bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protracted yet coordinated differentiation of long-lived SARS-CoV-2-specific CD8+ T cells during COVID-19 convalescence
Authors: Ma Tongcui , Ryu Heeju , McGregor Matthew , Babcock Benjamin , Neidleman Jason , Xie Guorui , George Ashley F. , Frouard Julie , Murray Victoria , Gill Gurjot , Ghosn Eliver , Newell Evan , Lee Sulggi , Roan Nadia R. 
Published: April 2021

ABSTRACTCD8+ T cells are important antiviral effectors that can potentiate long-lived immunity against COVID-19, but a detailed characterization of these cells has been hampered by technical challenges. We screened 21 well-characterized, longitudinally-sampled convalescent donors that recovered from mild COVID-19 against a collection of SARS-CoV-2 tetramers, and identified one participant with an immunodominant response against Nuc322-331, a peptide that is conserved in all the SARS-CoV-2 variants-of-concern reported to date. We conducted 38- parameter CyTOF phenotyping on tetramer-identified Nuc322-331-specific CD8+ T cells, and on CD4+ and CD8+ T cells recognizing the entire nucleocapsid and spike proteins from SARS- CoV-2, and took 32 serological measurements on longitudinal specimens from this participant. We discovered a coordination of the Nuc322-331-specific CD8+ T response with both the CD4+ T cell and antibody pillars of adaptive immunity. Nuc322-331-specific CD8+ T cells were predominantly central memory T cells, but continually evolved over a ∼6-month period of convalescence. We observed a slow and progressive decrease in the activation state and polyfunctionality of the Nuc322-331-specific CD8+ T cells, accompanied by an increase in their lymph-node homing and homeostatic proliferation potential. These results suggest that following a typical case of mild COVID-19, SARS-CoV-2-specific CD8+ T cells not only persist but continuously differentiate in a coordinated fashion well into convalescence, into a state characteristic of long-lived, self-renewing memory.
Ground tissue circuitry regulates organ complexity in cereal roots
Authors: Ortiz-Ramírez Carlos , Dias Araujo Poliana Coqueiro , Zhang Sanqiang , Demesa-Arevalo Edgar , Yan Zhe , Xu Xiosa , Rahni Ramin , Gingeras Thomas R. , Jackson David , Gallagher Kimberly L. , Birnbaum Kenneth D. 
Published: April 2021

AbstractMost plant roots have multiple cortex layers that make up the bulk of the organ and play key roles in physiology, such as flood tolerance and symbiosis. However, little is known about the formation of cortical layers outside of the highly reduced anatomy of the modelArabidopsis. Here we use single-cell RNAseq to rapidly generate a cell resolution map of the maize root, revealing an alternative configuration of the tissue formative SHORT-ROOT (SHR) signaling pathway adjacent to an expanded cortex. We show that maize SHR protein is hypermobile, moving at least eight cell layers into the cortex. Higher-order SHR mutants in both maize andSetariahave reduced numbers of cortical layers, showing that the SHR pathway controls expansion of cortical tissue in grasses that sets up anatomical complexity and a host of key traits.One sentence summarySingle-cell RNA-seq maps the maize root transcriptome uncovering a mechanism that regulates cortex layer number.
Virus-Targeted Transcriptomic Analyses Implicate Ranaviral Interaction with Host Interferon Response in Frog Virus 3-infected Frog Tissues
Authors: Tian Yun , De Jesús Andino Francisco , Robert Jacques , Sang Yongming 
Published: April 2021

AbstractFrog Virus 3 (FV3) is a large dsDNA virus that cause global infections in amphibians, fish and reptiles, and contribute to amphibian declines. FV3’s genome contains near 100 putative open reading frames (ORFs). Previous studies have classified these coding genes into temporal classes as immediate early, delayed early and late viral transcripts based on their sequential expression during FV3 infection. To genome-wide characterize ranaviral gene expression, we performed a whole transcriptomic analysis (RNA-Seq) using total RNA samples containing both viral and cellular transcripts from FV3-infectedXenopus laevisadult tissues using two FV3 strains, a wild type (FV3-WT) and an ORF64R-deleted recombinant (FV3-Δ64R). In samples from the infected intestine, liver, spleen, lung and especially kidney, a FV3-targeted transcriptomic analysis mapped reads spanning the full-genome coverage at ∼10× depth on both positive and negative strands. By contrast, reads were only mapped to partial genomic regions in samples from the infected thymus, skin and muscle. Extensive analyses validated the expression of almost all annotated 98 ORFs and profiled their differential expression in a tissue-, virus-, and temporal class-dependent manners. Further studies identified several putative ORFs that encode hypothetical proteins containing viral mimicking conserved domains found in host interferon (IFN) regulatory factors (IRFs) and IFN receptors. This study provides the first comprehensive genome-wide viral transcriptome profiling during infection and across multiple amphibian host tissues that will serve as instrumental reference. It also presents evidence implying that ranaviruses like FV3 have acquired previously unknown molecular mimics interfering with host IFN signaling during evolution.ImportanceFrog Virus 3 (FV3), are large dsDNA viruses that cause devastating infections globally in amphibians, fish and reptiles, and contribute to catastrophic amphibian declines. FV3’s large genome encodes near 100 coding genes, of which most have been functionally uncharacterized in the viral pathogenesis. Using a whole transcriptomic analysis (RNA-Seq) in FV3-infected amphibian samples, we determined a genome-wide virus transcriptome and profiled their differential expression in a tissue-, virus-, and temporal class-dependent manners. Further studies identified several putative ORFs that encode hypothetical proteins containing viral mimicking conserved domains found in host interferon (IFN) regulatory factors (IRFs) and IFN receptors. This study provides the first comprehensive genome-wide viral transcriptome profiling during infection and across multiple amphibian host tissues that will serve as instrumental reference. It also presents evidence implying that ranaviruses like FV3 have acquired previously unknown molecular mimics interfering with host IFN signaling during evolution.
Phosphorylation of the M1 muscarinic acetylcholine receptor mediates protection in neurodegenerative disease
Authors: Scarpa Miriam , Molloy Colin , Jenkins Laura , Tejeda Gonzalo , Rossi Mario , Dwomoh Louis , Marsango Sara , Ahmed Zeshan , Milligan Graeme , Hudson Brian D. , Tobin Andrew B. , Bradley Sophie J. 
Published: April 2021

AbstractThere are currently no treatments that can slow the progression of neurodegenerative diseases such as Alzheimer’s disease (AD). There is, however, a growing body of evidence that activation of the M1 muscarinic acetylcholine receptor (M1-receptor) can not only restore memory loss in AD patients, but in preclinical animal models can also slow neurodegenerative disease progression. The generation of an effective medicine targeting the M1-receptor has however been severely hampered by associated cholinergic adverse responses. By using genetically engineered mouse models that express a G protein-biased M1-receptor, we recently established that M1-receptor mediated adverse responses can be minimised by ensuring activating ligands maintain receptor phosphorylation/arrestin-dependent signalling. Here, we use these same genetic models in concert with murine prion disease, a terminal neurodegenerative disease showing key hallmarks of AD, to establish that phosphorylation/arrestin-dependent signalling delivers neuroprotection that both extends normal animal behaviour and prolongs the life span of prion diseased mice. Our data point to an important neuroprotective property inherent to the M1-receptor and indicate that next generation M1-receptor ligands designed to drive receptor phosphorylation/arrestin-dependent signalling would potentially show low adverse responses whilst delivering neuroprotection that will slow disease progression.
Cost-effective mapping of genetic interactions in mammalian cells
Authors: Khan Arshad H. , Smith Desmond J. 
Published: April 2021

AbstractComprehensive maps of genetic interactions in mammalian cells are daunting to construct because of the large number of potential interactions, ~ 2 × 108for protein coding genes. We previously used co-inheritance of distant genes from published radiation hybrid (RH) datasets to identify genetic interactions. However, it was necessary to combine six legacy datasets from four species to obtain adequate statistical power. Mapping resolution was also limited by the low density PCR genotyping. Here, we employ shallow sequencing of nascent human RH clones as an economical approach to constructing interaction maps. In this initial study, 15 clones were analyzed, enabling construction of a network with 225 genes and 2359 interactions (FDR < 0.05). Despite its small size, the network showed significant overlap with the previous RH network and with a protein-protein interaction network. Consumables were ≲ $50 per clone, showing that affordable, high quality genetic interaction maps are feasible in mammalian cells.
Effect of the shrimp farming wastes as co-feed on growth performance and digestibility of juvenile grey mullet,Mugil cephalus
Authors: Madrid Jorge , Ibarra-Zatarain Zohar , Viera-Pérez Jorge E. , Campos-Ezpinoza Abelardo , Peña-Messina Emilio 
Published: April 2021

AbstractA feeding trial was carried out to evaluate the utilization of residual nutrients from a shrimp farming wastes as co-feed in different proportions in juvenile grey mullets. Four treatments were designed offering shrimp farming wastes at 0, 33, 66, and 100%. The 4 % of feed respecting the total biomass of each experimental tank was offered daily. The total feed ratio was completed with commercial feed for marine fish in the treatments where it was needed. At the end of the feeding trial, final weight, weight gain, relative weight gain, and thermal growth coefficient were reduced in the fish when increasing the amount of SFW as feed. However, the fish showed a digestive capacity to use residual nutrients up to 66 %, increasing their initial weight by up to 25 %. The increase of shrimp farming waste as feed negatively affected the whole-body proximal composition. The digestibility results showed that the fish could digest up to 41 % of the shrimp farming waste protein. Results suggest that juvenile grey mullets are capable of utilizing residual nutrients from shrimp farming waste. However, it is necessary to use an alternative feed source to induce an optimal growth performance for the juvenile grey mullets. It is also recommended that mullets be fed with formulated feed to meet their nutritional requirements to maintain the protein and lipid content of the whole-body under culture conditions.
Crystal structures of the σ2receptor template large-library docking for selective chemotypes activein vivo
Authors: Alon Assaf , Lyu Jiankun , Braz Joao M. , Tummino Tia A. , Craik Veronica , O’Meara Matthew J. , Webb Chase M. , Radchenko Dmytro S. , Moroz Yurii S. , Huang Xi-Ping , Liu Yongfeng , Roth Bryan L. , Irwin John J. , Basbaum Allan I. , Shoichet Brian K. , Kruse Andrew C. 
Published: April 2021

AbstractThe σ2receptor is a poorly understood transmembrane receptor that has attracted intense interest in many areas of biology including cancer imaging, Alzheimer’s disease, schizophrenia, and neuropathic pain. However, little is known regarding the molecular details of the receptor, and few highly selective ligands are available. Here, we report the crystal structure of the σ2receptor in complex with the clinical drug candidate roluperidone and the probe compound PB28. These structures, in turn, templated a large-scale docking screen of 490 million make-on-demand molecules. Of these, 484 compounds were synthesized and tested, prioritizing not only high-ranking docked molecules, but also those with mediocre and poor scores. Overall, 127 compounds with binding affinities superior to 1 μM were identified, all in new chemotypes, 31 of which had affinities superior to 50 nM. Intriguingly, hit rate fell smoothly and monotonically with docking score. Seeking to develop selective and biologically active probe molecules, we optimized three of the original docking hits for potency and for selectivity, achieving affinities in the 3 to 48 nM range and to up to 250-fold selectivity vs. the σ1receptor. Crystal structures of the newly discovered ligands bound to the σ2receptor were subsequently determined, confirming the docked poses. To investigate the contribution of the σ2receptor in pain processing, and to distinguish it from the contribution of the σ1receptor, two potent σ2-selective and one potent σ1/σ2non-selective ligand were tested for efficacy in a mouse model of neuropathic pain. All three ligands demonstrated timedependent decreases in mechanical hypersensitivity in the spared nerve injury model, supporting a role for the σ2receptor in nociception, and a possible role for σ1/σ2polypharmacology. This study illustrates the opportunities for rapid discovery ofin vivoactive and selective probes to study under-explored areas of biology using structurebased screens of diverse, ultra-large libraries following the elucidation of protein structures.
Ecological basis and genetic architecture of crypsis polymorphism in the desert clicker grasshopper (Ligurotettix coquilletti)
Authors: O’Connor Timothy K. , Sandoval Marissa C. , Wang Jiarui , Hans Jacob C. , Takenaka Risa , Child Myron , Whiteman Noah K. 
Published: April 2021

ABSTRACTColor polymorphic species can offer exceptional insight into the ecology and genetics of adaptation. Although the genetic architecture of animal coloration is diverse, many color polymorphisms are associated with large structural variants and maintained by biotic interactions. Grasshoppers are exceptionally polymorphic in both color and karyotype, making them excellent models for understanding the ecological drivers and genetic underpinnings of color variation. Banded and uniform morphs of the desert clicker grasshopper (Ligurotettix coquilletti) are found across the western deserts of North America. To address the hypothesis that predation maintains local color polymorphism and shapes regional crypsis variation, we surveyed morph frequencies and tested for covariation with two predation environments. Morphs coexisted at intermediate frequencies at most sites, consistent with local balancing selection. Morph frequencies covaried with the appearance of desert substrate – an environment used only by females – indicating that ground-foraging predators are major agents of selection on crypsis. We next addressed the hypothesized link between morph variation and genome structure. To do so, we designed an approach for detecting inversions and indels using only RADseq data. The banded morph was perfectly correlated with a large putative indel. Remarkably, indel dominance differed among populations, a rare example of dominance evolution in nature.
Thein vivoRNA structurome of the malaria parasitePlasmodium falciparum, a protozoan with an A/T-rich transcriptome
Authors: Dumetz F , Enright AJ , Zhao J , Kwok CK , Merrick CJ 
Published: April 2021

ABSTRACTPlasmodium falciparum, a protozoan parasite and causative agent of human malaria, has one of the most A/T-biased genomes sequenced to date. This may give the genome and the transcriptome unusual structural features. Recent progress in sequencing techniques has made it possible to study the secondary structures of RNA molecules at the transcriptomic level. Thus, in this study we produced thein vivoRNA structurome of a protozoan parasite with a highly A/U-biased transcriptome. We showed that it is possible to probe the secondary structures ofP. falciparumRNA moleculesin vivousing two different chemical probes, and obtained structures for more than half of all transcripts in the transcriptome. These showed greater stability (lower free energy) than the same structures modelledin silico, and structural features appeared to influence translation efficiency and RNA decay. Finally, we compared theP. falciparumRNA structurome with the predicted RNA structurome of an A/T-balanced species,P. knowlesi, finding a bias towards lower overall transcript stability and more hairpins and multi-stem loops inP. falciparum. This unusual protozoan RNA structurome will provide a basis for similar studies in other protozoans and also in other unusual genomes.
Morphine exposure bidirectionally alters c-Fos expression in a sex-, age-, and brain region-specific manner during adolescence
Authors: Figueroa C , Yang H , DiSpirito J , Bourgeois JR , Kalyanasundaram G , Doshi I , Bilbo SD , Kopec AM 
Published: April 2021

AbstractDrug and alcohol use during adolescence is common, and data in both humans and preclinical animal models clearly indicate drug exposure during adolescence increases the risk of substance use and other mental health disorders later in life. Adolescence is a period of social, emotional, and cognitive development, and is characterized by increased exploratory behavior, risk-taking, and peer-centered social interactions. These are thought to be behavioral manifestations of developmental plasticity in ‘reward’ regions of the brain. Human data indicate that adolescence is not a unitary developmental period, but rather different neural and behavioral sequelae can be observed in early vs. late adolescence. However, most studies with rodent models examine a single adolescent age compared to a mature adult age, and often only in males. Herein, we sought to determine whether the acute response to the opioid morphine would also differ across adolescence, and by sex. By quantifying c-Fos positive cells, a proxy for neural activity, at different stages during adolescence (pre-, early, mid-, and late adolescence) and in multiple reward regions (prefrontal cortex, nucleus accumbens, caudate/putamen), we determined that acute morphine can either reduce or increase c-Fos expression dependent on adolescent age, sex, and brain region. These data suggest that heterogeneity in the consequences of adolescent opioid exposure may be due to the interaction between age- and sex-specific developmental profiles of reward processing in individual brain regions. In future studies, it will be important to add age within adolescence as an independent variable to fully capture the consequences of healthy or abnormal reward-related neural development.
Virtual partition digital PCR for high precision chromosomal counting applications
Authors: Jacky Lucien , Yurk Dominic , Alvarado John , Leatham Bryan , Schwartz Jerrod , MacDonald Chris , Rajagopal Aditya 
Published: April 2021

AbstractDigital PCR (dPCR) is the gold standard analytical platform for rapid high precision quantification of genomic fragments. However, current dPCR assays are generally limited to monitoring 1-2 analytes per sample, thereby limiting the platform’s ability to address some clinical applications that require the simultaneous monitoring of 20 – 50 analytes per sample. Here we present Virtual Partition dPCR (VPdPCR), a novel analysis methodology enabling the detection of 10 or more target regions per color channel using conventional dPCR hardware and workflow. Furthermore, VPdPCR enables dPCR instruments to overcome upper quantitation limits caused by partitioning error. While traditional dPCR analysis establishes a single threshold to separate negative and positive partitions, VPdPCR establishes multiple thresholds to identify the number of unique targets present in each positive droplet based on fluorescent intensity. Each physical partition is then divided into a series of virtual partitions, and the resulting increase in partition count substantially decreases partitioning error. We present both a theoretical analysis of the advantages of VPdPCR and an experimental demonstration in the form of a 20-plex assay for non-invasive fetal aneuploidy testing. This demonstration assay – tested on 432 samples contrived from sheared cell-line DNA at multiple input concentrations and simulated fractions of euploid or trisomy-21 “fetal” DNA – is analyzed using both traditional dPCR thresholding and VPdPCR. VPdPCR analysis significantly lowers variance of chromosome ratio across replicates and increases the accuracy of trisomy identification when compared to traditional dPCR, yielding >98% single-well sensitivity and specificity. VPdPCR has substantial promise for increasing the utility of dPCR in applications requiring ultra-high-precision quantitation.
Biofilm hydrophobicity in environmental isolates ofBacillus subtilis
Authors: Kalamara Margarita , Abbott James C. , MacPhee Cait E. , Stanley-Wall Nicola. R. 
Published: April 2021

AbstractBiofilms are communities of bacteria that are attached to a surface and surrounded by an extracellular matrix. The extracellular matrix protects the community from stressors in the environment, making biofilms robust. The Gram-positive soil bacteriumBacillus subtilis, particularly the isolate NCIB 3610, is widely used as a model for studying biofilm formation.B. subtilisNCIB 3610 forms colony biofilms that are architecturally complex and highly hydrophobic. The hydrophobicity is linked, in part, to the localisation of the protein BslA at the surface of the biofilm, which provides the community with increased resistance to biocides. As most of our knowledge aboutB. subtilisbiofilm formation comes from one isolate, it is unclear if biofilm hydrophobicity is a widely distributed feature of the species. To address this knowledge gap, we collated a library ofB. subtilissoil isolates and acquired their whole genome sequences. We used our new isolates to examine biofilm hydrophobicity and found that, although BslA is encoded and produced by all isolates in our collection, hydrophobicity is not a universal feature ofB. subtiliscolony biofilms. To test whether the matrix exopolymer poly γ-glutamic acid could be masking hydrophobicity in our hydrophilic isolates, we constructed deletion mutants and found, contrary to our hypothesis, that the presence of poly γ-glutamic acid was not the reason behind the observed hydrophilicity. This study highlights the natural variation in the properties of biofilms formed by different isolates and the importance of using a more diverse range of isolates as representatives of a species.RepositoriesRaw sequence reads and annotated assemblies have been submitted to the European Nucleotide Archive under accession PRJEB43128.