiomyces from the Thaxter collection %A Walter Rossi %A Haelewaters, Danny %A Donald H. Pfister %B Mycologia %V 108 %P 709-715 %G eng %U http://www.tandfonline.com/doi/pdf/10.3852/15-148?needAccess=true %N 4 %0 Book Section %B Synapse Development: Methods and Protocols, Methods in Molecular Biology %D 2016 %T Optimized Protocol for Imaging Cleared Neural TissuesUsing Light Microscopy %A Isogai, Yoh %A Richardson, Douglas S %A Dulac, Catherine %A Bergan, Joseph %B Synapse Development: Methods and Protocols, Methods in Molecular Biology %I Springer %V 1538 %P 137-153 %G eng %U http://download.springer.com/static/pdf/108/chp%253A10.1007%252F978-1-4939-6688-2_11.pdf?originUrl=http%3A%2F%2Flink.springer.com%2Fprotocol%2F10.1007%2F978-1-4939-6688-2_11&token2=exp=1481821688~acl=%2Fstatic%2Fpdf%2F108%2Fchp%25253A10.1007%25252F978-1-4 %0 Book Section %B Synapse Development: Methods and Protocols, Methods in Molecular Biology %D 2016 %T Structured Illumination Microscopy fortheInvestigationofSynaptic Structure andFunction %A Soyon Hong %A Daniel K Wilton %A Beth Stevens %A Richardson, Douglas S %B Synapse Development: Methods and Protocols, Methods in Molecular Biology %I Springer %V 1538 %G eng %U http://download.springer.com/static/pdf/107/chp%253A10.1007%252F978-1-4939-6688-2_12.pdf?originUrl=http%3A%2F%2Flink.springer.com%2Fprotocol%2F10.1007%2F978-1-4939-6688-2_12&token2=exp=1481821972~acl=%2Fstatic%2Fpdf%2F107%2Fchp%25253A10.1007%25252F978-1-4 %0 Journal Article %J Nature Methods %D 2016 %T Stable long-term chronic brain mapping at the single-neuron level %A Tian-Ming Fu %A Guosong Hong %A Zhou, Tao %A Thomas G Schuhmann %A Robert D Viveros %A Charles m Lieber %B Nature Methods %V 13 %P 875-882 %G eng %U http://www.nature.com/nmeth/journal/v13/n10/full/nmeth.3969.html?cookies=accepted#methods %0 Journal Article %J Genes & Development %D 2016 %T Hair follicles’ transit-amplifying cells govern concurrent dermal adipocyte production through Sonic Hedgehog %A Zhang, Bing %A Pai-Chi Tsai %A Meryem Gonzalez-Celeiro %A Oliver Chung %A Benjamin Boumard %A Carolina N. Perdigoto %A Elena Ezhkova %A Ya-Chieh Hsu %B Genes & Development %V 30 %P 2325-2338 %G eng %U http://genesdev.cshlp.org/content/30/20/2325.full %0 Journal Article %J Nature Methods %D 2016 %T Nanoscale imaging of RNA with expansion microscopy %A Chen, Fei %A Asmamaw T Wassie %A Allison J Cote %A Anubhav Sinha %A Shahar Alon %A Shoh Asano %A Evan R Daugharthy %A Jae-Byum Chang %A Adam Marblestone %A Church, George M %A Arjun Raj %A Edward S Boyden %B Nature Methods %V 13 %P 679-684 %G eng %U http://www.nature.com/nmeth/journal/v13/n8/full/nmeth.3899.html#methods %0 Journal Article %J The Journal of Clinical Investigation %D 2016 %T Sortilin mediates vascular calcification via its recruitment into extracellular vesicles %A Claudia Goettsch %A Joshua D Hutcheson %A Aikawa, Masanori %A Hiroshi Iwata %A Tan Pham %A Anders Nykjaer %A Mads Kjolby %A Maximillian Rogers %A Thomas Michel %A Manabu Shibasaki %A Sumihiko Hagita %A Kramann, Rafael %A Daniel J Rader %A Libby, Peter %A Sasha A Singh %A Elena Aikawa %B The Journal of Clinical Investigation %V 126 %P 1323-1336 %G eng %U https://www.jci.org/articles/view/80851/pdf %N 4 %0 Journal Article %J Natutre Cell Biology %D 2016 %T Yap reprograms glutamine metabolism to increase nucleotide biosynthesis and enable liver growth %A Andrew G. Cox %A Katie L. Hwang %A Kristin K. Brown %A Kimberley J. Evason %A Sebastian Beltz %A Allison Tsomides %A Keelin O’Connor %A Giorgio G. Galli %A Dean Yimlamai %A Sagar Chhangawala %A Yuan, Min %A Evan C. Lien %A Julia Wucherpfennig %A Sahar Nissim %A Akihiro Minami %A David E. Cohen %A Fernando D. Camargo %A John M. Asara %A Yariv Houvras %A Didier Y. R. Stainier %A Wolfram Goessling %B Natutre Cell Biology %V 18 %P 886-896 %G eng %U http://www.nature.com/ncb/journal/v18/n8/full/ncb3389.html#methods %0 Journal Article %J Development %D 2016 %T Asialoglycoprotein receptor 1 is a specific cell-surface marker for isolating hepatocytes derived from human pluripotent stem cells %A Derek T. Peters %A Christopher A. Henderson %A Curtis R. Warren %A Max Friesen %A Fang Xia %A Caroline E. Becker %A Kiran Musunuru %A Chad A. Cowan %B Development %V 143 %P 1475-1481 %G eng %U http://dev.biologists.org/content/143/9/1475.long#sec-8 %0 Journal Article %J Stem Cell Reports %D 2016 %T Large-Scale Production of Mature Neurons from Human Pluripotent Stem Cells in a Three-Dimensional Suspension Culture System %A Alessandra Rigamonti %A Giuliana G. Repetti %A Chicheng Sun %A Feodor D. Price %A Danielle C. Reny %A Francesca Rapino %A Karen Weisinger %A Chen Benkler %A Quinn P. Peterson %A Lance S. Davidow %A Emil M. Hansson %A Lee L. Rubin %B Stem Cell Reports %V 6 %P 993-1008 %G eng %U http://www.sciencedirect.com/science/article/pii/S2213671116300650 %N 6 %0 Journal Article %J Neuron %D 2016 %T Corticothalamic Projection Neuron Development beyond Subtype Specification: Fog2 and Intersectional Controls Regulate Intraclass Neuronal Diversity %A Maria J Galazo %A Jason G Emsley %A Jeffrey D Macklis %B Neuron %V 91 %P 90-106 %G eng %U http://www.sciencedirect.com/science/article/pii/S0896627316302033 %N 1 %0 Journal Article %J Fluids Barriers CNS %D 2016 %T Directional cerebrospinal fluid movement between brain ventricles in larval zebrafish %A Ryann M Fame %A Chang, Jessica T %A Alex Hong %A Nicole A Apontw-Santiago %A Hazel Sive %B Fluids Barriers CNS %V 13 %P 11 %G eng %U http://fluidsbarrierscns.biomedcentral.com/articles/10.1186/s12987-016-0036-z %N 1 %0 Journal Article %J Development %D 2016 %T The transcriptional repressor Blimp-1 acts downstream of BMP signaling to generate primordial germ cells in the cricket Gryllus bimaculatus. %A T Nakamura %A C G Extavour %B Development %V 143 %P 255-263 %G eng %U http://neurodiscovery.harvard.edu/enhanced-neuroimaging-core %N 2 %0 Journal Article %J Nature %D 2016 %T A complement–microglial axis drives synapse loss during virus-induced memory impairment %A Michael J. Vasek %A Charise Garber %A Denise Dorsey %A Douglas M. Durrant %A Bryan Bollman %A Allison Soung %A Jinsheng Yu %A Carlos Perez-Torres %A Arnaud Frouin %A Daniel K. Wilton %A Kristen Funk %A Bette K. DeMasters %A Xiaoping Jiang %A James R. Bowen %A Steven Mennerick %A John K. Robinson %A Joel R. Garbow %A Kenneth L. Tyler %A Mehul S. Suthar %A Robert E. Schmidt %A Beth Stevens %A Robyn S. Klein %B Nature %V 534 %P 538-543 %G eng %U http://www.nature.com/nature/journal/v534/n7608/full/nature18283.html %0 Journal Article %J eLIFE %D 2016 %T Adult axolotls can regenerate original neuronal diversity in response to brain injury %A Ryoji Amamoto %A Violeta Gisselle Lopez Huerta %A Emi Takahashi %A Guangping Dai %A Aaron K Grant %A Zhanyan Fu %A Arlotta, Paola %B eLIFE %P e13998 %G eng %U https://elifesciences.org/content/5/e13998 %N 5 %0 Journal Article %J PNAS %D 2016 %T Prevalent presence of periodic actin–spectrin-based membrane skeleton in a broad range of neuronal cell types and animal species %A He, Jiang %A Ruobo Zhou %A Zhuhoa Wu %A Carrasco, Monica A %A Peri T Kurshan %A Johnathon E Farley %A David J Simon %A Guiping Wang %A Boran Han %A Junjie Hao %A Evan Heller %A Marc R Freeman %A Kang Shen %A Maniatis, Tom %A Tessier-Lavigne, Marc %A Zhuang, Xiaowei %B PNAS %V 113 %P 6029-6034 %G eng %U http://www.pnas.org/content/113/21/6029.long#sec-16 %N 21 %0 Journal Article %J Nature Communications %D 2016 %T An essential malaria protein defines the architecture of blood-stage and transmission-stage parasites %A Sabrina Absalon %A Jonathan A Robbins %A Jeffrey D. Dvorin %B Nature Communications %V 7 %G eng %U http://www.nature.com/ncomms/2016/160428/ncomms11449/full/ncomms11449.html %N 11449 %0 Journal Article %J Cell Biology and Toxicology %D 2016 %T Success of transdisciplinary science requires monodisciplinary support %A Richardson, Douglas S %B Cell Biology and Toxicology %V 32 %P 5-6 %G eng %U http://download.springer.com/static/pdf/601/art%253A10.1007%252Fs10565-016-9317-1.pdf?originUrl=http%3A%2F%2Flink.springer.com%2Farticle%2F10.1007%2Fs10565-016-9317-1&token2=exp=1461467364~acl=%2Fstatic%2Fpdf%2F601%2Fart%25253A10.1007%25252Fs10565-016-931 %0 Journal Article %J Science %D 2016 %T Complement and microglia mediate early synapse loss in Alzheimer mouse models %A Soyon Hong %A Victoria F Beja-Glasser %A Bianca M. Nfonoyim %A Arnaud Frouin %A Shaomin Li %A Saranya Ramakrishnan %A Katherine M. Merry %A Qiaoqiao Shi %A Arnon Rosenthal %A Ben A. Barres %A Cynthia A. Lemere %A Dennis J. Selkoe %A Beth Stevens %B Science %V early release %8 March 31 2016 %G eng %U http://science.sciencemag.org/content/early/2016/03/30/science.aad8373 %0 Journal Article %J Nature Communications %D 2016 %T Function and evolution of local repeats in the Firre locus %A Ezgi Hacisuleyman %A Chinmay J Shukla %A Catherine L Weiner %A Rinn, John L %B Nature Communications %V 7 %8 03/24/2016 %G eng %U http://www.nature.com/ncomms/2016/160324/ncomms11021/full/ncomms11021.html#methods %0 Journal Article %J Nature Materials %D 2016 %T Genesis and growth of extracellular-vesicle-derived microcalcification in atherosclerotic plaques %A Joshua D. Hutcheson %A Claudia Goettsch %A Sergio Bertazzo %A Natalia Maldonado %A Jessica L. Ruiz %A Wilson Goh %A Katsumi Yabusaki %A Tyler Faits %A Carlijn Bouten %A Gregory Franck %A Thibaut Quillard %A Libby, Peter %A Aikawa, Masanori %A Sheldon Weinbaum %A Elena Aikawa %B Nature Materials %G eng %U http://www.nature.com/nmat/journal/vaop/ncurrent/pdf/nmat4519.pdf %0 Journal Article %J Cell %D 2015 %T Chromosomes Progress to Metaphase in Multiple Discrete Steps via Global Compaction/Expansion Cycles %A Liang, Zhangyi %A Zickler, Denise %A Prentiss, Mara %A Frederick S. Chang %A Witz, Guillaume %A Kazuhiro Maeshima %A Kleckner, Nancy %B Cell %V 161 %P 1124-1137 %G eng %U http://www.sciencedirect.com/science/article/pii/S0092867415004869 %N 5 %0 Journal Article %J Nature %D 2015 %T Acute off-target effects of neural circuit manipulations %A Timothy M Otchy %A Steffen B E Wolff %A Juliana Y Rhee %A Cengiz Pehlevan %A Risa Kawai %A Alexandre Kempf %A Sharon M H Gobes %A Bence P Olveczky %B Nature %V 528 %P 358-363 %G eng %U http://www.nature.com/nature/journal/v528/n7582/full/nature16442.html#methods %0 Journal Article %J Neuron %D 2015 %T Instructing Perisomatic Inhibition by Direct Lineage Reprogramming of Neocortical Projection Neurons %A Zhanlei Ye %A Mohammed A Mostajo-Radji %A Juliana R Brown %A Caroline Rouaux %A Giulio Srubek Tomassy %A Takao K Hensch %A Arlotta, Paola %B Neuron %V 88 %P 475-483 %G eng %U http://www.sciencedirect.com/science/article/pii/S0896627315008727 %N 3 %0 Journal Article %J Nature Nanotechnology %D 2015 %T Syringe-injectable electronics %A Jia Liu %A Tian-Ming Fu %A Zengguang Cheng %A Guosong Hong %A Zhou, Tao %A Jin, Lihua %A Madhavi Duvvuri %A Zhe Jiang %A Peter Kruskal %A Chong Xie %A Zhigang Suo %A Ying Fang %A Charles m Lieber %B Nature Nanotechnology %V 10 %P 629-636 %G eng %U http://www.nature.com/nnano/journal/v10/n7/full/nnano.2015.115.html#methods %0 Journal Article %J Nature Materials %D 2015 %T Three-dimensional macroporous nanoelectronic networks as minimally invasive brain probes %A Chong Xie %A Jia Liu %A Tian-Ming Fu %A Xiaochuan Dai %A Wei Zhou %A Charles m Lieber %B Nature Materials %V 14 %P 1286-1292 %G eng %U http://www.nature.com/nmat/journal/v14/n12/full/nmat4427.html %0 Journal Article %J eLIFE %D 2015 %T Asymmetric division triggers cell-specific gene expression through coupled capture and stabilization of a phosphatase %A Niels Bradshaw %A Losick, Richard %B eLIFE %V 10 %P 08145 %G eng %U http://elifesciences.org/content/early/2015/10/14/eLife.08145 %N 7554 %0 Journal Article %J eLIFE %D 2015 %T Dopamine neurons projecting to the posterior striatum form ananatomically distinct subclass %A Menegas, William %A Joseph F Bergen %A Ogawa, Sachie K %A Isogai, Yoh %A Venkataraju, Kannan Umadevi %A Osten, Pavel %A Uchida, Naoshige %A Watabe-Uchida, Mitsuko %B eLIFE %V 10 %G eng %U http://elifesciences.org/content/early/2015/08/31/eLife.10032 %N 7554 %0 Journal Article %J Nature Methods %D 2015 %T Whole-brain activity mapping onto a zebrafish brain atlas %A Randlett, Owen %A Caroline L Wee %A Naumann, Eva A %A Onyeka Nnaemeka %A Schoppik, David %A James E Fitzgerald %A Portugues, Ruben %A Alix M B Lacoste %A Clemens Riegler %A Engert, Florian %A Schier, Alexander F %B Nature Methods %V 12 %P 1039-1046 %G eng %U http://www.nature.com/nmeth/journal/v12/n11/full/nmeth.3581.html %0 Journal Article %J Biochemical and Biophysical Research Communications %D 2015 %T Intracellular Distribution of TM4SF1 and Internalization of TM4SF1-antibody Complex in Vascular Endothelial Cells %A Tracey E Sciuto %A Anne Merley %A Chi-lou Lin %A Douglas Richardson %A Yu Liu %A Dan Li %A Ann M Dvorak %A Harold F Dvorak %A Shou-Ching S Jaminet %B Biochemical and Biophysical Research Communications %V 465 %P 338-343 %8 2015 %G eng %U http://www.sciencedirect.com/science/article/pii/S0006291X15303739 %N 3 %0 Journal Article %J eLIFE %D 2015 %T Quantitative and functional interrogation of parent-of-origin allelic expression biases in the brain %A Julio D Perez %A Nimrod D Rubinstein %A Daniel E Fernandez %A Santoro, Stephen W %A Leigh A Needleman %A Olivia Ho-Shing %A John J Choi %A Zirlinger, Mariela %A Shau-Kwaun Chen %A Dulac, Catherine %B eLIFE %V 4 %P e07860 %G eng %U http://elifesciences.org/content/4/e07860 %0 Journal Article %J Cell %D 2015 %T Clarifying Tissue Clearing %A Richardson, Douglas S %A Lichtman, Jeff W %B Cell %V 162 %P 246-257 %G eng %U http://www.cell.com/cell/abstract/S0092-8674%2815%2900837-5 %N 2 %0 Journal Article %J PLOS One %D 2015 %T Testing Pancreatic Islet Function at the Single Cell Level by Calcium Influx with Associated Marker Expression %A Jennifer HR Kenty %A Douglas A Melton %B PLOS One %V 10 %P e0122044 %G eng %U http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0122044#ack %N 4 %0 Journal Article %J Cell %D 2015 %T One Cell at a Time %A Martha Koch %B Cell %V 161 %P 1479-1481 %G eng %U http://www.sciencedirect.com/science/article/pii/S0092867415007035 %N 7 %0 Journal Article %J Developmental Biology %D 2015 %T Embryonic development of the cricket Gryllus bimaculatus %A Seth Donoughe %A Cassandra G. Extavour %B Developmental Biology %V Epub %G eng %U http://www.sciencedirect.com/science/article/pii/S001216061500189X %0 Journal Article %J Nature Methods %D 2015 %T Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display %A David M Shechner %A Ezgi Hacisuleyman %A Scott T Younger %A Rinn, John L %B Nature Methods %V Epub %G eng %U http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3433.html#methods %0 Journal Article %J Developmental Biology %D 2015 %T PAR-6, but not E-cadherin and β-integrin, is necessary for epithelial polarization in C. elegans %A Von Stetina, Stephen E %A Mango, Susan E %B Developmental Biology %V 403 %P 5-14 %G eng %U http://www.sciencedirect.com.ezp-prod1.hul.harvard.edu/science/article/pii/S0012160615001062 %N 1 %0 Journal Article %J PNAS %D 2015 %T Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain %A Loyal A Goff %A Abigail F Groff %A Martin Sauvageau %A Zachary Trayes-Gibson %A Diana B Sanchez-Gomez %A Michael Morse %A Ryan D Martin %A Lara E Elcavage %A Stephen C Liapis %A Meryem Gonzalez-Celeiro %A Olivia Plana %A Eric Li %A Chiara Gerhardinger %A Giulio S Tomassy %A Arlotta, Paola %A Rinn, John L %B PNAS %V 112 %P 6855-6862 %G eng %U http://www.pnas.org/content/112/22/6855.long %N 22 %0 Journal Article %J Cell %D 2015 %T Chromosomes Progress to Metaphase in Multiple Discrete Steps via Global Compaction/Expansion Cycles %A Liang, Zhangyi %A Zickler, Denise %A Prentiss, Mara %A Chang, Frederick S %A Witz, Guillaume %A Kazuhiro Maeshima %A Kleckner, Nancy %B Cell %V 161 %P 1124-1137 %G eng %U http://www.cell.com/cell/abstract/S0092-8674%2815%2900486-9 %N 5 %0 Journal Article %J eLIFE %D 2015 %T Response to Nodal morphogen gradient is determined by the kinetics of target gene induction %A Dubrulle, Julien %A Jordan, Benjamin %A Akhmetova, Laila %A Farrell, Jeffrey A %A Kim, Seok-Hyung %A Solnica-Krezel, Lilianna %A Schier, Alexander F %B eLIFE %V 4 %G eng %U http://elifesciences.org/content/4/e05042 %N e5042 %0 Journal Article %J Nature Biotechnology %D 2015 %T Spatial reconstruction of single-cell gene expression data %A Rahul Satija %A Jeffery A Farrell %A David Gennert %A Alex F Schier %A Regev, Aviv %B Nature Biotechnology %G eng %U http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3192.html#acknowledgments %0 Journal Article %J Cell %D 2014 %T Generation of Functional Human Pancreaticβ Cells in Vitro %A Felicia W Pagliuca %A Jeffrey R Millman %A Mads Gurtler %A Michael Segel %A Alana Van Dervort %A Jennifer Hyoje Ryu %A Quinn P Peterson %A Dale Greiner %A Douglas A Melton %B Cell %V 159 %P 428-439 %G eng %U http://www.sciencedirect.com/science/article/pii/S0092867414012288 %N 2 %0 Journal Article %J mBio %D 2014 %T The Extracellular Matrix of Staphylococcus aureaus Biofilms Comprises Cytoplasmic Proteins That Associate with the Cell Surface in Response to Decreasing pH %A Foulston, Lucy %A Elsholz, Alexander K W %A DeFrancesco, Alicia S %A Losick, Richard %B mBio %V 5 %P e01667-14 %G eng %U http://mbio.asm.org/content/5/5/e01667-14.full %N 5 %0 Journal Article %J Chinese Science Bulletin %D 2014 %T Hesperomyces virescens (Fungi, Ascomycota, Laboulbeniales) attacking Harmonia axyridis (Coleoptera, Coccinellidae) in its native range %A Haelewaters, Danny %A Comont, Richard F %A Zhao, Serena Y %A Pfister, Donald H %B Chinese Science Bulletin %V 59 %P 528-532 %G eng %U http://link.springer.com/article/10.1007%2Fs11434-013-0060-1 %N 5-6 %0 Journal Article %J Science Translational Medicine %D 2014 %T Genetic validation of a therapeutic target in a mouse model of ALS %A AS de Boer %A K Koszka %A E Kiskinis %A N. Suzuki %A BN Davis-Dusenbery %A K Eggan %B Science Translational Medicine %V 6 %P 248ra104 %G eng %U http://stm.sciencemag.org/content/6/248/248ra104.full %N 248 %0 Journal Article %J eLIFE %D 2014 %T

Lis1 regulates dynein by sterically blocking its mechanochemical cycle

%A Toropova, Katerina %A Zou, Sirui %A Roberts, Anthony J %A Redwine, William B %A Goodman, Brian S %A Reck-Peterson, Samara L %A Leschziner, Andres E %B eLIFE %V 3 %G eng %U http://elifesciences.org/content/3/e03372 %N e03372 %0 Journal Article %J PNAS %D 2014 %T

BMP signaling is required for the generation of primordial germ cells in an insect

%A S Donoughe %A T Nakamura %A B Ewen-Campen %A D A Green II %A L Henderson %A C G Extavour %B PNAS %V 111 %P 4133-4138 %G eng %U http://www.pnas.org/content/111/11/4133.full %N 11 %0 Journal Article %J Science Translational Medicine %D 2014 %T

Genetic validation of a therapeutic target in a mouse model of ALS

%A AS de Boer %A K Koszka %A E Kiskinis %A N. Suzuki %A BN Davis-Dusenbery %A K Eggan %B Science Translational Medicine %V 6 %G eng %U http://stm.sciencemag.org/content/6/248/248ra104.short %N 248 %0 Journal Article %J eLIFE %D 2014 %T

In vivo reprogramming of pancreatic acinar cells to three islet endocrine subtypes

%A W Li %A M Nakanishi %A A Zumsteg %A M Shear %A C Wright %A DA Melton %A Q Zhou %B eLIFE %V 3 %G eng %U http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3977343/ %N e01846 %0 Journal Article %J Cell Reports %D 2014 %T

Organization of Monosynaptic inputs to the Serotonin and Dopamine Neuromodulatory Systems

%A S.K. Ogawa %A J.Y. Cohen %A D Hwang %A N. Uchida %A M. Watabe-Uchida %B Cell Reports %V 8 %P 1105-1118 %G eng %U http://www.cell.com/cell-reports/abstract/S2211-1247%2814%2900526-9 %N 4 %0 Journal Article %J Journal of Biomolecular Techniques %D 2014 %T

Mercury Free Microscopy: An Opportunity for Core Facility Directors

%A R Baird %A D Kaufman %A C Brown %B Journal of Biomolecular Techniques %V 25 %P 48-53 %G eng %U http://goo.gl/AtZlIK %N 2 %0 Journal Article %J Science %D 2014 %T

Niche engineering demonstrates a latent capacity for fungal-algal mutualism

%A E Hom %A A Murray %B Science %V 345 %P 94-98 %G eng %U http://goo.gl/6AxdTg %N 6192 %0 Journal Article %J eLife %D 2014 %T
Mechanisms of organelle biogenesis govern stochastic fluctuations in organelle abundance.
%A Mukherji, S %A O'Shea, E %B eLife %V 3 %P e02678 %G eng %U http://goo.gl/RyLCuH %0 Magazine Article %D 2014 %T

The planar truth about light-sheet microscopy

%A May, M %B BioOptics World %V 7 %G eng %U http://goo.gl/dcKRNO %N 1 %0 Journal Article %J Science %D 2014 %T

Life Science Technologies: Souping Up Your 'Scope

%A May, M %B Science %V 344 %P 536-538 %G eng %U http://goo.gl/Vl0LaT %N 6138 %0 Journal Article %J Science %D 2014 %T

Vascular and neurogenic Rejuvenation of the Aging Mouse Brain by Young Systemic Factors

%A Katsimpardi, L %A Litterman, N %A Schein, P %A Miller, C %A Loffredo, F %A Wojtkiewicz, G %A Chen, J %A Lee, R %A Wagers, A %A Rubin, L %B Science %V 344 %P 630-634 %G eng %U http://goo.gl/MrOpVr %N 6184 %0 Journal Article %J Science %D 2014 %T

Toddler: An Embryonic Signal That Promotes Cell Movement via Apelin Receptors

%A Pauli, A %A Norris, M %A Valen, E %A Chew, G %A Gagnon, J %A Zimmerman, S %A Mitchell, A %A Ma, J %A Dubrulle, J %A Reyon, D %A Tsai, S %A Joung, J %A Saghatelian, A. %A Schier, A %B Science %V 343 %G eng %U http://goo.gl/EYvtet %N 6172 %0 Journal Article %J Current Biology %D 2013 %T Germ Cell Specification Requires Zygotic Mechanisms Rather Than Germ Plasm in a Basally Branching Insect %A Ewen-Campen, Ben %A Seth Donoughe %A Donald Nat Clarke %A Cassandra G. Extavour %B Current Biology %V 23 %P 835-842 %G eng %U https://www.sciencedirect.com/science/article/pii/S0960982213003655?via%3Dihub#app3 %N 10 %0 Journal Article %J Science %D 2013 %T

Robust Circadian Oscillations in Growing Cyanobacteria Require Transcriptional Feedback

%A Teng, S %A Mukherji, S %A Moffitt, J %A de Buyl, S %A O'Shea, E %B Science %V 340 %P 737-740 %G eng %U http://goo.gl/SMEBw2 %N 6133 %0 Journal Article %J Current Biology %D 2012 %T

oskar Predates the Evolution of Germ plasm in Insects

%A B Ewen-Campen %A JR Srouji %A EE Schwager %A C G Extavour %B Current Biology %V 22 %P 2278-2283 %G eng %U http://www.sciencedirect.com/science/article/pii/S0960982212012043 %N 23 %0 Journal Article %J Nature %D 2011 %T

Molecular organization of vomeronasal chemoreception

%A Isogai, Y %A Si, S %A Pont-Lezica, L %A Tan, T %A Kapoor, V %A V.N. Murthy %A Dulac, C %B Nature %V 478 %P 241-245 %G eng %U http://goo.gl/VHvqu3 %N 7368