bluuebunny/crossref_metadata_2025_split huggingface dataset:
Imaging Microglia Surveillance during Sleep-wake Cycles in Freely Behaving Mice
Authors: Gu Xiaochun , Zhao Zhong , Chen Xueli , Zhang Lifeng , Fang Huaqiang , Zhao Ting , Ju Shenghong , Gao Weizheng , Qian Xiaoyu , Wang Xianhua , Zhang Jue , Cheng Heping 
Published: February 2023

AbstractMicroglia surveillance manifests itself as dynamic changes in cell morphology and functional remodeling. Whether and how microglia surveillance is coupled to brain state switches during natural sleep-wake cycles remain unclear. To address this question, we used miniature two-photon microscopy (mTPM) to acquire time-lapse high-resolution microglia images of the somatosensory cortex, along with EEG/EMG recordings and behavioral video, in freely-behaving mice. We uncovered fast and robust brain state-dependent changes in microglia surveillance, occurring in parallel with sleep dynamics and early-onset phagocytic microglial contraction during sleep deprivation stress. We also detected local norepinephrine fluctuation occurring in a sleep state-dependent manner. We showed that the locus coeruleus-norepinephrine system, which is crucial to sleep homeostasis, is required for both sleep state-dependent and stress-induced microglial responses and β2-adrenergic receptor signaling plays a significant role in this process. These results provide direct evidence that microglial surveillance is exquisitely tuned to signals and stressors that regulate sleep dynamics and homeostasis so as to adjust its varied roles to complement those of neurons in the brain.In vivoimaging with mTPM in freely behaving animals, as demonstrated here, opens a new avenue for future investigation of microglia dynamics and sleep biology in freely behaving animals.
Single molecule DNA methylation and hydroxymethylation reveal unique epigenetic identity profiles of T helper cells
Authors: Goldsmith Chloe , Fesneau Olivier , Thevin Valentin , Matias Maria I. , Perrault Julie , Abid Ali Hani , Taylor Naomi , Dardalhon Valérie , Marie Julien C. , Hernandez-Vargas Hector 
Published: February 2023

AbstractBoth identity and plasticity of CD4 T helper (Th) cells are regulated in part by epigenetic mechanisms. However, a method that reliably and readily profiles DNA base modifications is still needed to finely study Th cell differentiation. Cytosine methylation (5mC) and cytosine hydroxymethylation (5hmC) are DNA modifications that identify stable cell phenotypes but their potential to characterize intermediate cell transitions has not yet been evaluated. To assess transition states in Th cells, we developed a new method to profile Th cell identity using cas9-targeted single molecule nanopore sequencing and found that 5mC and 5hmC can be used as markers of cellular identity. Targeting as few as 10 selected genomic loci, we were able to distinguish major differentiated T cell subtypes as well as intermediate phenotypes by their native DNA 5mC/5hmC patterns. Moreover, by using off-target sequences we were able to infer transcription factor activities relevant to each cell subtype. Our analysis demonstrates the importance of epigenetic regulation by 5mC and 5hmC modifications in the establishment of Th cell identity. Furthermore, our data highlight the potential to exploit this immune profiling application to elucidate the pathogenic role of Th transition states in autoimmune diseases.
FarmGTEx TWAS-server: an interactive web server for customized TWAS analysis in both human and farm animals
Authors: Zhang Zhenyang , Chen Zitao , Teng Jinyan , Liu Shuli , Lin Qing , Gao Yahui , Bai Zhonghao ,   The FarmGTEx Consortium, Li Bingjie , Liu George , Zhang Zhe , Pan Yuchun , Zhang Zhe , Fang Lingzhao , Wang Qishan 
Published: February 2023

AbstractTranscriptome-wide association study (TWAS) is a powerful strategy for elucidating the molecular mechanisms behind the genetic loci of complex phenotypes. However, TWAS analysis is still daunting in many species due to the complication of the TWAS analysis pipeline, including the construction of the gene expression reference panel, gene expression prediction, and the subsequent association analysis in the large cohorts of genome-wide association study (GWAS). Farm animals are major protein sources and biomedical models for humans. To facilitate the translation of genetic findings across species, here we provide an interactive and easy-to-use multi-species TWAS web server for the entire community, called the FarmGTEx TWAS-server (http://twas.farmgtex.org), which is based on the GTEx and FarmGTEx projects. It includes gene expression data from 49, 34, and 23 tissues in 838 humans, 5,457 pigs, and 4,889 cattle, representing 38,180, 21,037, and 17,942 distinct eGenes in prediction models for humans, pigs, and cattle, respectively. It allows users to conduct gene expression prediction for any individuals with genotypes, GWAS summary statistics imputation, customized TWAS, and popular downstream functional annotation. It also provides 479,203, 1,208, and 657 tissue-gene-trait association trios for the research community, representing 1,129 human traits, 41 cattle traits, and 11 pig traits. In summary, the FarmGTEx TWAS-server is a one-stop solution for performing TWAS analysis for researchers without programming skills in both human and farm animal research communities. It will be maintained and updated timely within the FarmGTEx project to facilitate gene mapping and phenotype prediction within and across species.
A Structural Classification of the Variant Surface Glycoproteins of the African Trypanosome
Authors: Đaković Sara , Zeelen Johan , Gkeka Anastasia , Chandra Monica , Foti Konstantina , van Straaten Monique , Vlachou Evi P. , Aresta-Branco Francisco , Verdi Joseph P. , Papavasiliou F. Nina , Stebbins C. Erec 
Published: February 2023

ABSTRACTLong-term immune evasion by the African trypanosome is achieved through repetitive cycles of surface protein replacement with antigenically distinct versions of the dense Variant Surface Glycoprotein (VSG) coat. Thousands of VSG genes and pseudo-genes exist in the parasite genome that, together with genetic recombination mechanisms, allow for essentially unlimited immune escape from the host’s adaptive immune system. The diversity space of the “VSGnome” at the protein level was thought to be limited to a few related folds whose structures were determined more than 30 years ago. However, recent progress has shown that the VSGs possess significantly more architectural variation than had been appreciated. Here we combine experimental X-ray crystallography with deep-learning structural prediction using Alphafold to produce models of hundreds of VSG proteins. We classify the VSGnome into groups based on protein architecture and oligomerization state, contextualize recent bioinformatics clustering schemes, and extensively map VSG-diversity space. We demonstrate that in addition to the structural variability and post-translational modifications observed thus far, VSGs are also characterized by variations in oligomerization state and possess inherent flexibility and alternative conformations, lending additional variability to what is exposed to the immune system. Finally, these additional experimental structures and the hundreds of Alphafold predictions confirm that the molecular surfaces of the VSGs remain distinct from variant to variant, supporting the hypothesis that protein surface diversity is central to the process of antigenic variation used by this organism during infection.
Role of acetoacetyl-CoA synthetase in glucose uptake by HepG2 cells
Authors: Hasegawa Shinya , Imai Masahiko , Takahashi Noriko 
Published: February 2023

AbstractAccelerated glucose metabolism is a common feature of cancer cells and represents a potential therapeutic target. Recent studies have revealed that lipid metabolism is related to glucose me-tabolism, especially glucose uptake. Acetoacetyl-CoA synthetase (AACS) converts acetoacetate, a ketone body, to acetoacetyl-CoA, which is incorporated into cholesterol and fatty acids. The AACS gene is highly expressed in HepG2 cells but not in the human normal liver. These results suggest a correlation between AACS and glucose metabolism. Therefore, we examined the relationship between AACS and glucose uptake in hepatocellular carcinoma (HepG2) cells. The expression of AACS was significantly upregulated when HepG2 cells were exposed to high concentrations of glucose. Lentiviruses, which code for shRNA against AACS (shAACS), were used to determine whether AACS knockdown affects the glucose uptake in HepG2 cells. AACS knockdown signifi-cantly reduced glucose uptake and increased the concentration of ketone bodies in the media, and treatment with β-hydroxybutyrate, a ketone body, attenuated glucose uptake. Moreover, the knockdown of AACS, i.e., the increased concentration of the intracellular ketone body, slightly attenuated cell proliferation and significantly increased the sensitivity to the anticancer agent sorafenib. These results suggest that AACS plays an important role in glucose uptake and cell proliferation and that ketone bodies may compete with glucose as an important energy source for cancer cells.
Mechanistic Modeling Explains the Production Dynamics of Recombinant Adeno-Associated Virus with the Baculovirus Expression Vector System
Authors: Destro Francesco , Srinivasan Prasanna , Kanter Joshua M. , Neufeld Caleb , Wolfrum Jacqueline M. , Barone Paul W. , Springs Stacy L. , Sinskey Anthony J. , Cecchini Sylvain , Kotin Robert M. , Braatz Richard D. 
Published: February 2023

AbstractThe demand for recombinant adeno-associated virus (rAAV) for gene therapy is expected to soon exceed current manufacturing capabilities, considering the expanding number of approved products and of pre-clinical and clinical stage studies. Current rAAV manufacturing processes have less-than-desired yields and produce a significant amount of empty capsids. Recently, FDA approved the first rAAV-based gene therapy product manufactured in the baculovirus expression vector system (BEVS). The BEVS technology, based on an invertebrate cell line derived fromSpodoptera frugiperda, demonstrated scalable production of high volumetric titers of full capsids. In this work, we develop a mechanistic model describing the key extracellular and intracellular phenomena occurring during baculovirus infection and rAAV virion maturation in the BEVS. The predictions of the model show good agreement with experimental measurements reported in the literature on rAAV manufacturing in the BEVS, including for TwoBac, ThreeBac, and OneBac constructs. The model is successfully validated against measured concentrations of structural and non-structural protein components, and of vector genome. We carry out a model-based analysis of the process, to provide insights on potential bottlenecks that limit the formation of full capsids. The analysis suggests that vector genome amplification is the limiting step for rAAV production in TwoBac. In turn, vector genome amplification is limited by low Rep78 levels. For ThreeBac, low vector genome amplification dictated by Rep78 limitation appears even more severe than in TwoBac. Transgene expression in the insect cell during rAAV manufacturing is also found to negatively influence the final rAAV production yields.
Multimodal meta-analysis of fecal metagenomes reveals microbial single nucleotide variants as superior biomarkers for early detection of colorectal cancer
Authors: Gao Wenxing , Gao Xiang , Zhu Lixin , Gao Sheng , Sun Ruicong , Feng Zhongsheng , Wu Dingfeng , Liu Zhanju , Zhu Ruixin , Jiao Na 
Published: February 2023

AbstractMicrobial signatures show remarkable potentials in predicting colorectal cancer (CRC). This study aimed to evaluate the diagnostic powers of multimodal microbial signatures, multi-kingdom species, genes, and single-nucleotide variants (SNVs) for detecting pre-cancerous adenomas. We performed cross-cohort analyses on whole metagenome sequencing data of 750 samples via xMarkerFinder to identify adenoma-associated microbial multimodal signatures. Our data revealed that fungal species outperformed species from other kingdoms with an area under the ROC curve (AUC) of 0.71 in distinguishing adenomas from controls, while classifier based on SNVs of bacterial species displayed the strongest diagnostic capability (AUC=0.89). SNV biomarkers also exhibited outstanding performances in three independent validation cohorts (AUCs = 0.83, 0.82, and 0.76, respectively) and were highly specific to adenoma. In further support of the above results, functional analyses revealed more frequent inter-kingdom associations between bacteria and fungi, and abnormalities in quorum sensing, purine and butanoate metabolism in adenoma, which were further validated in a newly-recruited cohort via qRT-PCR. Therefore, these data extend our understanding of adenoma-associated multimodal alterations in the gut microbiome and provide a rationale of microbial SNVs for the early detection of CRC.
Protein Sequence Design by Entropy-based Iterative Refinement
Authors: Zhou Xinyi , Chen Guangyong , Ye Junjie , Wang Ercheng , Zhang Jun , Mao Cong , Li Zhanwei , Hao Jianye , Huang Xingxu , Tang Jin , Ann Heng Pheng 
Published: February 2023

AbstractInverse Protein Folding (IPF) is an important task of protein design, which aims to design sequences compatible with a given backbone structure. Despite the prosperous development of algorithms for this task, existing methods tend to leverage limited and noisy residue environment when generating sequences. In this paper, we develop an iterative sequence refinement pipeline, which can refine the sequence generated by existing sequence design models. It selects and retains reliable predictions based on the model’s confidence in predicted distributions, and decodes the residue type based on a partially visible environment. The proposed scheme can consistently improve the performance of a number of IPF models on several sequence design benchmarks, and increase sequence recovery of the SOTA model by up to 10%. We finally show that the proposed model can be applied to redesign Transposon-associated transposase B. 8 variants exhibit improved gene editing activity among the 20 variants we proposed. Our code and a demo of the refinement pipeline are provided in the online colab.
A network-based analysis of signal use during approach interactions across sexes in chacma baboons (Papio ursinus griseipes)
Authors: Muschinski Jana , Mielke Alexander , Carvalho Susana 
Published: February 2023

AbstractGreetings in primates fulfil important functions including navigation of rank, maintenance of social relationships, and potentially establishing coalition partnerships.Papiomakes a particularly valuable study genus as baboons show variation in greeting, male-male cooperation, philopatry, and social system. However, baboon greeting research has largely focused on male-male interactions, with female approach behaviour neglected except in relation to friendships and grunting. Most if not all signals seen in male-male greetings are also present in approaches between other sex combinations. To understand these signals further, their use in all sex combinations should be explored. We investigated approaches between male and female adult chacma baboons (Papio ursinus griseipes), the only savannah baboon reportedly lacking male-male cooperation, recorded in Gorongosa National Park, Mozambique. We compared male-male greetings with those of other baboon species, identified network clusters of co-occurring signals, and compared male and female approaches more broadly. Male-male approaches were similar to those in other baboon species. We identified several predictable signal combinations, ear-flattening with lip-smacking being a particularly strong signal of benign intent across sexes. Further research comparing greeting across sex combinations and species will help disentangle links between risk, cooperation, and greeting behaviour.
ORFanes in mitochondrial genomes of marine polychaetePolydora
Authors: Selifanova Maria , Demianchenko Oleg , Noskova Elizaveta , Pitikov Egor , Skvortsov Denis , Drozd Jana , Vatolkina Nika , Apel Polina , Kolodyazhnaya Ekaterina , Ezhova Margarita A. , Tzetlin Alexander B. , Neretina Tatiana V. , Knorre Dmitry A. 
Published: February 2023

AbstractMost characterised metazoan mitochondrial genomes are compact and encode a small set of proteins that are essential for oxidative phosphorylation. However, in rare cases, invertebrate taxa have additional open reading frames (ORFs) in their mtDNA sequences. Here, we sequenced and analysed the mitochondrial genome of a polychaete worm,Polydora cf. ciliata, part of whose life cycle takes place in low-oxygen conditions. In the mitogenome, we found three “ORFane” regions (1063, 427, and 519 bp) that have no resemblance to any standard metazoan mtDNA gene but lack stop codons in one of the reading frames. Similar regions are found in the mitochondrial genomes of three other Polydora species andBocardiella hamata. All five species share the same gene order in their mitogenomes, which differ from that of other known spionidae mitogenomes. By analysing the ORFane sequences, we found that they are under negative selection pressure, contain conservative regions, and harbour predicted transmembrane domains.The codon adaptation indices (CAIs) of the ORFan genes were in the same range of values as the CAI of conventional protein-coding genes in corresponding mitochondrial genomes. Together, this suggests that ORFanes encode functional proteins. We speculate that the ORFanes originated from the conventional mitochondrial protein-coding genes which were duplicated when the Polydora/Bocardiella species complex separated from the rest of the Spionidae.Significance statementMetazoan mitochondrial genomes usually contain a conservative set of genes and features. However, mitogenomes of some species contain ORFanes – putative protein-coding genes without clear homology with other known sequences. In this study, we analysed three ORFanes in mitochondria of species of the genera Polydora and Bocardiella, which were absent in all other representatives of Spionidae. To the best of our knowledge, ORFanes haven’t been described in Annelida before. Sequence analysis of the ORFanes suggests they contain conservative regions and are likely translated into functional proteins. Our study features an uncommon case where new protein-coding genes emerged in the mitochondrial genomes of metazoa.
Mammalian Milk Glycomes: Connecting the Dots between Evolutionary Conservation and Biosynthetic Pathways
Authors: Thomès Luc , Karlsson Viktoria , Lundstrøm Jon , Bojar Daniel 
Published: February 2023

SummaryMilk oligosaccharides (MOs) are among the most abundant constituents of breast milk and are essential for health and development. Biosynthesized from monosaccharides into complex sequences, MOs differ considerably between taxonomic groups. Even human MO biosynthesis is insufficiently understood, hampering evolutionary and functional analyses. Using a comprehensive resource of all published MOs from >100 mammals, we develop a nonparametric pipeline for generating and analyzing MO biosynthetic networks, which readily generalizes to other glycan classes. We then use evolutionary relationships and inferred intermediates of these networks to discover (i) distributional glycome biases, (ii) biosynthetic restrictions, such as reaction path dependence, and (iii) conserved biosynthetic modules. This allows us to prune and pinpoint biosynthetic pathways despite missing information. Machine learning and network analysis cluster species by their milk glycome, identifying characteristic sequence relationships and evolutionary gains/losses of motifs, MOs, and biosynthetic modules. These resources and analyses will advance our understanding of glycan biosynthesis and the evolution of breast milk.
NaV1.7 mRNA and protein expression in putative projection neurons of the human spinal dorsal horn
Authors: Shiers Stephanie , Funk Geoffrey , Cervantes Anna , Horton Peter , Dussor Gregory , Hennen Stephanie , Price Theodore J. 
Published: February 2023

AbstractNaV1.7, a membrane-bound voltage-gated sodium channel, is preferentially expressed along primary sensory neurons, including their peripheral & central nerve endings, axons, and soma within the dorsal root ganglia and plays an integral role in amplifying membrane depolarization and pain neurotransmission. Loss- and gain-of-function mutations in the gene encoding NaV1.7,SCN9A, are associated with a complete loss of pain sensation or exacerbated pain in humans, respectively. As an enticing pain target supported by human genetic validation, many compounds have been developed to inhibit NaV1.7 but have disappointed in clinical trials. The underlying reasons are still unclear, but recent reports suggest that inhibiting NaV1.7 in central terminals of nociceptor afferents is critical for achieving pain relief by pharmacological inhibition of NaV1.7. We report for the first time that NaV1.7 mRNA is expressed in putative projection neurons (NK1R+) in the human spinal dorsal horn, predominantly in lamina 1 and 2, as well as in deep dorsal horn neurons and motor neurons in the ventral horn. NaV1.7 protein was found in the central axons of sensory neurons terminating in lamina 1-2, but also was detected in the axon initial segment of resident spinal dorsal horn neurons and in axons entering the anterior commissure. Given that projection neurons are critical for conveying nociceptive information from the dorsal horn to the brain, these data support that dorsal horn NaV1.7 expression may play an unappreciated role in pain phenotypes observed in humans with geneticSCN9Amutations, and in achieving analgesic efficacy in clinical trials.
Effect ofLantana camaraethanolic leaf extract on survival and migration of MDA-MB-231 triple negative breast cancer cell line
Authors: Pal Arundhaty , Sanyal Sourav , Das Sayantani , Sengupta Tapas Kumar 
Published: February 2023

AbstractIntroductionBreast cancer is a leading cause of cancer-related death worldwide.Lantana camarahas been reported to cure a number of ailments, with few studies showing its cytotoxic effects on breast cancer cells. However, the impact ofLantana camaraon triple negative breast cancer cells is largely obscure to date. The present study investigated the effect of ethanolic extract ofLantana camaraleaves on the triple negative breast cancer cell line, MDA-MB-231.MethodsCytotoxic effect of the extract on the cells was determined by cell survival assay. Cell cycle phase distribution was analysed using flow cytometry. To study the effect on nuclear morphology, nuclear stained cells were visualized using epifluorescence microscopy. The induction of apoptosis and generation of reactive oxygen species was conducted using flow cytometry. Cellular migration was studied by performing wound healing assay. Real-time polymerase chain reaction was done to determine the mRNA levels of some key genes.ResultsLantana camaraleaf extract induced cytomorphological changes and growth inhibitory effect on MDA-MB-231 cells in a dose-dependent manner. The extract also induced G0/G1 cell cycle arrest and nuclear condensation. Flow cytometry analysis confirmed cell death by apoptosis.Lantana camaraleaf extract also reduced the migration of MDA-MB-231 cells. mRNA expression levels also supported the above observations.ConclusionsThis study demonstrates the efficacy of the extract to induce growth-inhibitory and anti-migratory effects on MDA-MB-231 cells. Our results thus suggest thatLantana camaraleaf extract can be considered as a potent source of chemotherapeutic agents for triple negative breast cancer.