bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dandelionutilizes single cell adaptive immune receptor repertoire to explore lymphocyte developmental origins
Authors: Suo Chenqu , Polanski Krzysztof , Dann Emma , Lindeboom Rik G.H. , Vilarrasa-Blasi Roser , Vento-Tormo Roser , Haniffa Muzlifah , Meyer Kerstin B. , Dratva Lisa M. , Tuong Zewen Kelvin , Clatworthy Menna R. , Teichmann Sarah A. 
Published: November 2022

AbstractAssessment of single-cell gene expression (scRNA-seq) and adaptive immune receptor sequencing (scVDJ-seq) has been invaluable in studying lymphocyte biology. Here, we introduceDandelion, a computational pipeline for scVDJ-seq analysis. It enables the application of standard V(D)J analysis workflows to single-cell datasets, delivering improved V(D)J contig annotation and the identification of non-productive and partially spliced contigs. We devised a novel strategy to create an adaptive immune receptor feature space that can be used for both differential V(D)J usage analysis and pseudotime trajectory inference. The application ofDandelionimproved the alignment of human thymic development trajectories of double positive T cells to mature single-positive CD4/CD8 T cells, with important new predictions of factors regulating lineage commitment.Dandelionanalysis of other cell compartments provided novel insights into the origins of human B1 cells and ILC/NK cell development, illustrating the power of our approach.Dandelionis an open access resource (https://www.github.com/zktuong/dandelion)that will enable future discoveries.
Structural, functional and evolutionary analysis of wheat WRKY45 protein: A combined bioinformatics and MD simulation approach
Authors: Ranjan Prashant , Yadav Ashok , Behera Ananta Keshari , Singh Dhiraj Kumar , Singh Premkant , Singh Ganga Prasad 
Published: November 2022

AbstractBread wheat (Triticum aestivum L.) is the world’s second-most important cereal crop, as well as India’s. It is an allohexaploid composed of three homeologous sub-genomes (AA, BB, and DD), which is a constraint in determining the complete genome sequence. Several transcription factors have been implicated in both abiotic and biotic stress. WRKY transcription factors are among the best characterised in the context of pathogen defence mechanisms. Different members of the WRKY transcription factors have been shown to confer resistance to stress. But very little is known about the wheat WRKY transcription factors. In silico analysis of the TaWRKY45 protein was performed in the present study using several bioinformatics tools like motif scan, CD search, Netphos, NGlycos, GRAVY, and the SWISS MODEL. The study revealed that TaWRKY45 belongs to the group III family and contains hydrophilic proteins with 19 potential phosphorylation sites. TaWRKY45 protein was found to be orthologous to rice OsWRKY45 by phylogenetic analysis. The catalytic domain was analysed by motif scan which showed that TaWRKY45 has one WRKY domain and a C2-HC zinc finger motif. TaWRKY45’s structure was determined to be more stable, more constrained, more compact, and have greater potential to interact with other molecules than OsWRKY45, according to MD simulation analysis. Thus, in silico analysis of transcription factors helps study protein function, interaction, and regulatory pathways.
A therapeutic hepatitis B mRNA vaccine with strong immunogenicity and persistent virological suppression
Authors: Zhao Huajun , Shao Xianyu , Yu Yating , Huang Lulu , Amor Narh Philip , Guo Kun , Weng Changzhen , Zhao Weijun , Yang Ailu , Hu Jiesen , Yang Hongbao , Liu Zhenguang , Han Qiuju , Shi Leilei , Sun Shiyu , Zhang Jian , Yang Yong , Lin Ang 
Published: November 2022

BRIEF ABSTRACTHere we report on the development and comprehensive evaluations of an mRNA vaccine for chronic hepatitis B (CHB) treatment. In two different HBV carrier mouse models generated by viral vector-mediated HBV transfection (pAAV-HBV1.2 and rAAV8-HBV1.3), this vaccine demonstrates sufficient and persistent virological suppression, and robust immunogenicity in terms of induction of strong innate immune activation, high-level virus-specific antibodies, memory B cells and T cells. mRNA platform therefore holds prospects for therapeutic vaccine development to combat CHB.
Transcriptomic profiling of reward and sensory brain areas in perinatal fentanyl exposed juvenile mice
Authors: Olusakin Jimmy , Kumar Gautam , Basu Mahashweta , Calarco Cali A. , Fox Megan E. , Alipio Jason B. , Haga Catherine , Turner Makeda D. , Keller Asaf , Ament Seth A. , Lobo Mary Kay 
Published: November 2022

ABSTRACTUse of the synthetic opioid fentanyl increased ∼300% in the last decade, including among women of reproductive ages. Adverse neonatal outcomes and long-term behavioral disruptions are associated with perinatal opioid exposure. Our previous work demonstrated that perinatal fentanyl exposed mice displayed enhanced negative affect and somatosensory circuit and behavioral disruptions during adolescence. However, little is known about molecular adaptations across brain regions that underlie these outcomes. We performed RNA-sequencing across three reward and two sensory brain areas to study transcriptional programs in perinatal fentanyl exposed juvenile mice. Pregnant dams received 10μg/ml fentanyl in the drinking water from embryonic day 0 (E0) through gestational periods until weaning at postnatal day 21 (P21). RNA was extracted from nucleus accumbens (NAc), prelimbic cortex (PrL), ventral tegmental area (VTA), somatosensory cortex (S1) and ventrobasal thalamus (VBT) from perinatal fentanyl exposed mice of both sexes at P35. RNA-sequencing was performed, followed by analysis of differentially expressed genes (DEGs) and gene co-expression networks. Transcriptome analysis revealed DEGs and gene modules significantly associated with exposure to perinatal fentanyl in a sex-wise manner. The VTA had the most DEGs, while robust gene enrichment occurred in NAc. Genes enriched in mitochondrial respiration were pronounced in NAc and VTA of perinatal fentanyl exposed males, extracellular matrix (ECM) and neuronal migration enrichment were pronounced in NAc and VTA of perinatal fentanyl exposed males, while genes associated with vesicular cycling and synaptic signaling were markedly altered in NAc of perinatal fentanyl exposed female mice. In sensory areas from perinatal fentanyl exposed females, we found alterations in mitochondrial respiration, synaptic and ciliary organization processes. Our findings demonstrate distinct transcriptomes across reward and sensory brain regions, with some showing discordance between sexes. These transcriptome adaptations may underlie structural, functional, and behavioral changes observed in perinatal fentanyl exposed mice.
Interferon-γ Elicits Pathological Hallmarks of ALS in Human Motor Neurons
Authors: Chun Changho , Lee Jung Hyun , Smith Alec S.T. , Mack David L. , Bothwell Mark , Nghiem Paul 
Published: November 2022

AbstractNeuroinflammation is an established factor contributing to amyotrophic lateral sclerosis (ALS) pathology, implicating the possible detrimental effects of inflammatory cytokines on motor neurons. The RNA/DNA-binding protein TDP-43 has emerged as a pivotal actor in ALS, because TDP-43 mutations cause familial ALS and loss of nuclear TDP-43, associated with its redistribution into cytoplasmic aggregates (TDP-43 proteinopathy) in motor neurons occurs in 97% of ALS cases. However, mechanisms linking neuroinflammation to TDP-43 mislocalization have not been described. Programmed death-ligand 1 (PD-L1) is an immune-modulatory protein, highly expressed on cell surfaces following acute inflammatory stress. To determine which inflammatory cytokines might impact motor neuron function, seven cytokines known to be elevated in ALS patients’ cerebrospinal fluid were tested for their effects on PD-L1 expression in human iPSC-derived motor neurons. Among the tested cytokines, only interferon-γ (IFN-γ) was found to strongly promote PD-L1 expression. Thus, we hypothesized that excessive exposure to IFN-γ may contribute to motor neuron degeneration in ALS. We observed that neuronal populations exposed to IFN-γ exhibited severe TDP-43 cytoplasmic aggregation and excitotoxic behavior correlated with impaired neural firing activity, hallmarks of ALS pathology, in both normal and ALS mutant (TARDB1K+/-) neurons. Single-cell RNA sequencing revealed possible mechanisms for these effects. Motor neurons exposed to IFN-γ exhibited an extensive shift of their gene expression profile toward a neurodegenerative phenotype. Notably, IFN-γ treatment induced aberrant expression levels for 70 genes that are listed in the recent literature as being dysregulated in various ALS subtypes. Additionally, we found that genes related to neuronal electrophysiology, protein aggregation, and TDP-43 misregulation were abnormally expressed in IFN-γ treated cells. Moreover, IFN-γ induced a significant reduction in the expression of genes that encode indispensable proteins for neuromuscular synapse development and maintenance, implying that the continuous cytokine exposure could directly impair signal transmission between motor axons and muscle membranes. Our findings suggest that IFN-γ could be a potent upstream pathogenic driver of ALS and provide potential candidates for future therapeutic targets to treat sporadic forms of ALS, which account for roughly 90% of reported cases.
Vascular fungi alter the apoplastic purinergic signaling in plants by deregulating the homeostasis of extracellular ATP and its metabolite adenosine
Authors: Kesten Christopher , Leitner Valentin , Dora Susanne , Sims James W. , Dindas Julian , Zipfel Cyril , De Moraes Consuelo M. , Sánchez-Rodríguez Clara 
Published: November 2022

AbstractPurinergic signaling activated by extracellular nucleotides and their derivative nucleosides trigger sophisticated signaling networks. The outcome of these pathways determine the capacity of the organism to survive under challenging conditions. Both extracellular ATP (eATP) and Adenosine (eAdo) act as secondary messengers in mammals, essential for immunosuppressive responses. Despite the clear role of eATP as a plant damage-associated molecular pattern, the function of its nucleoside, eAdo, and of the eAdo/eATP balance in plant stress response remain to be fully elucidated. This is particularly relevant in the context of plant/microbe interaction, where the intruder manipulates the extracellular matrix. Here, we identify Ado as a main elicitor secreted by the vascular fungusFusarium oxysporum. We show that eAdo modulates the plant’s susceptibility to fungal colonization by altering eATP-mediated physiological immune responses, such as apoplastic pH and calcium homeostasis. Our work indicates that plant pathogens actively imbalance the eAdo/eATP levels as a virulence mechanism.One Sentence SummaryThe apoplastic Adenosine/ATP balance is a messenger for plant defense and can be manipulated by the fungal pathogenF. oxysporum.
Runx factors launch T-cell and innate lymphoid programs via direct and gene network-based mechanisms
Authors: Shin Boyoung , Zhou Wen , Wang Jue , Gao Fan , Rothenberg Ellen V. 
Published: November 2022

AbstractRunx factors are essential for lineage specification of various hematopoietic cells, including T lymphocytes. However, they regulate context-specific genes and occupy distinct genomic regions in different cell types. Here, we show that dynamic Runx binding shifts in early T-cell development are mostly not restricted by local chromatin state but regulated by Runx dosage and functional partners. Runx co-factors compete to recruit a limited pool of Runx factors in early T-progenitors, and a modest increase in Runx protein availability at pre-commitment stages causes premature Runx occupancy at post-commitment binding sites. This results in striking T-lineage developmental acceleration by selectively activating T-identity and innate lymphoid cell programs. These are collectively regulated by Runx together with other, Runx-induced transcription factors that co-occupy Runx target genes and propagate gene network changes.
CryoEM Reveals Oligomeric Isomers of a Multienzyme Complex and Assembly Mechanics
Authors: Lee Jane K.J. , Liu Yun-Tao , Hu Jason J. , Aphasizheva Inna , Aphasizhev Ruslan , Zhou Z. Hong 
Published: November 2022

AbstractPropionyl-CoA carboxylase (PCC) is a multienzyme complex consisting of up to six α-subunits and six ß-subunits. Belonging to a metabolic pathway converging on the citric acid cycle, it is present in most forms of life and irregularities in its assembly lead to serious illness in humans, known as propionic acidemia. Here, we report the cryogenic electron microscopy (cryoEM) structures and assembly of different oligomeric isomers of endogenous PCC from the parasitic protozoanLeishmania tarentolae(LtPCC). These structures and their statistical distribution reveal the mechanics of PCC assembly and disassembly at equilibrium. We show that, in solution, endogenous LtPCC ß-subunits form stable homohexamers, to which different numbers of α-subunits attach. Sorting LtPCC particles into seven classes (i.e., oligomeric formulas α0β6, α1β6, α2β6, α3β6, α4β6, α5β6, α6β6) enables formulation of a model for PCC assembly. Our results suggest how multimerization regulates PCC enzymatic activity and showcase the utility of cryoEM in revealing the statistical mechanics of reaction pathways.
Distinct states of nucleolar stress induced by anti-cancer drugs
Authors: Potapova Tamara A. , Unruh Jay R. , Conkright-Fincham Juliana , Banks Charles A. S. , Florens Laurence , Schneider David A. , Gerton Jennifer L. 
Published: November 2022

AbstractRibosome biogenesis is a vital and energy-consuming cellular function occurring primarily in the nucleolus. Cancer cells have an especially high demand for ribosomes to sustain continuous proliferation. This study evaluated the impact of existing anticancer drugs on the nucleolus by screening a library of anticancer compounds for drugs that induce nucleolar stress. For a readout, a novel parameter termed “nucleolar normality score” was developed that measures the ratio of the fibrillar center and granular component proteins in the nucleolus and nucleoplasm. Multiple classes of drugs were found to induce nucleolar stress, including DNA intercalators, inhibitors of mTOR/PI3K, heat shock proteins, proteasome, and cyclin-dependent kinases (CDKs). Each class of drugs induced morphologically and molecularly distinct states of nucleolar stress accompanied by changes in nucleolar biophysical properties. In-depth characterization focused on the nucleolar stress induced by inhibition of transcriptional CDKs, particularly CDK9, the main CDK that regulates RNA Pol II. Multiple CDK substrates were identified in the nucleolus, including RNA Pol I – recruiting protein Treacle, which was phosphorylated by CDK9in vitro. These results revealed a concerted regulation of RNA Pol I and Pol II by transcriptional CDKs. Our findings exposed many classes of chemotherapy compounds that are capable of inducing nucleolar stress, and we recommend considering this in anticancer drug development.Types of nucleolar stresses identified in this study(1) DNA intercalators and RNA Pol inhibitors induced canonical nucleolar stress manifested by partial dispersion of granular component (GC) and segregation of rDNA and fibrillar center (FC) components UBF, Treacle, and POLR1A within nucleolar stress caps. (2) Inhibition of mTOR and PI3K growth pathways induced a metabolic suppression of function accompanied by the decrease in nucleolar normality score, size, and rRNA production, without dramatic re-organization of nucleolar anatomy. (3) Inhibitors targeting HSP90 and proteasome induced proteotoxicity, resulting in the disruption of protein homeostasis and the accumulation of misfolded and/or undegraded proteins. These effects were accompanied by a decrease in nucleolar normality score, rRNA output, and in some cases formation of protein aggregates (aggresomes) inside the nucleolus. (4) Inhibition of transcriptional CDK activity led to the disruption of interactions between rDNA, RNA Pol I, and GC proteins. This resulted in almost complete nucleolar dissolution, leaving behind an extended bare rDNA scaffold with only a few associated FC proteins remaining. UBF and PolI-recruiting protein Treacle remained associated with the rDNA, while POLR1A and GC dispersed in the nucleoplasm. rRNA production ceased and the nucleolar normality score was greatly reduced.
Mapping single-cell responses to population-level dynamics during antibiotic treatment
Authors: Kim Kyeri , Wang Teng , Ma Helena R. , Şimşek Emrah , Li Boyan , Andreani Virgile , You Lingchong 
Published: November 2022

AbstractTreatment of sensitive bacteria with beta-lactam antibiotics often leads to two salient population-level features: a transient increase in total population biomass before a subsequent decline, and a linear correlation between growth and killing rates. However, it remains unclear how these population-level responses emerge from collective single-cell responses. During beta-lactam treatment, it is well recognized that individual cells often exhibit varying degrees of filamentation before lysis. We show that the probability of cell lysis increases with the extent of filamentation and that this dependence is characterized by unique parameters that are specific to bacterial strain, antibiotic dose, and growth condition. Modeling demonstrates how the single-cell lysis probabilities can give rise to population-level biomass dynamics, which were experimentally validated. This mapping provides insights into how the population biomass time-kill curve emerges from single cells and allows the representation of both single-and population-level responses with universal parameters.
Germline variation contributes to false negatives in CRISPR-based experiments with varying burden across ancestries
Authors: Misek Sean A. , Fultineer Aaron , Kalfon Jeremie , Noorbakhsh Javad , Boyle Isabella , Dempster Joshua , Petronio Lia , Huang Katherine , Saadat Alham , Green Thomas , Brown Adam , Doench John G. , Root David , McFarland James , Beroukhim Rameen , Boehm Jesse S. 
Published: November 2022

AbstractReducing disparities is critical to promote equity of access to precision treatments for all patients with cancer. While socioenvironmental factors are a major driver behind such disparities, biological differences also are likely to contribute. The prioritization of cancer drug targets is foundational for drug discovery, yet whether ancestry-related signals in target discovery pipelines exist has not been systematically explored due to the absence of data at the appropriate scale. Here, we analyzed data from 611 genome-scale CRISPR/Cas9 viability experiments in human cell line models as part of the Cancer Dependency Map to identify ancestry-associated genetic dependencies. Surprisingly, we found that most putative associations between ancestry and dependency arose from artifacts related to germline variants that are present at different frequencies across ancestry groups. In 2-5% of genes profiled in each cellular model, germline variants in sgRNA targeting sequences likely reduced cutting by the CRISPR/Cas9 nuclease. Unfortunately, this bias disproportionately affected cell models derived from individuals of recent African descent because their genomes tended to diverge more from the consensus genome typically used for CRISPR/Cas9 guide design. To help the scientific community begin to resolve this source of bias, we report three complementary methods for ancestry-agnostic CRISPR experiments. This report adds to a growing body of literature describing ways in which ancestry bias impacts cancer research in underappreciated ways.
Biofilm characterization in the maize pathogen,Fusarium verticillioides
Authors: Peremore Chizné , Wingfield Brenda , Santana Quentin , Steenkamp Emma T , Motaung Thabiso E 
Published: November 2022

AbstractNearly all microbes, including fungal pathogens, form biofilms, which are structured communities of microbial aggregates enclosed in self-produced extracellular polymeric substances (EPS) and attached to a surface. Studying plant-associated fungal biofilms can enhance understanding of fungal biology and knowledge of the links between fungal diseases and plants. However, only a few plant-associated fungi are reported to form biofilms. This study aimed to examine the ability of a mycotoxigenic fungus of maize,Fusarium verticillioides, to form biofilms under laboratory conditions. During our investigation,F. verticillioidesstationary phase cultures incubated in liquid media developed a biofilm-like pellicle with a hyphal assemblage that appears in the form of a cloudy and thin slime material. Under the microscope, the biofilms exhibited a highly heterogeneous architecture made of dense, entangled, and compact hyphae, which were accompanied by a quantifiable EPS and extracellular DNA (eDNA). The biofilm was also found to respond to different abiotic conditions including pH and temperature, suggesting their relevance in a field setting. We further demonstrate the biofilm structural maintenance role of eDNA through treatment with DNase, which was only marginally effective during late biofilm stages, suggesting that it forms complex interactions with the EPS during biofilm maturation. Based on these results, we propose thatF. verticillioidesforms a ‘true’ biofilm that may act as a potential virulence factor.
Subcellular niche segregation of co-obligate symbionts in whiteflies
Authors: Fujiwara Akiko , Meng Xian-Ying , Kamagata Yoichi , Tsuchida Tsutomu 
Published: November 2022

AbstractMany insects contain endosymbiotic bacteria within their bodies. In multiple endosymbiotic systems comprising two or more symbionts, each of the symbionts is generally localized in a different host cell or tissue.Bemisia tabaci(Sweet potato whitefly)possesses a unique endosymbiotic system where co-obligate symbionts are localized in the same bacteriocytes. Using fluorescencein situhybridization, we found that endosymbionts inB. tabaciMEAM1 occupy distinct subcellular habitats, or niches, within a single bacteriocyte.Hamiltonellawas located adjacent to the nucleus of the bacteriocyte, whilePortierawas present in the cytoplasm surroundingHamiltonella. Immunohistochemical analysis revealed that the endoplasmic reticulum separates the two symbionts. Habitat segregation was maintained for longer durations in female bacteriocytes. The same segregation was observed in three genetically distinctB. tabacigroups (MEAM1, MED Q1, and Asia II 6) andTrialeurodes vaporariorum, which shared a common ancestor withBemisiaover 80 million years ago, even though the coexisting symbionts and the size of bacteriocytes were different. These results suggest that the habitat segregation system existed in the common ancestor and was conserved in both lineages, despite different bacterial partners coexisting withPortiera. Our findings provide insights into the evolution and maintenance of complex endosymbiotic systems and highlight the importance of organelles for the construction of separate niches for endosymbionts.ImportanceCo-obligate endosymbionts inB. tabaciare exceptionally localized within the same bacteriocyte (a specialized cell for endosymbiosis), but the underlying mechanism for their coexistence remains largely unknown. This study provides evidence for niche segregation at the subcellular level between the two symbionts. We showed that the endoplasmic reticulum is a physical barrier separating the two species. Despite differences in co-obligate partners, this subcellular niche segregation was conserved across various whitefly species. The physical proximity of symbionts may enable the efficient biosynthesis of essential nutrients via shared metabolic pathways. The expression “Good fences make good neighbors” appears to be true for insect endosymbiotic systems.