Department of Biological Science

: A PRIMITIVE HADROSAURID FROM SOUTHEASTERN NORTH AMERICA AND THE ORIGIN AND EARLY EVOLUTION OF 'DUCK- BILLED' DINOSAURS; Eotrachodon orientalis gen. et sp. nov. (latest Santonian of Alabama, southeastern U.S.A.) is one of the oldest and most basal hadrosaurid dinosaurs and the only hadrosaurid from Appalachia (present day eastern North America) with a preserved skull. This taxon possesses a relatively derived narial structure that was until now regarded as synapomorphic for saurolophine (solid-crested or crestless) hadrosaurids. Maximum parsimony analysis places E. orientalis as the sister taxon to Saurolophidae (Saurolophinae + Lambeosaurinae). Character optimization on the phylogeny indicates that the saurolophine-like circumnarial structure evolved by the Santonian following the split between saurolophines and lambeosaurines but prior to the major hadrosaurid radiation. Statistical dispersal-vicariance analysis posits an Appalachian ancestral area for Hadrosauridae and subsequent dispersal of their ancestors into Laramidia (present-day western North America) during the Cenomanian.http://zoobank.org/urn:lsid:zoobank.org:pub:3AD914D2-A3A5-45FD-8C94-5EE80461FEBCSUPPLEMENTAL DATASupplemental materials are available for this article for free at www.tandfonline.com/UJVPCitation for this article: Prieto-Marquez, A., G. M. Erickson, and J. A. Ebersole. 2016. A primitive hadrosaurid from southeastern North America and the origin and early evolution of duck-billed' dinosaurs. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2015.1054495, Keywords: Anatomy, china, dispersal-vicariance analysis, historical biogeography, homologies, lambeosaurine dinosaurs, nasal cavity, ornithischia, ornithopoda, phylogenetic position, Publication Note: The publisher’s version of record is available at http://www.dx.doi.org/10.1080/02724634.2015.1054495

: A new Arctic hadrosaurid from the Prince Creek Formation (lower Maastrichtian) of northern Alaska; The Liscomb bonebed in the Price Creek Formation of northern Alaska has produced thousands of individual bones of a saurolophine hadrosaurid similar to Edmontosaurus; however, the specific identity of this taxon has been unclear, in part because the vast majority of the remains represent immature individuals. In this study, we address the taxonomic status of the Alaskan material through a comparative and quantitative morphological analysis of juvenile as well several near adult-sized specimens with particular reference to the two known species of Edmontosaurus, as well as a cladistic analysis using two different matrices for Hadrosauroidea. In the comparative morphological analysis, we introduce a quantitative method using bivariate plots to address ontogenetic variation. Our comparative anatomical analysis reveals that the Alaskan saurolophine possesses a unique suite of characters that distinguishes it from Edmontosaurus, including a premaxillary circumnarial ridge that projects posterolaterally without a premaxillary vestibular promontory, a shallow groove lateral to the posterodorsal premaxillary foramen, a relatively narrow jugal process of the postorbital lacking a postorbital pocket, a relatively tall maxilla, a relatively gracile jugal, a more strongly angled posterior margin of the anterior process of the jugal, wide lateral exposure of the quadratojugal, and a short symphyseal process of the dentary. The cladistic analyses consistently recover the Alaskan saurolophine as the sister taxon to Edmontosaurus annectens + Edmontosaurus regalis. This phylogenetic assessment is robust even when accounting for ontogenetically variable characters. Based on these results, we erect a new taxon, Ugrunaaluk kuukpikensis gen. et sp. nov. that contributes to growing evidence for a distinct, early Maastrichtian Arctic dinosaur community that existed at the northernmost extent of Laramidia during the Late Cretaceous., Keywords: Alaska, america, Arctic, coastal-plain, Cretaceous, Dinosauria, dinosauria ornithischia, Edmontosaurini, edmontosaurus, Hadrosauridae, high-latitude, ontogeny, ornithopoda, Prince Creek Formation, relative growth, Saurolophinae, slope, USA, Publication Note: The publisher’s version of record is available at http://www.dx.doi.org/10.4202/app.00152.2015

: AIM2 inflammasome activation and regulation; Absent in melanoma 2 (AIM2) inflammasome is a multi-protein platform that recognizes aberrant cytoplasmic dsDNA and induces cytokine maturation, release and pyroptosis. It is composed of AIM2, apoptosis-associated speck-like protein containing a CARD (ASC), and caspase-1. Recent X-ray crystallographic and high resolution cryo-electron microscopic (cryo-EM) studies have revealed a series of structures in AIM2 inflammasome activation and regulation. One prominent feature common in multiple steps is the assembly of high-order structures, especially helical filaments nucleated by upstream molecules, rather than stoichiometric complexes. In this review, we track the AIM2 inflammasome activation process step by step, using high-resolution structures to illustrate the overall architecture of AIM2 inflammasome and its assembly and regulatory mechanisms., Keywords: AIM2, ASC, CARD, Caspase-1, Helical filament, High-order assembly, INCA, Inflammasome, P202, PYD, Polymerization, Grant Number: R00 AI108793, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5733693.

: Active And Repressed Biosynthetic Gene Clusters Have Distinct Chromosome States; While colocalization within a bacterial operon enables coexpression of the constituent genes, the mechanistic logic of clustering of nonhomologous monocistronic genes in eukaryotes is not immediately obvious. Biosynthetic gene clusters that encode pathways for specialized metabolites are an exception to the classical eukaryote rule of random gene location and provide paradigmatic exemplars with which to understand eukaryotic cluster dynamics and regulation. Here, using 3C, Hi-C, and Capture Hi-C (CHi-C) organ-specific chromosome conformation capture techniques along with highresolution microscopy, we investigate how chromosome topology relates to transcriptional activity of clustered biosynthetic pathway genes in Arabidopsis thaliana. Our analyses reveal that biosynthetic gene clusters are embedded in local hot spots of 3D contacts that segregate cluster regions from the surrounding chromosome environment. The spatial conformation of these cluster-associated domains differs between transcriptionally active and silenced clusters. We further show that silenced clusters associate with heterochromatic chromosomal domains toward the periphery of the nucleus, while transcriptionally active clusters relocate away from the nuclear periphery. Examination of chromosome structure at unrelated clusters in maize, rice, and tomato indicates that integration of clustered pathway genes into distinct topological domains is a common feature in plant genomes. Our results shed light on the potential mechanisms that constrain coexpression within clusters of nonhomologous eukaryotic genes and suggest that gene clustering in the one-dimensional chromosome is accompanied by compartmentalization of the 3D chromosome., identification, domains, diversification, organization, arabidopsis, Arabidopsis thaliana, architecture, chromatin packing, chromosome, coexpression, gene cluster, genome-wide analysis, H3K27me3, Hi-C, plant genomes, The publisher's version of record is availible at https://doi.org/10.1073/pnas.1920474117

: Acute Sleep Deprivation Blocks Short- and Long-Term Operant Memory in .; Insufficient sleep in individuals appears increasingly common due to the demands of modern work schedules and technology use. Consequently, there is a growing need to understand the interactions between sleep deprivation and memory. The current study determined the effects of acute sleep deprivation on short and long-term associative memory using the marine mollusk , a relatively simple model system well known for studies of learning and memory. were sleep deprived for 9 hours using context changes and tactile stimulation either prior to or after training for the operant learning paradigm, learning that food is inedible (LFI). The effects of sleep deprivation on short-term (STM) and long-term memory (LTM) were assessed. Acute sleep deprivation prior to LFI training impaired the induction of STM and LTM with persistent effects lasting at least 24 h. Sleep deprivation immediately after training blocked the consolidation of LTM. However, sleep deprivation following the period of molecular consolidation did not affect memory recall. Memory impairments were independent of handling-induced stress, as daytime handled control animals demonstrated no memory deficits. Additional training immediately after sleep deprivation failed to rescue the induction of memory, but additional training alleviated the persistent impairment in memory induction when training occurred 24 h following sleep deprivation. Acute sleep deprivation inhibited the induction and consolidation, but not the recall of memory. These behavioral studies establish as an effective model system for studying the interactions between sleep and memory formation., Keywords: Aplysia, Learning and memory, Sleep deprivation, Grant Number: R21 NS088835, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5103805.

: Advances in Zika Virus Research; The re-emergence of Zika virus (ZIKV) and its suspected link with various disorders in newborns and adults led the World Health Organization to declare a global health emergency. In response, the stem cell field quickly established platforms for modeling ZIKV exposure using human pluripotent stem cell-derived neural progenitors and brain organoids, fetal tissues, and animal models. These efforts provided significant insight into cellular targets, pathogenesis, and underlying biological mechanisms of ZIKV infection as well as platforms for drug testing. Here we review the remarkable progress in stem cell-based ZIKV research and discuss current challenges and future opportunities., Keywords: SpinΩ, Zika, IPSC, Microcephaly, Neurogenesis, Organoid, Outer radial glia cell, Radial glia cell, Grant Number: R01 HD069184, P01 NS097206, R35 NS097370, RM1 HG008935, R01 AG024984, R37 NS047344, U19 MH106434, R21 AI111250, R21 NS095348, R21 MH110160, R21 AI119530, R01 AI079150, R01 NS048271, R01 NS047344, R21 HD086820, R01 MH105128, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5218815.

: Advancing Behavioural Genomics By Considering Timescale; Animal behavioural traits often covary with gene expression, pointing towards a genomic constraint on organismal responses to environmental cues. This pattern highlights a gap in our understanding of the time course of environmentally responsive gene expression, and moreover, how these dynamics are regulated. Advances in behavioural genomics explore how gene expression dynamics are correlated with behavioural traits that range from stable to highly labile. We consider the idea that certain genomic regulatory mechanisms may predict the timescale of an environmental effect on behaviour. This temporally minded approach could inform both organismal and evolutionary questions ranging from the remediation of early life social trauma to understanding the evolution of trait plasticity., Keywords: drosophila-melanogaster, molecular-mechanisms, adaptive phenotypic plasticity, brain gene-expression, dna methylation, early-life experience, epigenetic marking, honey-bee aggression, social challenge, stress reactivity, Publication Note: The publisher's version of record is available at https://doi.org/10.1038/s41467-018-02971-0

: Advancing Cognitively Demanding Tasks In Undergraduate Classrooms; With ink teasing focus on active learning in college classrooms, many institutions of higher education are redesigning introductory laboratory classes to provide more active-learning opportunities for students and to more authentically recreate the practices of scientists. These classes are primarily taught by graduate teaching assistants (GTAs), who often lack the pedagogical training necessary to plan for and support students' intellectual engagement in rich science tasks that require deep engagement in the practices of science and the core disciplinary ideas. We believe that graduate student discussion groups can provide an opportunity to encourage and equip GTAs with pedagogical knowledge and skills to select and use cognitively demanding instructional tasks. In this article, we describe our planning and facilitation of one such meeting with a group of GTAs about the relative cognitive demands of various laboratory activities. We propose that regularly scheduled meetings of discussion groups like this can help build learning communities among GTAs. We provide strategies to support GTAs' professional development and help them think critically about the tasks they use in their classes. In particular, we highlight the importance of the cognitive demands of tasks for engaging students in active and rigorous opportunities for science learning., impact, professional development, professional-development, knowledge, instruction, education, inquiry, discussion group, graduate teaching assistant, gta, teaching assistant gta, The publisher's version of record is availible at https://doi.org/10.1525/abt.2019.82.1.53

: Advancing behavioural genomics by considering timescale.; Animal behavioural traits often covary with gene expression, pointing towards a genomic constraint on organismal responses to environmental cues. This pattern highlights a gap in our understanding of the time course of environmentally responsive gene expression, and moreover, how these dynamics are regulated. Advances in behavioural genomics explore how gene expression dynamics are correlated with behavioural traits that range from stable to highly labile. We consider the idea that certain genomic regulatory mechanisms may predict the timescale of an environmental effect on behaviour. This temporally minded approach could inform both organismal and evolutionary questions ranging from the remediation of early life social trauma to understanding the evolution of trait plasticity., Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5809431.

: Aging and circadian dysfunction increase alcohol sensitivity and exacerbate mortality in Drosophila melanogaster.; Alcohol abuse is a rising problem in middle-aged and older individuals resulting in serious health, family and economic consequences. Effective treatment necessitates the identification of factors influencing alcohol toxicity with aging. We investigated the interaction between aging, alcohol toxicity and circadian function using Drosophila as a model system. We found as wild type flies age, sensitivity to alcohol increases and circadian regulation of alcohol-induced behaviors weakens. Decreased circadian modulation is correlated with significantly greater alcohol sensitivity during the subjective day. The circadian clock modulates alcohol-induced mortality in younger flies with increased mortality following alcohol exposure at night. Older flies exhibit significantly longer recovery times following alcohol-induced sedation and increased mortality following binge-like or chronic alcohol exposure. Flies rendered arrhythmic either genetically or environmentally exhibit significantly increased alcohol sensitivity, longer recovery times and increased mortality. We hypothesize that the circadian clock phase specifically buffers behavioral and cellular alcohol sensitivity with this protection diminishing as the circadian clock weakens with age., Keywords: Aging, Alcohol, Circadian rhythms, Drosophila, Grant Number: R21 AA021233, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6158789.

: Allele-specific Control Of Replication Timing And Genome Organization During Development; DNA replication occurs in a defined temporal order known as the replication-timing (RT) program. RT is regulated during development in discrete chromosomal units, coordinated with transcriptional activity and 3D genome organization. Here, we derived distinct cell types from F1 hybrid musculus x castaneus mouse crosses and exploited the high single-nucleotide polymorphism (SNP) density to characterize allelic differences in RT (Repli-seq), genome organization (Hi-C and promoter-capture Hi-C), gene expression (total nuclear RNA-seq), and chromatin accessibility (ATAC-seq). We also present HARP, a new computational tool for sorting SNPs in phased genomes to efficiently measure allele-specific genome-wide data. Analysis of six different hybrid mESC clones with different genomes (C57BL/ 6,129 /sv, and CAST/ Ei), parental configurations, and gender revealed significant RT asynchrony between alleles across similar to 12% of the autosomal genome linked to subspecies genomes but not to parental origin, growth conditions, or gender. RT asynchrony in mESCs strongly correlated with changes in Hi-C compartments between alleles but not as strongly with SNP density, gene expression, imprinting, or chromatin accessibility. We then tracked mESC RT asynchronous regions during development by analyzing differentiated cell types, including extraembryonic endoderm stem (XEN) cells, four male and female primary mouse embryonic fibroblasts (MEFs), and neural precursor cells (NPCs) differentiated in vitro from mESCs with opposite parental configurations. We found that RT asynchrony and allelic discordance in Hi-C compartments seen in mESCs were largely lost in all differentiated cell types, accompanied by novel sites of allelic asynchrony at a considerably smaller proportion of the genome, suggesting that genome organization of homologs converges to similar folding patterns during cell fate commitment., Keywords: mouse, dna-replication, embryonic stem-cells, in-situ hybridization, hi-c, stable units, acute lymphoblastic-leukemia, asynchronous replication, es cells, x-chromosome inactivation, Publication Note: The publisher’s version of record is available at https://doi.org/10.1101/gr.232561.117

: An improved smaller biotin ligase for BioID proximity labeling; The BioID method uses a promiscuous biotin ligase to detect protein-protein associations as well as proximate proteins in living cells. Here we report improvements to the BioID method centered on BioID2, a substantially smaller promiscuous biotin ligase. BioID2 enables more-selective targeting of fusion proteins, requires less biotin supplementation, and exhibits enhanced labeling of proximate proteins. Thus BioID2 improves the efficiency of screening for protein-protein associations. We also demonstrate that the biotinylation range of BioID2 can be considerably modulated using flexible linkers, thus enabling application-specific adjustment of the biotin-labeling radius., Keywords: dependent biotinylation, e-cadherin, interacting partners, mammalian-cells, membrane, messenger-rna export, nuclear-pore complex, promiscuous protein biotinylation, proteomic analysis, trypanosoma-brucei, Publication Note: The publisher’s version of record is available at http://www.dx.doi.org/10.1091/mbc.E15-12-0844

: Analysis Of The Temporal Patterning Of Notch Downstream Targets During Drosophila Melanogaster Egg Chamber Development; Living organisms require complex signaling interactions and proper regulation of these interactions to influence biological processes. Of these complex networks, one of the most distinguished is the Notch pathway. Dysregulation of this pathway often results in defects during organismal development and can be a causative mechanism for initiation and progression of cancer. Despite previous research entailing the importance of this signaling pathway and the organismal processes that it is involved in, less is known concerning the major Notch downstream targets, especially the onset and sequence in which they are modulated during normal development. As timing of regulation may be linked to many biological processes, we investigated and established a model of temporal patterning of major Notch downstream targets including broad, cut, and hindsight during Drosophila melanogaster egg chamber development. We confirmed the sequential order of Broad upregulation, Hindsight upregulation, and Cut downregulation. In addition, we showed that Notch signaling could be activated at stage 4, one stage earlier than the stage 5, a previously long-held belief. However, our further mitotic marker analysis re-stated that mitotic cycle continues until stage 5. Through our study, we once again validated the effectiveness and reliability of our MATLAB toolbox designed to systematically identify egg chamber stages based on area size, ratio, and additional morphological characteristics., expression, cells, differentiation, cut, germ-line, switch, The publisher's version of record is availible at https://doi.org/10.1038/s41598-020-64247-2

: Anatomy and osteohistology of the basal hadrosaurid dinosaur Eotrachodon from the uppermost Santonian (Cretaceous) of southern Appalachia.; The cranial and postcranial anatomy of the basal hadrosaurid dinosaur Eotrachodon orientalis, from the uppermost Santonian of southern Appalachia (southeastern U.S.A.), is described in detail. This animal is the only known pre-Campanian non-lambeosaurine hadrosaurid, and the most complete hadrosauroid known from Appalachia. E. orientalis possesses a mosaic of plesiomorphic and derived characters in the context of Hadrosauroidea. Characters shared with basal hadrosauroids include a short and sloping maxillary ectopterygoid shelf, caudally prominent maxillary jugal process, one functional tooth per alveolus on the maxillary occlusal plane, a jugal rostral process with a shallow caudodorsal margin and medioventrally facing articular facet, a vertical dentary coronoid process with a poorly expanded apex, and tooth crowns with accessory ridges. Derived characters shared with other hadrosaurids include a circumnarial depression compartmented into three fossae (as in brachylophosaurins and Edmontosaurus), a thin everted premaxillary oral margin (as in Gryposaurus, Prosaurolophus, and Saurolophus), and a maxilla with a deep and rostrocaudally extensive rostrodorsal region with a steeply sloping premaxillary margin (as in Gryposaurus). Eotrachodon orientalis differs primarily from the other hadrosauroid from the Mooreville Chalk of Alabama, Lophorhothon atopus, in having a slender and crestless nasal whose caudodorsal margin is not invaded by the circumnarial depression. Hadrosaurus foulkii, the only other known hadrosaurid from Appalachia, is distinct from E. orientalis in having dentary teeth lacking accessory ridges and a dorsally curved shaft of the ischium. A histological section of the tibia of the E. orientalis holotype (MSC 7949) suggests that this individual was actively growing at the time of death and, thus, had the potential to become a larger animal later in development., Keywords: Anatomy, Appalachia, Cretaceous, Dinosaur, Evolution, Hadrosaurid, Histology, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4841272.

: Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae); Background: Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly diverse nature, importance as pollinators, and historical instability with regard to subfamilial and tribal classification, Syrphidae (flower flies or hoverflies) are an ideal candidate for anchored hybrid enrichment-based phylogenetics, especially since recent molecular phylogenies of the syrphids using only a few markers have resulted in highly unresolved topologies. Over 6200 syrphids are currently known and uncovering their phylogeny will help us to understand how these species have diversified, providing insight into an array of ecological processes, from the development of adult mimicry, the origin of adult migration, to pollination patterns and the evolution of larval resource utilization. Results: We present the first use of anchored hybrid enrichment in insect phylogenetics on a dataset containing 30 flower fly species from across all four subfamilies and 11 tribes out of 15. To produce a phylogenetic hypothesis, 559 loci were sampled to produce a final dataset containing 217,702 sites. We recovered a well resolved topology with bootstrap support values that were almost universally >95 %. The subfamily Eristalinae is recovered as paraphyletic, with the strongest support for this hypothesis to date. The ant predators in the Microdontinae are sister to all other syrphids. Syrphinae and Pipizinae are monophyletic and sister to each other. Larval predation on soft-bodied hemipterans evolved only once in this family. Conclusions: Anchored hybrid enrichment was successful in producing a robustly supported phylogenetic hypothesis for the syrphids. Subfamilial reconstruction is concordant with recent phylogenetic hypotheses, but with much higher support values. With the newly designed probe kit this analysis could be rapidly expanded with further sampling, opening the door to more comprehensive analyses targeting problem areas in syrphid phylogenetics and ecology., Keywords: Anchored phylogenetics, biology, chemical mimicry, classification, Eristalinae, Evolution, Flower flies, history, Hoverflies, Hybrid enrichment, larval, Microdontinae, obligate predator, Pipizinae, pollination, Syrphinae, Systematics, Publication Note: The publisher’s version of record is available at https://doi.org/10.1186/s12862-016-0714-0

: Anchored enrichment dataset for true flies (order Diptera) reveals insights into the phylogeny of flower flies (family Syrphidae).; Anchored hybrid enrichment is a form of next-generation sequencing that uses oligonucleotide probes to target conserved regions of the genome flanked by less conserved regions in order to acquire data useful for phylogenetic inference from a broad range of taxa. Once a probe kit is developed, anchored hybrid enrichment is superior to traditional PCR-based Sanger sequencing in terms of both the amount of genomic data that can be recovered and effective cost. Due to their incredibly diverse nature, importance as pollinators, and historical instability with regard to subfamilial and tribal classification, Syrphidae (flower flies or hoverflies) are an ideal candidate for anchored hybrid enrichment-based phylogenetics, especially since recent molecular phylogenies of the syrphids using only a few markers have resulted in highly unresolved topologies. Over 6200 syrphids are currently known and uncovering their phylogeny will help us to understand how these species have diversified, providing insight into an array of ecological processes, from the development of adult mimicry, the origin of adult migration, to pollination patterns and the evolution of larval resource utilization. We present the first use of anchored hybrid enrichment in insect phylogenetics on a dataset containing 30 flower fly species from across all four subfamilies and 11 tribes out of 15. To produce a phylogenetic hypothesis, 559 loci were sampled to produce a final dataset containing 217,702 sites. We recovered a well resolved topology with bootstrap support values that were almost universally >95 %. The subfamily Eristalinae is recovered as paraphyletic, with the strongest support for this hypothesis to date. The ant predators in the Microdontinae are sister to all other syrphids. Syrphinae and Pipizinae are monophyletic and sister to each other. Larval predation on soft-bodied hemipterans evolved only once in this family. Anchored hybrid enrichment was successful in producing a robustly supported phylogenetic hypothesis for the syrphids. Subfamilial reconstruction is concordant with recent phylogenetic hypotheses, but with much higher support values. With the newly designed probe kit this analysis could be rapidly expanded with further sampling, opening the door to more comprehensive analyses targeting problem areas in syrphid phylogenetics and ecology., Keywords: Anchored phylogenetics, Eristalinae, Flower flies, Hoverflies, Hybrid enrichment, Microdontinae, Pipizinae, Syrphinae, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4928351.

: Anti-Inflammatory Mechanism of Neural Stem Cell Transplantation in Spinal Cord Injury; Neural stem cell (NSC) transplantation has been proposed to promote functional recovery after spinal cord injury. However, a detailed understanding of the mechanisms of how NSCs exert their therapeutic plasticity is lacking. We transplanted mouse NSCs into the injured spinal cord seven days after SCI, and the Basso Mouse Scale (BMS) score was performed to assess locomotor function. The anti-inflammatory effects of NSC transplantation was analyzed by immunofluorescence staining of neutrophil and macrophages and the detection of mRNA levels of tumor necrosis factor- (TNF-), interleukin-1 (IL-1), interleukin-6 (IL-6) and interleukin-12 (IL-12). Furthermore, bone marrow-derived macrophages (BMDMs) were co-cultured with NSCs and followed by analyzing the mRNA levels of inducible nitric oxide synthase (iNOS), TNF-, IL-1, IL-6 and IL-10 with quantitative real-time PCR. The production of TNF- and IL-1 by BMDMs was examined using the enzyme-linked immunosorbent assay (ELISA). Transplanted NSCs had significantly increased BMS scores (p < 0.05). Histological results showed that the grafted NSCs migrated from the injection site toward the injured area. NSCs transplantation significantly reduced the number of neutrophils and iNOS+/Mac-2+ cells at the epicenter of the injured area (p < 0.05). Meanwhile, mRNA levels of TNF-, IL-1, IL-6 and IL-12 in the NSCs transplantation group were significantly decreased compared to the control group. Furthermore, NSCs inhibited the iNOS expression of BMDMs and the release of inflammatory factors by macrophages in vitro (p < 0.05). These results suggest that NSC transplantation could modulate SCI-induced inflammatory responses and enhance neurological function after SCI via reducing M1 macrophage activation and infiltrating neutrophils. Thus, this study provides a new insight into the mechanisms responsible for the anti-inflammatory effect of NSC transplantation after SCI., Keywords: central-nervous-system, encephalomyelitis, factor-alpha, functional recovery, inflammatory cytokine, macrophage, macrophages, Microglia, neural stem cells, promotes, regeneration, Spinal cord injury, stem/progenitor cells, tumor-necrosis-factor, Publication Note: The publisher’s version of record is available at http://www.dx.doi.org/10.3390/ijms17091380

: Applying systems-level spectral imaging and analysis to reveal the organelle interactome.; The organization of the eukaryotic cell into discrete membrane-bound organelles allows for the separation of incompatible biochemical processes, but the activities of these organelles must be coordinated. For example, lipid metabolism is distributed between the endoplasmic reticulum for lipid synthesis, lipid droplets for storage and transport, mitochondria and peroxisomes for β-oxidation, and lysosomes for lipid hydrolysis and recycling. It is increasingly recognized that organelle contacts have a vital role in diverse cellular functions. However, the spatial and temporal organization of organelles within the cell remains poorly characterized, as fluorescence imaging approaches are limited in the number of different labels that can be distinguished in a single image. Here we present a systems-level analysis of the organelle interactome using a multispectral image acquisition method that overcomes the challenge of spectral overlap in the fluorescent protein palette. We used confocal and lattice light sheet instrumentation and an imaging informatics pipeline of five steps to achieve mapping of organelle numbers, volumes, speeds, positions and dynamic inter-organelle contacts in live cells from a monkey fibroblast cell line. We describe the frequency and locality of two-, three-, four- and five-way interactions among six different membrane-bound organelles (endoplasmic reticulum, Golgi, lysosome, peroxisome, mitochondria and lipid droplet) and show how these relationships change over time. We demonstrate that each organelle has a characteristic distribution and dispersion pattern in three-dimensional space and that there is a reproducible pattern of contacts among the six organelles, that is affected by microtubule and cell nutrient status. These live-cell confocal and lattice light sheet spectral imaging approaches are applicable to any cell system expressing multiple fluorescent probes, whether in normal conditions or when cells are exposed to disturbances such as drugs, pathogens or stress. This methodology thus offers a powerful descriptive tool and can be used to develop hypotheses about cellular organization and dynamics., Grant Number: , R01 AG041861, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5536967.

: Artificial incubation does not affect the post-hatch development, health, or survival of the Lance-tailed Manakin (Chiroxiphia lanceolata); Artificial incubation of avian eggs is used in scientific research, conservation, zoo husbandry, and the commercial poultry industry. However, whether artificial incubation negatively impacts post-hatch nestling phenotypes and survival compared to naturally incubated young has not been explicitly tested. Here, we assess whether nestlings artificially incubated as eggs and returned to their natal nest after hatching experienced negative impacts in development, health, and survival. From 2007 to 2017, we measured mass, mass growth rate, tarsus length, tarsus growth rate, external lesions, ejection from the nest, fledging success, and recruitment of Lance-tailed Manakin (Chiroxiphia lanceolata) nestlings from 209 nests where 1 of 2 eggs was artificially incubated, along with 230 unmanipulated nests. We found no statistically significant difference in the development, health, and survival among nestlings artificially incubated as eggs, their naturally incubated nestmates, and nestlings from unmanipulated nests. Our results indicate that artificial incubation can be a safe and effective tool in the study of free-living birds., avian, bird, fledging, growth rate, nestling, recruitment, Data and R code for analyses in DOI: 10.1093/condor/duy022, NSF 1453408, NSF 0843334

: Atomic Resolution Structures Of Human Bufaviruses Determined By Cryo-electron Microscopy; Bufavirus strain 1 (BuV1), a member of the Protoparvovirus genus of the Parvoviridae, was first isolated from fecal samples of children with acute diarrhea in Burkina Faso. Since this initial discovery, BuVs have been isolated in several countries, including Finland, the Netherlands, and Bhutan, in pediatric patients exhibiting similar symptoms. Towards their characterization, the structures of virus-like particles of BuV1, BuV2, and BuV3, the current known genotypes, have been determined by cryo-electron microscopy and image reconstruction to 2.84, 3.79, and 3.25 angstrom, respectively. The BuVs, 65-73% identical in amino acid sequence, conserve the major viral protein, VP2, structure and general capsid surface features of parvoviruses. These include a core -barrel (B-I), -helix A, and large surface loops inserted between these elements in VP2. The capsid contains depressions at the icosahedral 2-fold and around the 5-fold axes, and has three separated protrusions surrounding the 3-fold axes. Structure comparison among the BuVs and to available parvovirus structures revealed capsid surface variations and capsid 3-fold protrusions that depart from the single pinwheel arrangement of the animal protoparvoviruses. These structures provide a platform to begin the molecular characterization of these potentially pathogenic viruses., Keywords: complex, adenoassociated virus-2, bufavirus, cellular receptor, cryo-EM and image reconstruction, diarrhea, electron-microscopy, empty capsids, human parvovirus b19, human protoparvoviruses, parvoviruses, porcine parvovirus, single-stranded DNA virus, surface loops, Publication Note: The publisher's version of record is available at https://doi.org/10.3390/v10010022

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