bluuebunny/crossref_metadata_2025_split huggingface dataset:
Satellite cell expansion is mediated by P-eIF2α dependentTacc3translation
Authors: Fujita Ryo , Lean Graham , Jamet Solène , Hébert Steven , Kleinman Claudia L. , Crist Colin 
Published: May 2020

AbstractTranslational control of gene expression is an important regulator of adult stem cell quiescence, activation and self-renewal. In skeletal muscle, quiescent satellite cells maintain low levels of protein synthesis, mediated in part through the phosphorylation of eIF2α (P-eIF2α). Pharmacological inhibition of the eIF2α phosphatase with the small molecule sal003 maintains P-eIF2α and permits the expansion of satellite cellsex vivo. Paradoxically, P-eIF2α also increases the translation of specific mRNAs, which is mediated by P-eIF2α dependent readthrough of inhibitory upstream open reading frames (uORFs). Here, we ask whether P-eIF2α dependent mRNA translation enables expansion of satellite cells. Using transcriptomic and proteomic analyses, we show a number of genes associated with the assembly of the spindle pole to be upregulated at the level of protein, without corresponding change in mRNA levels, in satellite cells expanded in the presence of sal003. We show that uORFs in the 5’UTR of mRNA for the mitotic spindle stability geneTacc3direct P-eIF2α dependent translation. Satellite cells deficient for TACC3 exhibit defects in expansion, self-renewal and regeneration of skeletal muscle.SignificanceTranslational control of gene expression has emerged as an important regulator of adult stem cell populations, which maintain low levels of protein synthesis. In adult muscle stem cells, or satellite cells, a portrait of translational control has emerged whereby multiple repression mechanisms prevent the translation of specific mRNAs. It remains unclear how other mRNAs escape repression and are efficiently translated. We show that within the context of low global rates of protein synthesis, satellite cell expansion occurs through the selective translation ofTacc3mRNA.Tacc3deficient satellite cells expand poorly, leading to defects in skeletal muscle regeneration. Our study provides a more complete picture of translational control of gene expression in adult stem cell populations.
Methamphetamine enhances caveolar transport of therapeutic drugs across the rodent blood-brain barrier
Authors: Chang Jui-Hsien , Greene Chris , Futter Clare , Nichols Benjamin J. , Campbell Matthew , Turowski Patric 
Published: May 2020

AbstractThe blood-brain barrier (BBB) is a multifactorial and multicellular vascular interface separating the systemic environment from the central nervous system (CNS). It gates cerebral penetration of circulating molecules and cells and is the principal reason for low accumulation of many therapeutics in the brain. Low dose methamphetamine (METH) induces fluid phase transcytosis across the BBBin vitroand could therefore be used to enhance CNS drug delivery. Here we show, that low dose intravascular METH induced significant leakage exclusively via caveolar transport at the intact BBB in rodentsex vivo. Notably, METH-induced leakage was suppressed at 4°C and in Caveolin-1 (CAV1) knockout mice. Furthermore, METH strongly enhanced brain penetration of therapeutic molecules, namely doxorubicin (DOX), a small chemotherapeutic agent, and aflibercept (AFL), a ca. 100 kDA recombinant protein. Lastly, METH improved the therapeutic efficacy of DOX in a mouse model of human glioblastoma (GBM), as measured by a 25% increase in median survival time (p = 0.0024). Collectively, our data indicated that METH can facilitate preclinical assessment of novel experimental treatments and has the potential to enhance drug delivery to the diseased CNS.
Fast purification of recombinant monomeric amyloid-β fromE. coliand amyloid-β-mCherry aggregates from mammalian cells
Authors: Stephens Amberley D. , Lu Meng , Kaminski Schierle Gabriele S. 
Published: May 2020

AbstractThe Alzheimer’s disease related peptide, Amyloid-beta (Aβ)1-40 and 1-42, has proven difficult to be purified as a recombinant monomeric protein due its expression inE. colileading to the formation of insoluble inclusion bodies and its tendency to quickly form insoluble aggregates. A vast array of methods have been used so far, yet many have pitfalls, such as the use of tags for ease of Aβ isolation, the formation of Aβ multimers within the time frame of extraction or the need to reconstitute Aβ from a freeze dried state. Here, we present a rapid protocol to produce highly pure and monomeric recombinant Aβ using a one-step ion exchange purification method and to label the peptide using a maleimide dye. The solublisation and purification steps take only three hours. We also present a protocol for the isolation of Aβ-mCherry from mammalian cells.HighlightsPurification of untagged, monomeric recombinant Aβ fromE. coli.A fast protocol; 6 hours forE. coligrowth and Aβ expression, 2 hours to clean inclusion bodies, 45 mins to solublise and purify the peptide.No freeze drying step that can lead to oligomer formation.Purification of fluorescent Aβ-mCherry from mammalian cells.
MET Receptor Tyrosine Kinase Regulates Vagal Laryngeal Motor Neuron Development and Lifespan Ultrasonic Vocal Communication
Authors: Kamitakahara Anna K. , Marandi Ghoddousi Ramin Ali , Lanjewar Alexandra L. , Magalong Valerie M. , Wu Hsiao-Huei , Levitt Pat 
Published: May 2020

SummaryThe vagal motor nucleus ambiguus (nAmb) innervates the intrinsic muscles of the larynx, providing direct motor control over vocal production in humans and rodents. Here, we demonstrate that early developmental signaling through the MET receptor tyrosine kinase (MET) is required for proper formation of the nAmb. Embryonic deletion ofMetin the developing brainstem resulted in a loss of one-third of motor neurons in the nAmb. While the remaining neurons were able to establish connections with target muscles in the larynx, advanced signal processing analyses revealed severe deficits in ultrasonic vocalization in early postnatal life. Abnormal vocalization patterns persisted into adulthood in the majority of mice tested. Interestingly, 28% of adult mice recovered the ability to vocalize demonstrating heterogeneity in circuit restitution. Together, the data establish MET as a factor necessary for development of a specific subset of neurons in the nAmb required for normal ultrasonic vocalization.
PALLAS: Penalized mAximum LikeLihood and pArticle Swarms for Inference of Gene Regulatory Networks from Time Series Data
Authors: Tan Yukun , Neto Fernando B. Lima , Neto Ulisses Braga 
Published: May 2020

AbstractWe present PALLAS, a practical method for gene regulatory network (GRN) inference from time series data, which employs penalized maximum likelihood and particle swarms for optimization. PALLAS is based on the Partially-Observable Boolean Dynamical System (POBDS) model and thus does not require ad-hoc binarization of the data. The penalty in the likelihood is a LASSO regularization term, which encourages the resulting network to be sparse. PALLAS is able to scale to large networks under no prior knowledge, by virtue of a novel continuous-discrete Fish School Search particle swarm algorithm for efficient simultaneous maximization of the penalized likelihood over the discrete space of networks and the continuous space of observational parameters. The performance of PALLAS is demonstrated by a comprehensive set of experiments using synthetic data generated from real and artificial networks, as well as real time series microarray and RNA-seq data, where it is compared to several other well-known methods for gene regulatory network inference. The results show that PALLAS can infer GRNs efficiently and accurately. PALLAS is a fully-fledged program with a commandline user interface, written in python, and available on GitHub (https://github.com/yukuntan92/PALLAS).
ZEB1 is Required for NHEJ-Mediated DSB Repair in Euchromatin
Authors: Genetta Thomas L. , Abbas Tarek , Pandta Raj , Hunt Clayton R. , Pandita Tej. K. , Larner James M. 
Published: May 2020

AbstractIonizing radiation-induced DSBs are repaired primarily by the Non-Homologous End Joining (NHEJ) pathway, but the details of how this is regulated in different chromatin contexts are far from understood. We have discovered a novel response to DSBs that promotes NHEJ selectively in euchromatin, based on a novel interaction between the EMT-inducing transcriptional repressor ZEB1, and the well-studied NHEJ-promoting DNA repair factor 53BP1. Using a number of approaches, we have discovered that the ZEB1-53BP1 association is amplified following exposure of cells to IR and that they co-localize at IR-induced foci (IRIF). Depletion of ZEB1 enhances radio-sensitivity and increases IR-induced chromosomal aberrations in an ATM-independent manner. The very rapid recruitment–within 2 seconds–of ZEB1 to euchromatic DSBs is like-wise ATM-independent, but DNA-PK-dependent and is required for subsequent recruitment of 53BP1. ZEB1 promotes NHEJ and inhibits HR through its homeodomain by inducing 53BP1-permissive, pro-NHEJ/anti-HR chromatin modifications. Lastly, depletion of ZEB1 increases hyper-resection at DSBs and inhibits physiological DSB repair. These results support the argument that ZEB1 plays an essential role in DSB repair in euchromatin by establishing a 53BP1-permissive/pro-NHEJ chromatin environment.
Regional, layer, and cell-class specific connectivity of the mouse default mode network
Authors: Whitesell Jennifer D. , Liska Adam , Coletta Ludovico , Hirokawa Karla E. , Bohn Phillip , Williford Ali , Groblewski Peter A. , Graddis Nile , Kuan Leonard , Knox Joseph E. , Ho Anh , Wakeman Wayne , Nicovich Philip R. , Nguyen Thuc Nghi , Garren Emma , van Velthoven Cindy T. J. , Fong Olivia , Feng David , Naeemi Maitham , Henry Alex M. , Dee Nick , Smith Kimberly A. , Levi Boaz P. , Ng Lydia , Tasic Bosiljka , Zeng Hongkui , Mihalas Stefan , Gozzi Alessandro , Harris Julie A. 
Published: May 2020

AbstractThe evolutionarily conserved default mode network (DMN) is characterized by temporally correlated activity between brain regions during resting states. The DMN has emerged as a selectively vulnerable network in multiple disorders, so understanding its anatomical composition will provide fundamental insight into how its function is impacted by disease. Reproducible rodent analogs of the human DMN offer an opportunity to investigate the underlying brain regions and structural connectivity (SC) with high spatial and cell type resolution. Here, we performed systematic analyses using mouse resting state functional magnetic resonance imaging to identify the DMN and whole brain axonal tracing data, co-registered to the 3D Allen Mouse Common Coordinate Framework reference atlas. We identified the specific, predominantly cortical, brain regions comprising the mouse DMN and report preferential SC between these regions. Next, at the cell class level, we report that cortical layer (L) 2/3 neurons in DMN regions project almost exclusively to other DMN regions, whereas L5 neurons project to targets both in and out of the DMN. We then test the hypothesis that in- and out-DMN projection patterns originate from distinct L5 neuron sub-classes using an intersectional viral tracing strategy to label all the axons from neurons defined by a single target. In the ventral retrosplenial cortex, a core DMN region, we found two L5 projection types related to the DMN and mapped them to unique transcriptomically-defined cell types. Together, our results provide a multi-scale description of the anatomical correlates of the mouse DMN.
Reference-free Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network
Authors: Shao Xin , Yang Haihong , Zhuang Xiang , Liao Jie , Yang Yueren , Yang Penghui , Cheng Junyun , Lu Xiaoyan , Chen Huajun , Fan Xiaohui 
Published: May 2020

AbstractAdvances in single-cell RNA sequencing (scRNA-seq) have furthered the simultaneous classification of thousands of cells in a single assay based on transcriptome profiling. In most analysis protocols, single-cell type annotation relies on marker genes or RNA-seq profiles, resulting in poor extrapolation. Here, we introduce scDeepSort (https://github.com/ZJUFanLab/scDeepSort), a reference-free cell-type annotation tool for single-cell transcriptomics that uses a deep learning model with a weighted graph neural network. Using human and mouse scRNA-seq data resources, we demonstrate the feasibility of scDeepSort and its high accuracy in labeling 764,741 cells involving 56 human and 32 mouse tissues. Significantly, scDeepSort outperformed reference-dependent methods in annotating 76 external testing scRNA-seq datasets, including 126,384 cells (85.79%) from ten human tissues and 134,604 cells from 12 mouse tissues (81.30%). scDeepSort accurately revealed cell identities without prior reference knowledge, thus potentially providing new insights into mechanisms underlying biological processes, disease pathogenesis, and disease progression at a single-cell resolution.
Chromosome-level genome assembly of the African pike,Hepsetus odoe
Authors: Du Xiao , Hong Xiaoning , Fan Guangyi , Huang Xiaoyun , Sun Shuai , Bingjie Ouyang , Zhang He , Zhang Mengqi , Liu Shanshan , Liu Xin , Zhang Wenwei 
Published: May 2020

AbstractThe order Characiformes is one of the largest components of the freshwater teleost fauna inhabiting exclusively in South America and Africa with great ecological and economical significance. Yet, quite limited genomic resources are available to study this group and their transatlantic vicariance. In this study we present a chromosome-level genome assembly of the African pike (Hepsetus odoe), a representative member of the African Characiformes. To this end, we generated 119, 11, and 67 Gb reads using the single tube long fragment read (stLFR), Oxford Nanopore, and Hi-C sequencing technologies, respectively. We obtained an 862.1 Mb genome assembly with the contig and scaffold N50 of 347.4 kb and 25.8 Mb, respectively. Hi-C sequencing produced 29 chromosomes with 742.5 Mb, representing 86.1% of the genome. 24,314 protein-coding genes were predicted and 23,999 (98.7%) genes were functionally annotated. The chromosomal-scale genome assembly will be useful for functional and evolutionary studies of the African pike and promote the study of Characiformes speciation and evolution.
Evolutionary Dynamics And Geographic Dispersal Of Beta Coronaviruses In African Bats
Authors: Motayo Babatunde Olanrewaju , Oluwasemowo Olukunle Oluwapamilerin , Akinduti Paul Akiniyi 
Published: May 2020

ABSTRACTBats have been shown to serve as reservoir host of various viral agents including coronaviruses. They have also been associated with the novel coronavirus SARS-CoV-2. This has made them an all important agent for CoV evolution and transmission. Our objective in this study was to investigate the dispersal, phylogenomics and evolution ofbetacoronavirus(βCoV) among African bats. We retrieved sequence data from established databases such as GenBank and Virus Pathogen Resource, covering the partial RNA dependent RNA polymerase (RdRP) gene of Bat coronaviruses from eight African, three Asian, five European, two South American countries and Australia. We analyzed for Phylogeographic information relating to genetic diversity and evolutionary dynamics. Our study revealed that majority of the African strains fell withinNorbecovirussubgenera, with an Evolutionary rate of 1.301 × 10−3, HPD (1.064 × 10−3– 1.434 × 10−3) subs/site/year. The African strains diversified into three main subgenera,Norbecovirus, HibecovirusandMarbecovirus. The time to most common recent ancestor forNorbecovirusstrains was 1968, and 2010, for the AfricanMarbecovirusstrains. There was evidence of inter species transmission ofNorbecovirusamong bats in Cameroun and DRC. Phlylogeography showed that there were inter-continental spread of Bt-CoV from Europe, China and Hong Kong into Central and Southern Africa, highlighting the possibility of long distance transmission. Our study has elucidated the possible evolutionary origins of βCoV among African bats, we therefore advocate for broader studies of whole genome sequences of BtCoV to further understand the drivers for their emergence and zoonotic spillovers into human population.
Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale
Authors: Carnevali Paula B. Matheus , Lavy Adi , Thomas Alex D. , Crits-Christoph Alexander , Diamond Spencer , Meéheust Raphaeël , Olm Matthew R. , Sharrar Allison , Lei Shufei , Dong Wenming , Falco Nicola , Bouskill Nicholas , Newcomer Michelle , Nico Peter , Wainwright Haruko , Dwivedi Dipankar , Williams Kenneth H. , Hubbard Susan , Banfield Jillian F. 
Published: May 2020

AbstractBiogeochemical exports of C, N, S and H2from watersheds are modulated by the activity of microorganisms that function over micron scales. This disparity of scales presents a substantial challenge for development of predictive models describing watershed function. Here, we tested the hypothesis that meander-bound regions exhibit patterns of microbial metabolic potential that are broadly predictive of biogeochemical processes in floodplain soils along a river corridor. We intensively sampled floodplain soils located in the upper, middle, and lower reaches of the East River in Colorado and reconstructed 248 draft quality genomes representative at a sub-species level. Approximately one third of the representative genomes were detected across all three locations with similar levels of abundance, and despite the very high microbial diversity and complexity of the soils, ~15% of species were detected in two consecutive years. A core floodplain microbiome was enriched in bacterial capacities for aerobic respiration, aerobic CO oxidation, and thiosulfate oxidation with the formation of elemental sulfur. We did not detect systematic patterns of gene abundance based on sampling position relative to the river. However, at the watershed scale meander-bound floodplains appear to serve as scaling motifs that predict aggregate capacities for biogeochemical transformations in floodplain soils. Given this, we conducted a transcriptomic analysis of the middle site. Overall, the most highly transcribed genes wereamoCABandnxrAB(for nitrification) followed by genes involved in methanol and formate oxidation, and nitrogen and CO2fixation. Low soil organic carbon correlated with high activity of genes involved in methanol, formate, sulfide, hydrogen, and ammonia oxidation, nitrite oxidoreduction, and nitrate and nitrite reduction. Thus, widely represented genetic capacities did not predictin situactivity at one time point, but rather they define a reservoir of biogeochemical potential available as conditions change.
Visualizing cassava bacterial blight at the molecular level using CRISPR-mediated homology-directed repair
Authors: Veley Kira M. , Okwuonu Ihuoma , Jensen Greg , Yoder Marisa , Taylor Nigel J. , Meyers Blake C. , Bart Rebecca S. 
Published: May 2020

SUMMARYResearch on a few model, plant-pathogen systems has benefitted from years of tool and resource development. This is not the case for the vast majority of economically and nutritionally important plants, creating a crop improvement bottleneck. Cassava bacterial blight (CBB), caused byXanthomonas axonopodispv.manihotis(Xam), is an important disease in all regions where cassava (Manihot esculentaCrantz) is grown. Here we describe development of a tool for molecular-level visualization of CBB dynamicsin vivo. Using CRISPR-mediated homology-directed repair (HDR), we generated plants containing scarless insertion of a GFP reporter at the CBB susceptibility (S) geneMeSWEET10a. Activation ofMeSWEET10a-GFPbyXamwas subsequently visualized at transcriptional and translational levels. Development of this tool was facilitated by a time-saving, adaptable strategy for identifying successful products of HDR, currently a limiting factor in plant research. This strategy has the potential to enable such research in other systems, improving the practicality of HDR-based experimentation.
ACE2-Variants Indicate Potential SARS-CoV-2-Susceptibility in Animals: An Extensive Molecular Dynamics Study
Authors: Pach Szymon , Nguyen Trung Ngoc , Trimpert Jakob , Kunec Dusan , Osterrieder Nikolaus , Wolber Gerhard 
Published: May 2020

AbstractSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) emerged in late 2019 and since evolved into a global threat with nearly 4.4 million infected people and over 290,000 confirmed deaths worldwide.1 SARS-CoV-2 is an enveloped virus presenting spike (S) glycoproteins on its outer surface. Binding of S to host cell angiotensin converting enzyme 2 (ACE2) is thought to be critical for cellular entry. The host range of the virus extends far beyond humans and non-human primates. Natural and experimental infections have confirmed high susceptibility of cats, ferrets, and hamsters, whereas dogs, mice, rats, pigs, and chickens seem refractory to SARS-CoV-2 infection. To investigate the reason for the variable susceptibility observed in different species, we have developed molecular descriptors to efficiently analyze our dynamic simulation models of complexes between SARS-CoV-2 S and ACE2. Based on our analyses we predict that: (i) the red squirrel is likely susceptible to SARS-CoV-2 infection and (ii) specific mutations in ACE2 of dogs, rats, and mice render them susceptible to SARS-CoV-2 infection.
An NMR-based biosensor to measure stereo-specific methionine sulfoxide reductase (MSR) activitiesin vitroandin vivo
Authors: Sánchez-López Carolina , Labadie Natalia , Lombardo Verónica A. , Biglione Franco A. , Manta Bruno , Jacob Reeba S. , Gladyshev Vadim N. , Abdelilah-Seyfried Salim , Selenko Philipp , Binolfi Andres 
Published: May 2020

AbstractOxidation of protein methionines to methionine-sulfoxides (MetOx) is associated with several age-related diseases. In healthy cells, MetOx is reduced to methionine by two families of conserved methionine sulfoxide reductase enzymes, MSRA and MSRB that specifically target theS- orR-diastereoisomers of methionine-sulfoxides, respectively. To directly interrogate MSRA and MSRB functions in cellular settings, we developed an NMR-based biosensor that we call CarMetOx to simultaneously measure both enzyme activities in single reaction setups. We demonstrate the suitability of our strategy to delineate MSR functions in complex biological environments that range from native cell lysates to zebrafish embryos. Thereby, we establish differences in substrate specificities between prokaryotic and eukaryotic MSRs and introduce CarMetOx as a highly sensitive tool for studying therapeutic targets of oxidative stress-related human diseases and redox regulated signaling pathways. Our approach further extends high-resolution in-cell NMR measurements of exogenously delivered biomolecules to an entire multicellular organism.