bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nuclear Ribosomal Internal Transcribed Spacer 1 (ITS1) variation in Lady Bird Beetles (Coccinellidae)
Authors: Aruggoda A. G. B. , Ren Shun-Xiang 
Published: May 2022

AbstractThe seventeen taxa of the family Coccinellidae were analyzed by sequencing the Internal Transcribed Spacer 1 region followed by analyzing the presence of significantly simple motifs (SSMs), to investigate the presence of functionally important areas in the gene if any and to find phylogenetic inference of the ITSI region between sequenced species. Length comparisons among the ITS 1 region indicated the absence of intraspecific variability. Further, length differences observed were among Adalia bipunctata showing a 3 bp maximum size difference and Psyllobora vigintiduopunctata with 1 bp size difference. The base composition showed highly similar values of A, T, G and C. Except Harmonia axyridis, Phyllobora vigintiduopunctata, Chilocorus renipustulatu, Lemnia duvauceli all other species showed significant number of simple repetitions. Adalia bipunctata showed the highest simple repetition with the RSF value of 1.4440. Thirteen ladybird beetles had higher SSM regions. Adalia bipunctata, Adalia decempunctata, Exochomus quadripustulatus shows high accumulation of AT repeats in 5 prime end flanking region and GC repeats in 3 prime end flanking region. Amida nigropectoralis, Amida quingquefasiata, Menochilus sexmaculata, Phaenochilus mesternalis, Coccidula rufa, Platynaspis luterubra shows a higher concentration of GC repeats towards the 3 prime end flanking regions. Phylogenetic analysis revealed that the tribe Psylloborini of the subfamily Coccinellidae was monophyletic. The members of the Subfamily Chilocorinae first associate with the tribes of subfamily Coccinellidae and then relate with the tribe Scymnini. Exochomus quadripustulatus which shows the highest length variably showed a relationship with Phaenochilus mesternalis 77 bootstrap and 84 posterior probabilities.
Serotonin coordinates reproductive functions in Caenorhabditis elegans
Authors: Aprison Erin Z. , Dzitoyeva Svetlana , Ruvinsky Ilya 
Published: May 2022

ABSTRACTReproduction alters animal behavior and physiology, but neuronal circuits that coordinate these changes remain largely unknown. Insights into mechanisms that regulate and possibly coordinate reproduction-related traits could be gleaned from the study of sex pheromones that manipulate potential mating partners to improve reproductive success. In C. elegans, the prominent male pheromone, ascr#10, modifies reproductive behavior and several aspects of reproductive physiology in hermaphrodite recipients, including improving oocyte quality. Here we show that a circuit that contains serotonin-producing and serotonin-uptaking neurons plays a key role in mediating these beneficial effects of ascr#10. We also demonstrate that increased serotonergic signaling promotes proliferation of germline progenitors in adult hermaphrodites. Our results establish a role for serotonin in maintaining germline quality and highlight a simple neuronal circuit that acts as a linchpin that couples food intake, mating behavior, reproductive output, and germline renewal and provisioning.
Paths to adaptation under fluctuating nitrogen starvation: The spectrum of adaptive mutations in Saccharomyces cerevisiae is shaped by transposons and microhomology-mediated recombination
Authors: Hays Michelle , Schwartz Katja , Schmidtke Danica T. , Aggeli Dimitra , Sherlock Gavin 
Published: May 2022

AbstractThere are many mechanisms that give rise to genomic change: while point mutations are often emphasized in genomic analyses, evolution acts upon many other types of genetic changes that can result in less subtle perturbations. Changes in chromosome structure, DNA copy number, and novel transposon insertions all create large genomic changes, which can have correspondingly large impacts on phenotypes and fitness. In this study we investigate the spectrum of adaptive mutations that arise in a population under consistently fluctuating nitrogen conditions. We specifically contrast these adaptive alleles and the mutational mechanisms that create them, with mechanisms of adaptation under batch glucose limitation and constant selection in low, non-fluctuating nitrogen conditions. We observe that retrotransposon activity accounts for a substantial number of adaptive events, along with microhomology-mediated mechanisms of insertion, deletion, and gene conversion. In addition to loss of function alleles, which are often exploited in genetic screens, we identify adaptive gain of function alleles and alleles acting through as-of-yet unclear mechanisms. Taken together, our findings emphasize that how selection (fluctuating vs. non-fluctuating) is applied also shapes adaptation, just as the selective pressure (nitrogen vs. glucose) does itself. Fluctuating environments can activate different mutational mechanisms, shaping adaptive events accordingly. Experimental evolution, which allows a wider array of adaptive events to be assessed, is thus a complementary approach to both classical genetic screens and natural variation studies to characterize the genotype-to-phenotype-to-fitness map.
MicroRNAs contribute to the host response to Coxiella burnetii
Authors: Sachan Madhur , Brann Katelynn R. , Voth Daniel E. , Raghavan Rahul 
Published: May 2022

ABSTRACTMicroRNAs (miRNAs), a class of small non-coding RNAs, are critical to gene regulation in eukaryotes. They are involved in modulating a variety of physiological processes, including the host response to intracellular infections. Little is known about miRNA functions during infection by Coxiella burnetii, the causative agent of human Q fever. This bacterial pathogen establishes a large replicative vacuole within macrophages by manipulating host processes such as apoptosis and autophagy. We investigated miRNA expression in C. burnetii-infected macrophages and identified several miRNAs that were down- or up-regulated during infection. We further explored the functions of miR-143-3p, an miRNA whose expression is down-regulated in macrophages infected with C. burnetii, and show that increasing the abundance of this miRNA in human cells results in increased apoptosis and reduced autophagy – conditions that are unfavorable to C. burnetii intracellular growth. In sum, this study demonstrates that C. burnetii infection elicits a robust miRNA-based host response, and because miR-143-3p promotes apoptosis and inhibits autophagy, down-regulation of miR-143-3p expression during C. burnetii infection likely benefits the pathogen.
A Bispecific Antibody Targeting RBD and S2 Potently Neutralizes SARS-CoV-2 Omicron and Other Variants of Concern
Authors: Yuan Mengqi , Chen Xiangyu , Zhu Yanzhi , Dong Xiaoqing , Liu Yan , Qian Zhaohui , Ye Lilin , Liu Pinghuang 
Published: May 2022

AbstractEmerging severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) variants, especially the Omicron variant, have impaired the efficacy of existing vaccines and most therapeutic antibodies, highlighting the need for additional antibody-based tools that can efficiently neutralize emerging SARS-CoV-2 variants. The use of a “single” agent to simultaneously target multiple distinct epitopes on the spike is desirable to overcome the neutralizing escape of SARS-CoV-2 variants. Herein, we generated a human-derived IgG-like bispecific antibody (bsAb), Bi-Nab35B5-47D10, which successfully retained the specificity and simultaneously bound to the two distinct epitopes on RBD and S2. Bi-Nab35B5-47D10showed improved spike binding breadth among wild-type (WT) SARS-CoV-2, variants of concern (VOCs) and variants being monitored (VBMs) compared with its parental mAbs. Furthermore, pseudotyped virus neutralization demonstrated that Bi-Nab35B5-47D10can efficiently neutralize VBMs including Alpha (B.1.1.7), Beta (B.1.351) and Kappa (B.1.617.1) and VOCs including Delta (B.1.617.2), Omicron BA.1 and Omicron BA.2. Crucially, Bi-Nab35B5-47D10substantially improved neutralizing activity against Omicron BA.1 (IC50= 27.3 ng/mL) and Omicron BA.2 (IC50= 121.1 ng/mL) compared with their parental mAbs. Therefore, Bi-Nab35B5-47D10represents a potential effective countermeasure against SARS-CoV-2 Omicron and other variants of concern.ImportanceThe new highly contagious SARS-CoV-2 Omicron variant caused substantial breakthrough infections and has become the dominant strain in countries across the world. Omicron variants usually bear high mutations in the spike protein and exhibit considerable escape of most potent neutralization monoclonal antibodies and reduced efficacy of current COVID-19 vaccines. The development of neutralizing antibodies with potent efficacy against the Omicron variant is still an urgent priority. Here, we generated a bsAb, Bi-Nab35B5-47D10,that simultaneously targets SARS-CoV-2 RBD and S2 and improved neutralizing potency and breadth against SARS-CoV-2 WT and the tested variants compared with their parental antibodies. Notably, Bi-Nab35B5-47D10has more potent neutralizing activity against the VOC Omicron pseudotyped virus. Therefore, Bi-Nab35B5-47D10is a feasible and potentially effective strategy to treat and prevent COVID-19.
MAP Kinase and mammalian target of rapamycin are main pathways of gallbladder carcinogenesis: Results from bioinformatic analysis of Next Generation Sequencing data from a hospital-based cohort
Authors: Rajput Monika , Chigurupati SatyaVjiay j , Purwar Roli , Shukla Mridula , Pandey Manoj 
Published: May 2022

ABSTRACTBackgroundGallbladder Cancer (GBC) is one of the most common cancers of the biliary tract and the third commonest gastrointestinal (GI) malignancy worldwide. The disease is characterized by the late presentation and poor outcome despite treatment, and hence, newer therapies and targets need to be identified.MethodsThe current study investigated various functionally enriched pathways in GBC pathogenesis involving the genes identified through Next Generation Sequencing (NGS). The Pathway enrichment analysis and Gene Ontology (GO) were carried out after NGS, followed by the construction of the protein-protein interaction (PPI) network to discover associations among the genes.ResultsOf the thirty-three patients with GBC who were screened through next-generation sequencing (NGS), 27somatic mutations were identified. These mutations involved a total of 14 genes. The p53 and KRAS were commonly found to be mutated, while mutations in other genes were seen in one case each, the mean number of mutations were 1.2, and maximum mutation in a single case (eight) was seen in one case. The bioinformatics analysis identified MAP kinase, PI3K-AKT, EGF/EGFR, and Focal Adhesion PI3K-AKT-mTOR signaling pathways and cross-talk between these.ConclusionThe results suggest that the complex crosstalk between the mTOR, MAPK, and multiple interacting cell signaling cascades can promote GBC progression, and hence, mTOR - MAPK targeted treatment will be an attractive option.
Myofiber reconstruction at micron scale reveals longitudinal bands in heart ventricular walls
Authors: Dileep Drisya , Syed Tabish A. , Sloan Tyler F. W. , Dhandapany Perundurai S. , Siddiqi Kaleem , Sirajuddin Minhajuddin 
Published: May 2022

AbstractThe coordinated contraction of myocytes drives the heart to beat and circulate blood. Due to the limited spatial resolution of whole heart imaging and the piecemeal nature of high-magnification studies, a confirmed model of myofiber geometry does not yet exist. Using microscopy and computer vision we report the first three-dimensional reconstruction of myofibers across entire mouse ventricular walls at the micron scale, representing a gain of three orders of magnitude in spatial resolution over the existing models. Our analysis reveals prominent longitudinal bands of fibers that are orthogonal to the well-known circumferential ones. Our discovery impacts present understanding of heart wall mechanics and electrical function, with fundamental implications for the study of diseases related to myofiber disorganization.
Development of a high dimensional imaging mass cytometry panel to investigate spatial organization of tissue microenvironment in formalin-fixed archival clinical tissues
Authors: Tornaas Stian , Kleftogiannis Dimitrios , Fromreide Siren , Ytre-Hauge Smeland Hilde , Aarstad Hans Jørgen , Karsten Vintermyr Olav , Andreas Akslen Lars , Elena Costea Daniela , Dongre Harsh Nitin 
Published: May 2022

SummaryTo decipher the interactions between various components of the tumor microenvironment (TME) and tumor cells in a preserved spatial context, a multiparametric approach is essential. In this pursuit, imaging mass cytometry (IMC) emerges as a valuable tool, capable of concurrently analyzing up to 40 parameters at subcellular resolution. In this study, a set of antibodies was selected to spatially resolve multiple cell types and TME elements, including a comprehensive panel targeted at dissecting the heterogeneity of cancer-associated fibroblasts (CAF), a pivotal TME component. This antibody panel was standardized and optimized using formalin-fixed paraffin-embedded tissue (FFPE) samples from different organs/lesions known to express the markers of interest. The final composition of the antibody panel was determined based on the performance of conjugated antibodies in both immunohistochemistry (IHC) and IMC. Tissue images were segmented employing the Steinbock framework. Unsupervised clustering of single-cell data was carried out using a bioinformatics pipeline developed in R program. This paper provides a detailed description of the staining procedure and analysis workflow. Subsequently, the panel underwent validation on clinical FFPE samples from head and neck squamous cell carcinoma (HNSCC). The panel and bioinformatics pipeline established here proved to be robust in characterizing different TME components of HNSCC while maintaining a high degree of spatial detail. The platform we describe shows promise for understanding the clinical implications of TMA heterogeneity in large patient cohorts with FFPE tissues available in diagnostic biobanks worldwide.
Low immune response after 1.5 years of primary SARS-CoV-2 infection and Covishield vaccination lead to SARS-CoV-2 reinfection
Authors: Shete Anita M. , Patil Deepak Y. , Sahay Rima R. , Sapkal Gajanan N. , Deshpande Gururaj R. , Yadav Pragya D. 
Published: May 2022

AbstractWe have investigated six COVID recovered cases with two doses of Covishield vaccination followed by reinfection. The primary SARS-CoV-2 infection found to occur with B.1 and reinfection with Omicron BA.1 and BA.2 variants. The genomic characterization and duration between two infections confirms these cases as SARS-CoV-2 reinfection. The mutation analysis of the reinfection cases correlated with immune evasion potential of BA.1 and BA.2 sub lineages. The immune response determined at different time intervals demonstrated boost post two dose vaccination, decline in pre-reinfection sera post 7 months and rise post reinfection. Apparently, these cases suffered from SARS-CoV-2 reinfection with the declined hybrid immunity acquired from primary infection and two dose covishield vaccination. This suggests the need for booster dose of vaccination. Besides this, multiple non-pharmaceutical interventions should be used to cope up with SARS-CoV-2 infection.
Proliferation drives quorum sensing of microbial products in human macrophage populations
Authors: Rajab Nadia , Gearing Linden J. , Lyu Ruqian , Prawer Yair D.J. , Angel Paul W. , Grimmond Sean M. , Laslett Andrew L. , McCarthy Davis J. , Wells Christine A. 
Published: May 2022

AbstractMacrophages coordinate the initial host inflammatory response to tissue infection, as well as mediating the reparative phase, by producing growth factors that promote tissue repair. One model of this functional dichotomy is that peripherally recruited monocyte-derived macrophages drive acute inflammatory responses to infection, whereas tissue-resident macrophages are responsible for tissue repair. Alternatively, inflammation and repair may be inter-dependent molecular programs, such that both recruited and resident cells have equivalent capacity to contribute. Repeated exposure to pathogenic challenge results in innate tolerance, which may also alter the contributions of discrete macrophage populations to inflammation or repair. In this study a village model of tissue resident and recruited macrophages was created using induced pluripotent stem cell-derived macrophages and peripheral blood monocyte-derived macrophages, respectively. Population responses to repeated exposure to lipopolysaccharide were assessed with single-cell RNA sequencing and donors demultiplexed with Vireo. A subset of genes escaped classical tolerance programs in the iPSC, but not monocyte-derived macrophages, and this was associated with differences in their proliferative capacity. This suggests that targeting the proliferative resident macrophages would be most effective to limit inflammatory signaling.
Tethering distinct molecular profiles of single cells by their lineage histories to investigate sources of cell state heterogeneity
Authors: Minkina Anna , Cao Junyue , Shendure Jay 
Published: May 2022

AbstractGene expression heterogeneity is ubiquitous within single cell datasets, even among cells of the same type. Heritable expression differences, defined here as those which persist over multiple cell divisions, are of particular interest, as they can underlie processes including cell differentiation during development as well as the clonal selection of drug-resistant cancer cells. However, heritable sources of variation are difficult to disentangle from non-heritable ones, such as cell cycle stage, asynchronous transcription, and measurement noise. Since heritable states should be shared by lineally related cells, we sought to leverage CRISPR-based lineage tracing, together with single cell molecular profiling, to discriminate between heritable and non-heritable variation in gene expression. We show that high efficiency capture of lineage profiles alongside single cell gene expression enables accurate lineage tree reconstruction and reveals an abundance of progressive, heritable gene expression changes. We find that a subset of these are likely mediated by structural genetic variation (copy number alterations, translocations), but that the stable attributes of others cannot be understood with expression data alone. Towards addressing this, we develop a method to capture cell lineage histories alongside single cell chromatin accessibility profiles, such that expression and chromatin accessibility of closely related cells can be linked via their lineage histories. We call this indirect “coassay” approach “THE LORAX” and leverage it to explore the genetic and epigenetic mechanisms underlying heritable gene expression changes. Using this approach, we show that we can discern between heritable gene expression differences mediated by large and small copy number changes, trans effects, and possible epigenetic variation.
Characterization of full-length CNBP expanded alleles in myotonic dystrophy type 2 patients by Cas9-mediated enrichment and nanopore sequencing
Authors: Alfano Massimiliano , De Antoni Luca , Centofanti Federica , Visconti Virginia Veronica , Maestri Simone , Esposti Chiara Degli , Massa Roberto , D’Apice Maria Rosaria , Novelli Giuseppe , Delledonne Massimo , Botta Annalisa , Rossato Marzia 
Published: May 2022

ABSTRACTMyotonic dystrophy type 2 (DM2) is caused by CCTG repeat expansions in the CNBP gene, comprising 75 to >11,000 units and featuring extensive mosaicism, making it challenging to sequence fully-expanded alleles. To overcome these limitations, we used PCR-free Cas9-mediated nanopore sequencing to characterize CNBP repeat expansions at the single-nucleotide level in nine DM2 patients. The length of normal and expanded alleles can be assessed precisely using this strategy, agreeing with traditional methods, and revealing the degree of mosaicism. We also sequenced an entire ∼50-kbp expansion, which has not been achieved previously for DM2 or any other repeat-expansion disorders. Our approach precisely counted the repeats and identified the repeat pattern for both short interrupted and uninterrupted alleles. Interestingly, in the expanded alleles, only two DM2 samples featured the expected pure CCTG repeat pattern, while the other seven presented also TCTG blocks at the 3′ end, which have not been reported before in DM2 patients, but confirmed hereby with orthogonal methods. The demonstrated approach simultaneously determines repeat length, structure/motif and the extent of somatic mosaicism, promising to improve the molecular diagnosis of DM2 and achieve more accurate genotype– phenotype correlations for the better stratification of DM2 patients in clinical trials.
RNA Methylome Reveals the m6A-Mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-Withering
Authors: Zhu Chen , Zhang Shuting , Zhou Chengzhe , Tian Caiyun , Shi Biying , Xu Kai , Huang Linjie , Sun Yun , Lin Yuling , Lai Zhongxiong , Guo Yuqiong 
Published: May 2022

AbstractEpitranscriptomic mark N6-methyladenosine (m6A) is the most predominant internal modification in RNAs, which plays pivotal roles in response to diverse stresses. Multiple environmental stresses caused by withering process can greatly influence the accumulation of specialized metabolites and the formation of tea flavor. However, little is known about the effects of m6A-mediated regulatory mechanism on flavor-related metabolisms in tea leaves. Here, we explored m6A-mediated regulatory mechanism and its impacts on flavonoid and terpenoid metabolisms under solar-withering using integrated RNA methylome and transcriptome. Dynamic changes in global m6A levels of tea leaves are mainly controlled by two m6A erasers (CsALKBH4A and CsALKBH4B) under solar-withering. Differentially methylated peak (DMP)-associated genes under different shading rates of solar-withering were identified and found to be enriched in terpenoid biosynthesis and spliceosome pathways. Further analyses indicated that CsALKBH4-driven RNA demethylation can not only directly affect the accumulation of volatile terpenoids by mediating the stability and abundance of terpenoid biosynthesis-related genes, but also indirectly influence the contents of flavonoids, catechins, and theaflavins via triggering the alternative splicing (AS)-mediated regulation. Our findings underscored a novel layer of epitranscriptomic gene regulation in tea flavor-related metabolic pathways and established a compelling link between m6A-mediated regulatory mechanism and the formation of high-quality flavor in tea leaves under solar-withering.