bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robust, Fiducial-Free Drift Correction for Super-resolution Imaging
Authors: Wester Michael J. , Schodt David J. , Mazloom-Farsibaf Hanieh , Fazel Mohamadreza , Pallikkuth Sandeep , Lidke Keith A. 
Published: March 2021

ABSTRACTWe describe a robust, fiducial-free method of drift correction for use in single molecule localization-based super-resolution methods. The method combines periodic 3D registration of the sample using brightfield images with a fast post-processing algorithm that corrects residual registration errors and drift between registration events. The method is robust to low numbers of collected localizations, requires no specialized hardware, and provides stability and drift correction for an indefinite time period.
Host genetic control of succession in the switchgrass leaf fungal microbiome
Authors: VanWallendael A. , Benucci G. M. N. , da Costa P. B. , Fraser L. , Sreedasyam A. , Fritschi F. , Juenger T. E. , Lovell J. T. , Bonito G. , Lowry D. B. 
Published: March 2021

AbstractLeaf fungal microbiomes can be fundamental drivers of host plant success, as they contain pathogens that devastate crop plants and taxa that enhance nutrient uptake, discourage herbivory, and antagonize pathogens. We measured leaf fungal diversity with amplicon sequencing across an entire growing season in a diversity panel of switchgrass (Panicum virgatum). We also sampled a replicated subset of genotypes across three additional sites to compare the importance of time, space, ecology, and genetics. We found a strong successional pattern in the microbiome shaped both by host genetics and environmental factors. Further, we used genome-wide association mapping and RNA-sequencing to show that three cysteine-rich receptor-like kinases were linked to a genetic locus associated with microbiome structure. These genes were more highly expressed in genotypes susceptible to fungal pathogens, which were central to microbial covariance networks, suggesting that host immune genes are a principal means of controlling the entire leaf microbiome.
Draft Genome of the Korean smeltHypomesus nipponensisand its transcriptomic responses to heat stress in the liver and muscle
Authors: Xuan Biao , Park Jongbin , Choi Sukjung , You Inhwan , Nam Bo-Hye , Noh Eun Soo , Kim Eun Mi , Song Mi-Young , Shin Younhee , Jeon Ji-Hyeon , Kim Eun Bae 
Published: March 2021

AbstractPond smelt (Hypomesus nipponensis) is a cold-freshwater fish species as a winter economic resource of aquaculture in South Korea. Due to its high susceptibility to abnormal water temperature from global warming, a large number of smelt die in hot summer. Here, we present the first draft genome ofH. nipponensisand transcriptomic changes in molecular mechanisms or intracellular responses under heat stress. We combined Illumina and PacBio sequencing technologies to generate the draft genome ofH. nipponensis. Based on the reference genome, we conducted transcriptome analysis of liver and muscle tissues under normal (NT, 5°C) versus warm (HT, 23°C) conditions, to identify heat stress-induced genes and gene categories. We observed a total of 1,987 contigs, with N50of 0.46 Mbp with a largest contig (3.03 Mbp) in the assembled genome. A total number of 20,644 protein coding genes were predicted, and 19,224 genes were functionally annotated: 15,955 genes for Gene Ontology (GO) terms; and 11,560 genes for KEGG Orthology (KO). We conducted the lost and gained genes analysis compared with three species that human, zebrafish and salmon. In the lost genes analysis, we detected smelt lost 4,461 (22.16%), 2,825 (10.62%), and 1,499 (3.09%) genes compare with above three species, respectively. In the gained genes analysis, we observed smelt gain 1,133 (5.49%), 1,670 (8.09%), and 229 (1.11%) genes compare with above species, respectively. From transcriptome analysis, a total of 297 and 331 differentially expressed genes (DEGs) with False discovery rate (FDR) < 0.05 were identified in the liver and muscle tissues, respectively. Gene enrichment analysis of DEGs indicates that up-regulated genes were significantly enriched for lipid biosynthetic process (GO:0008610, P < 0.001) and regulation of apoptotic process (GO:0042981, P < 0.01), and down-regulated genes by immune responses such as myeloid cell differentiation (GO:0030099, P < 0.001) in the liver under heat stress. In muscle tissue, up-regulated genes were enriched for hypoxia (GO:0001666, P < 0.05), transcription regulator activity (GO:0140110, P < 0.001) and calcium-release channel activity (GO:0015278, P < 0.01), and down-regulated genes for nicotinamide nucleotide biosynthetic process (GO:0019359, P < 0.01). The results of KEGG pathway analysis were similar to that of gene enrichment analysis. The draft genome and transcriptomic ofH. nipponensiswill be used as a useful genetic resource for functional and evolutionary studies. Our findings will improve understanding of the molecular mechanisms and heat responses and will be useful for predicting survival of the smelt and its closely related species under global warming.
Histone H3 dopaminylation in ventral tegmental area underlies heroin-induced maladaptive plasticity
Authors: Fulton Sasha L. , Mitra Swarup , Lepack Ashley E. , Martin Jennifer A. , Dietz David M. , Maze Ian 
Published: March 2021

ABSTRACTPersistent transcriptional eventsamples were incubated on ice for 30 min and then centrifugeds in ventral tegmental area (VTA) and other reward relevant brain regions contribute to enduring behavioral adaptations that characterize substance use disorder (SUD). Recent data from our laboratory indicate that aberrant accumulation of the newly discovered histone post-translational modification (PTM), H3 dopaminylation at glutamine 5 (H3Q5dop), contributes significantly to cocaine-seeking behavior following prolonged periods of abstinence. It remained unclear, however, whether this modification is important for relapse vulnerability in the context of other drugs of abuse, such as opioids. Here, we showed that H3Q5dop plays a critical role in heroin-mediated transcriptional plasticity in midbrain. In rats undergoing abstinence from heroin self-administration (SA), we found acute and persistent accumulation of H3Q5dop in VTA. By attenuating H3Q5dop during abstinence, we both altered gene expression programs associated with heroin withdrawal and reduced heroin-primed reinstatement behavior. These findings thus establish an essential role for H3Q5dop, and its downstream transcriptional consequences, in opioid-induced plasticity in VTA.SIGNIFICANCE STATEMENTOpioid addiction is a chronically relapsing disorder defined by pathological drug-seeking behavior. Persistent relapse vulnerability is hypothesized to reflect a functional “rewiring” of reward-processing circuitry in the brain. This phenomenon is precipitated by drug-induced alterations in transcriptional plasticity of midbrain dopamine neurons, indicating an important role for epigenetic regulatory mechanisms in opioid dependence. We found that the newly discovered histone modification, H3 dopaminylation at glutamine 5 (H3Q5dop), was increased in ventral tegmental area (VTA) during periods of abstinence. H3Q5dop accumulation was found to regulate transcriptional programs associated with chronic heroin exposure. Using viral-mediated gene therapy to reduce H3Q5dop accumulation during abstinence resulted in attenuated heroin-primed seeking behaviors. Together, our results indicate that H3Q5dop plays an abstinence-specific role in regulating heroin-induced behavioral plasticity during prolonged abstinence.
Dopaminergic regulation of vestibulo-cerebellar circuits through unipolar brush cells
Authors: Canton-Josh Jose Ernesto , Qin Joanna , Salvo Joseph , Kozorovitskiy Yevgenia 
Published: March 2021

SUMMARYWhile multiple monoamines modulate cerebellar output, the mechanistic details of dopaminergic signaling in the cerebellum remain poorly understood. Here we show that Drd1 dopamine receptors are expressed in unipolar brush cells (UBCs) of the cerebellar vermis. Drd1 activation increases UBC firing rate and postsynaptic NMDA receptor-mediated currents. Using anatomical tracing andin situhybridization, we tested three hypotheses about the source of cerebellar dopamine. We exclude midbrain dopaminergic nuclei and tyrosine hydroxylase-positive Purkinje cells as potential sources, supporting the possibility of dopaminergic co-release from locus coeruleus (LC) axons. Using an optical dopamine sensor GRABDA, electrical stimulation, and optogenetic activation of LC fibers in the acute slice, we find evidence for monoamine release onto Drd1-expressing UBCs. Altogether, we propose that the LC regulates cerebellar cortex activity by co-releasing dopamine onto UBCs to modulate their response to cerebellar inputs. Purkinje neurons directly inhibit these Drd1-positive UBCs, forming a dopamine-sensitive recurrent vestibulo-cerebellar circuit.
Manifestations of genetic risk for Alzheimer’s Disease in the blood: a cross-sectional multi-omic analysis in healthy adults aged 18-90+
Authors: Heath Laura , Earls John C. , Magis Andrew T. , Kornilov Sergey A. , Lovejoy Jennifer C. , Funk Cory C. , Rappaport Noa , Logsdon Benjamin A. , Mangravite Lara M. , Kunkle Brian W. , Martin Eden R. , Naj Adam C. , Ertekin-Taner Nilüfer , Golde Todd E. , Hood Leroy , Price Nathan D. ,   Alzheimer’s Disease Genetics Consortium
Published: March 2021

AbstractDeeply phenotyped cohort data can elucidate differences associated with genetic risk for common complex diseases across an age spectrum. Previous work has identified genetic variants associated with Alzheimer’s disease (AD) risk from large-scale genome-wide association study meta-analyses. To explore effects of known AD-risk variants, we performed a phenome-wide association study on ~2000 clinical, proteomic, and metabolic blood-based analytes obtained from 2,831 cognitively normal adult clients of a consumer-based scientific wellness company. Results uncovered statistically significant SNP-analyte associations for five genetic variants after correction for multiple testing (for SNPs in or nearNYAP1, ABCA7, INPP5D, andAPOE). These effects were detectable from early adulthood. Sex modified the effects of four genetic variants, with multiple interrelated immune-modulating effects associated with thePICALMvariant. Sex-stratified GWAS results from an independent AD case-control meta-analysis supported sexspecific disease effects of thePICALMvariant, highlighting the importance of sex as a biological variable. These analyses support evidence from previous functional genomics studies in the identification of a causal variant within thePILRAgene. Taken together, this study highlights clues to the earliest effects of AD genetic risk variants in individuals where disease symptoms have not (yet) arisen.
Modulation masking and fine structure shape neural envelope coding to predict speech intelligibility across diverse listening conditions
Authors: Viswanathan Vibha , Bharadwaj Hari M. , Shinn-Cunningham Barbara G. , Heinz Michael G. 
Published: March 2021

AbstractA fundamental question in the neuroscience of everyday communication is how scene acoustics shape the neural processing of attended speech sounds and in turn impact speech intelligibility. While it is well known that the temporal envelopes in target speech are important for intelligibility, how the neural encoding of target-speech envelopes is influenced by background sounds or other acoustic features of the scene is unknown. Here, we combine human electroencephalography with simultaneous intelligibility measurements to address this key gap. We find that the neural envelope-domain signal-to-noise ratio in target-speech encoding, which is shaped by masker modulations, predicts intelligibility over a range of strategically chosen realistic listening conditions unseen by the predictive model. This provides neurophysiological evidence for modulation masking. Moreover, using high-resolution vocoding to carefully control peripheral envelopes, we show that target-envelope coding fidelity in the brain depends not only on envelopes conveyed by the cochlea, but also on the temporal fine structure (TFS), which supports scene segregation. Our results are consistent with the notion that temporal coherence of sound elements across envelopes and/or TFS influences scene analysis and attentive selection of a target sound. Our findings also inform speech-intelligibility models and technologies attempting to improve real-world speech communication.
Insights intoin vivoadipocyte differentiation through cell-specific labeling in zebrafish
Authors: Lepanto Paola , Levin Florencia , Koziol Uriel , Malacrida Leonel , Badano José L. 
Published: March 2021

AbstractWhite adipose tissue hyperplasia has been shown to be crucial for handling excess energy in healthy ways. Though adipogenesis mechanisms have been underscoredin vitro, we lack information on how tissue and systemic factors influence the differentiation of new adipocytes. While this could be studied in zebrafish, adipocyte identification currently relies on neutral lipid labeling, thus precluding access to cells in early stages of differentiation. Here we report the generation and analysis of a zebrafish line with the transgenefabp4(-2.7):EGFPcaax. In vivoconfocal microscopy of the pancreatic and abdominal visceral depots of transgenic larvae, revealed the presence of labeled mature adipocytes as well as immature cells in earlier stages of differentiation. Through co-labeling for blood vessels, we observed a close interaction of differentiating adipocytes with endothelial cells through cell protrusions. Finally, we implemented hyperspectral imaging and spectral phasor analysis in Nile Red labeled transgenic larvae and revealed the lipid metabolic transition towards neutral lipid accumulation of differentiating adipocytes. Altogether our work presents the characterization of a novel adipocyte-specific label in zebrafish and uncovers previously unknown aspects ofin vivoadipogenesis.Summary statementAnalysis of the differentiation of adipocytesin vivothrough cell-specific labeling in zebrafish, revealed their early interaction with blood vessels as well as early lipid metabolic changes.
Cytogenotoxic effects of 3-epicaryoptin inAllium cepaL. root apical meristem cells
Authors: Barman Manabendu , Ray Sanjib 
Published: March 2021

AbstractDiterpenoid 3-epicaryoptin (C26H36O9) is abundant in the leaves ofClerodendrum inerme, a traditionally used medicinal plant, having insect antifeedant activities. Here, we aim to explore the cytogenotoxic effects of compound 3-epicaryoptin inAllium ceparoot apical meristem cells.A. ceparoots were treated with 3-epicaryoptin (100, 150 & 200 μg mL-1concentration) and the standard compound colchicine (200 μg mL-1concentration) for 2, 4, 4+16 h (4 h treatment followed by 16 h recovery). Cytogenotoxicity was analysed by studying the root growth retardation (RGR), mitotic index (MI), and cellular aberrations. The result showed statistically significant (p<0.01), concentration-dependent RGR effects of 3-epicaryoptin treatment compared with the negative control. Study of cell frequency in different phases of cell division observed a significant (p<0.001) increase in the metaphase cell percentage (66.2±0.58 %, 150 μg mL-1) and which subsequently caused an increase in the frequency of MI (12.29±0.34 %, 150 μg mL-1) at 4h of 3-epicaryoptin treatment and that was comparable with the colchicine action. The cytological study revealed that the 3-epicaryoptin treatment could induce different types of chromosomal abnormalities such as colchicine like metaphase, vagrant chromosomes, sticky chromosomes, anaphase-bridge, and an increased frequency of micronuclei and polyploid cells. These findings indicate that 3-epicaryoptin is cytogenotoxic, and thusC. inermeshould be used with caution in traditional medicine.
Detection of SARS-CoV-2 N501Y mutation by RT-PCR to identify the UK and the South African strains in the population of South Indian state of Telangana
Authors: Ahmed Safaa Muneer , Juvvadi Smita Rao , Kalapala Rakesh , Sreemanthula Jagadeesh Babu 
Published: March 2021

AbstractObjectiveTo detect N501Y mutation of the SARS-CoV-2 spike protein by RT-PCR to distinguish (B.1.1.7) UK and (501Y.V2) South African strains from others in the population of Telangana and to determine its clinical implications.MethodsA primer-probe mix that specifically detects the mutated N501Y strain by real time RT-PCR was designed. 93 samples that were reported positive for COVID-19 by our laboratory in the month of February 2021 were tested using our own primer-probe mix for the presence of N501Y by RT-PCR. The results of RT-PCR were validated by Sanger sequencing in representative samples. Sanger sequencing of other defining spike mutations of B.1.1.7 (del 69-70, del 144, N501Y, A570D, D614G, P681H, T716I, S982A and D1118H) and 501Y.V2 (K417N, E484K, N501Y and D614G) was also investigated.FindingsOut of 93 COVID-19 positive samples, 12 samples are detected positive for N501Y by RT-PCR. Sanger sequencing of these 12 samples further confirmed the presence of N501Y and other mutations that are characteristic of UK strain (B.1.1.7). The South African strain (501Y.V2) is not detected in any of our samples in this study. But, the E484K mutation that is characteristic of 501Y.V2 is detected in one N501Y negative sample.ConclusionStrain-specific RT-PCR for N501Y was developed and validated with Sanger sequencing. Such strategy facilitates quick surveillance for more transmissible and more vaccine resistant strains.
Structural variant selection for high-altitude adaptation using single-molecule long-read sequencing
Authors: Shi Jinlong , Jia Zhilong , Zhao Xiaojing , Sun Jinxiu , Liang Fan , Park Minsung , Zhao Chenghui , Wang Xiaoreng , Chen Qi , Song Xinyu , Yu Kang , Jia Qian , Wang Depeng , Xiao Yuhui , Liu Yinzhe , Wu Shijing , Zhong Qin , Wu Jue , Cui Saijia , Bo Xiaochen , Wu Zhenzhou , Kellis Manolis , He Kunlun 
Published: March 2021

AbstractStructural variants (SVs) can be important drivers of human adaptation with strong effects, but previous studies have focused primarily on common variants with weak effects. Here, we used large-scale single-molecule long-read sequencing of 320 Tibetan and Han samples, to show that SVs are key drivers of selection under high-altitude adaptation. We expand the landscape of global SVs, apply robust models of selection and population differentiation combining SVs, SNPs and InDels, and use epigenomic analyses to predict driver enhancers, target genes, upstream regulators, and biological functions, which we validate using enhancer reporter and DNA pull-down assays. We reveal diverse Tibetan-specific SVs affecting the cis- and trans-regulatory circuitry of diverse biological functions, including hypoxia response, energy metabolism, lung function, etc. Our study greatly expands the global SV landscape, reveals the central role of gene-regulatory circuitry rewiring in human adaptation, and illustrates the diverse functional roles that SVs can play in human biology.
Single Cell, Single Nucleus and Spatial RNA Sequencing of the Human Liver Identifies Hepatic Stellate Cell and Cholangiocyte Heterogeneity
Authors: Andrews Tallulah S. , Atif Jawairia , Liu Jeff C. , Perciani Catia T. , Ma Xue-Zhong , Thoeni Cornelia , Slyper Michal , Eraslan Gökcen , Segerstolpe Asa , Manuel Justin , Chung Sai , Winter Erin , Cirlan Iulia , Khuu Nicholas , Fischer Sandra , Rozenblatt-Rosen Orit , Regev Aviv , McGilvray Ian D. , Bader Gary D. , MacParland Sonya A. 
Published: March 2021

ABSTRACTThe critical functions of the human liver are coordinated through the interactions of hepatic parenchymal and non-parenchymal cells. Recent advances in single cell transcriptional approaches have enabled an examination of the human liver with unprecedented resolution. However, dissociation related cell perturbation can limit the ability to fully capture the human liver’s parenchymal cell fraction, which limits the ability to comprehensively profile this organ. Here, we report the transcriptional landscape of 73,295 cells from the human liver using matched single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA sequencing (snRNA-seq). The addition of snRNA-seq enabled the characterization of interzonal hepatocytes at single-cell resolution, revealed the presence of rare subtypes of hepatic stellate cells previously only seen in disease, and detection of cholangiocyte progenitors that had only been observed duringin vitrodifferentiation experiments. However, T and B lymphocytes and NK cells were only distinguishable using scRNA-seq, highlighting the importance of applying both technologies to obtain a complete map of tissue-resident cell-types. We validated the distinct spatial distribution of the hepatocyte, cholangiocyte and stellate cell populations by an independent spatial transcriptomics dataset and immunohistochemistry. Our study provides a systematic comparison of the transcriptomes captured by scRNA-seq and snRNA-seq and delivers a high-resolution map of the parenchymal cell populations in the healthy human liver.
The nucleotide addition cycle of the SARS-CoV-2 polymerase
Authors: Bera Subhas Chandra , Seifert Mona , Kirchdoerfer Robert N. , van Nies Pauline , Wubulikasimu Yibulayin , Quack Salina , Papini Flávia S. , Arnold Jamie J. , Canard Bruno , Cameron Craig E. , Depken Martin , Dulin David 
Published: March 2021

AbstractCoronaviruses have evolved elaborate multisubunit machines to replicate and transcribe their genomes. Central to these machines are the RNA-dependent RNA polymerase subunit (nsp12) and its intimately associated cofactors (nsp7 and nsp8). We have used a high-throughput magnetic-tweezers approach to develop a mechanochemical description of this core polymerase. The core polymerase exists in at least three catalytically distinct conformations, one being kinetically consistent with incorporation of incorrect nucleotides. We provide the first evidence that an RdRp uses a thermal ratchet instead of a power stroke to transition from the pre- to post-translocated state. Ultra-stable magnetic tweezers enables the direct observation of coronavirus polymerase deep and long-lived backtrack that are strongly stimulated by secondary structure in the template. The framework presented here elucidates one of the most important structure-dynamics-function relationships in human health today, and will form the grounds for understanding the regulation of this complex.