Transcriptomic analysis reinforces the implication of spatacsin in neuroinflammation and neurodevelopment by Liriopé Toupenet Marchesi, Daniel Stockholm, Typhaine Esteves, Marion Leblanc, Nicolas Auger, Julien Branchu, Khalid Hamid El Hachimi, Giovanni Stevanin

“…To elucidate its function, we conducted an extensive RNA sequencing (RNAseq) experiment and transcriptomic analysis in three distinct neural structures (cerebellum, cortex and hippocampus) and at three different ages (6 weeks, 4 months and 8 months) in both wild type and Spg11 −/− mice. …”
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Molecular Diversity of Arbuscular Mycorrhizal Fungi (AMF) Associated with Carissa edulis, an Endangered Plant Species along Lake Victoria Basin of Kenya by Benard O. Ogoma, Stephen F. Omondi, Jane Ngaira, Josephine W. Kimani

“…AMF was assessed through morphological characterization and sequencing of small subunit of ribosomal DNA. Morphological identification identified four genera of AMF (Gigaspora, Acaulospora, Scutellospora, and Glomus) with no significant difference among the sites. …”
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Profiling bacterial communities of irrigation water and leafy green vegetables produced by small-scale farms and sold in informal settlements in South Africa by D. M. Kgoale, J. K. Gokul, S. Duvenage, E. M. Du Plessis, L. Korsten

“…Illumina MiSeq high-throughput sequencing showed that each farm exhibited a unique bacterial community composition, with an overall high relative abundance of Proteobacteria, Firmicutes and Actinobacteria, including prominent families such as Burkholderiaceae (48%), Enterobacteriaceae (34%), Bacillales Family XII (8%), Rhodobacteraceae (3%), Micrococcaceae (1.98%) and Pseudomonadaceae (1.79%). …”
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Bioinformatics Analysis, Prokaryotic Expression and Biological Activity of Lysin from Vibrio parahaemolyticus Phage vB_VpP_1 by ZHANG Defu, YANG Wenjing, LIU Ke, LIU Qingqing, BAI Wutong, LI Fan, LÜ Xinran, BAI Xue, TAN Xiqian, LI Xuepeng, LI Jianrong

“…To study the in vitro cleavage effect of a recombinant lysin from bacteriophage vB_VpP_1 on Vibrio parahaemolyticus, the gp32 gene fragment of vB_VpP_1 was identified as a lysin gene according to the results of whole-genome sequencing (WGS) and functional analysis. The amino acid sequence and structure of gp32 were analyzed by various tools such as Expasy. …”
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Molecular epidemiology of foot-and-mouth disease (review) by A. V. Scherbakov

“…These tests are based on constantly progressing technologies of nucleic acid sequencing and phylogenetic analysis. The use of these technologies made it possible to assess the genetic diversity of the FMD virus, to analyze the evolution of the virus in the enzootic regions, and track the pathways of FMD epizootic and panzootic spread. …”
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Assessing the probiotic potential of Lactococcus lactis isolated from the intestine and gill of rainbow trout (Oncorhynchus mykiss) through in vitro analysis by Lucano Billy M., Feria Manuel A., Zatan Adrian E., Toledo Odalis E., Aguilar Jorge L., Diringer Benoit M., Castañeda Arnaldo E.

“…The isolates with the best characteristics were identified as Lactococcus lactis (n=7) by 16S rRNA gene sequencing.…”
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Genetic Diversity and Population Structure of Tomato (<i>Solanum lycopersicum</i>) from the USDA-GRIN Germplasm Collection by Ibtisam Alatawi, Haizheng Xiong, Hanan Alkabkabi, Kenani Chiwina, Qun Luo, Kai-Shu Ling, Yuejun Qu, Renjie Du, Ainong Shi

“…A total of 276 accessions from the USDA-GRIN collection were analyzed using single-nucleotide polymorphisms (SNPs) generated through genotyping by sequencing (GBS). After stringent filtering, 5162 high-quality polymorphic SNPs were retained for analysis. …”
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High-fidelity annotated triploid genome of the quarantine root-knot nematode, Meloidogyne enterolobii by Marine Poullet, Hemanth Konigopal, Corinne Rancurel, Marine Sallaberry, Celine Lopez-Roques, Ana Paula Zotta Mota, Joanna Lledo, Sebastian Kiewnick, Etienne G. J. Danchin

“…Here, we report a high-quality genome assembly of M. enterolobii using the high-fidelity long-read sequencing technology developed by Pacific Biosciences, combined with a gap-aware sequence transformer, DeepConsensus. …”
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Commercial bioinoculants improve colonization but do not alter the arbuscular mycorrhizal fungal community of greenhouse-grown grapevine roots by Mariam P. Berdeja, Nicole K. Reynolds, Teresa Pawlowska, Justine E. Vanden Heuvel

“…Root colonization, leaf nitrogen concentration, plant biomass and root morphology were assessed, and AMF communities of inoculated and non-inoculated grapevine roots were profiled using high-throughput sequencing. Results Contrary to our predictions, no differences in the microbiome of plants exposed to native AMF communities versus commercial AMF bioinoculants + native AMF communities were detected in roots. …”
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Association of Human Leukocyte Antigen Class I Polymorphism with Spontaneous Clearance of Hepatitis B Surface Antigen in Qidong Han Population by Fengqin Miao, Hang Sun, Ning Pan, Jinhuan Xu, Jie Qiu, Yuqing Shen, Wei Xie, Jianqiong Zhang

“…We genotyped HLA-A, -B, and -C loci of 448 individuals with HBV persistent infection and 140 persons with spontaneous clearance of HBsAg by polymerase chain reaction with sequencing based typing (PCR/SBT). All the individuals were unrelated males enrolled from Qidong Han population and were followed up for 10 years. …”
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Replication-IDentifier links epigenetic and metabolic pathways to the replication stress response by Sophie C. van der Horst, Leonie Kollenstart, Amandine Batté, Sander Keizer, Kees Vreeken, Praveen Pandey, Andrei Chabes, Haico van Attikum

“…During Repli-ID, the replicative polymerase epsilon (Pol ε) is tracked at a barcoded origin of replication by chromatin immunoprecipitation (ChIP) coupled to next-generation sequencing of the barcode in thousands of hydroxyurea-treated yeast mutants. …”
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Looks can be deceiving: the deceptive milkcaps (Lactifluus, Russulaceae) exhibit low morphological variance but harbour high genetic diversity by Lynn Delgat, Glen Dierickx, Serge De Wilde, Claudio Angelini, Eske De Crop, Ruben De Lange, Roy Halling, Cathrin Manz, Jorinde Nuytinck, Annemieke Verbeken

“…These species are morphologically very similar and are characterized by a tomentose pileus with thin-walled hyphae and a velvety stipe with thick-walled hyphae. An ITS1 sequence was obtained through Illumina sequencing for the lectotype of L. deceptivus, dating from 1885, revealing which clade represents the true L. deceptivus. …”
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Epithelial NSD2 maintains FMO‐mediated taurine biosynthesis to prevent intestinal barrier disruption by Yue Xu, Xiuying Xiao, Chunxiao Ma, Ziyi Wang, Wenxin Feng, Hanyu Rao, Wei Zhang, Ningyuan Liu, Rebiguli Aji, Xiangjun Meng, Wei‐Qiang Gao, Li Li

“…The IECs were isolated for RNA sequencing and chromatin immunoprecipitation sequencing to identify molecular signalling pathways and key molecules leading to IBD in mice. …”
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Molecular underpinnings of exceptional response in primary malignant melanoma of the esophagus to anti-PD-1 monotherapy by Yu Chen, Xuan Wang, Jie Dai, Li Zhou, Xuefeng Xia, Jun Guo, Xue Bai, Lu Si, Bixia Tang, Chuanliang Cui, Xiaoting Wei, Xinan Sheng, Siming Li, Zhihong Chi, Lili Mao, Bin Lian, Xieqiao Yan, Yan Kong, Caili Li, Xuan Gao, Lirui Tang, Linzi Sun, Zhonghui Qi, Zelong Xu

“…Genomic sequencing analysis revealed that the genomic aberration landscape of PMME predominated in classical cancer driver genes, with approximately half of PMME cases harboring mutations in BRAF, N/KRAS, and NF1. …”
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Risk of hereditary spherocytosis misdiagnosis due to limited effective diagnostic methods by Hien Thanh Dao, Triet Hy Van, Tuyet Thi Bach Tran, Dat Quoc Ngo, Anh Thi Mai Nguyen

“…The percentage of spherocytes was scored from peripheral blood smear observation; the percentage of decreased mean fluorescent intensity from Eosin-5'-maleimide binding assay was used to determine red cell membrane protein deficiency, and hereditary spherocytosis was finally confirmed by gene sequencing as a gold standard. Results: Eosin-5'-maleimide binding assay demonstrated high sensitivity (93.33%), specificity (100%), and accuracy (97.3%) in detecting hereditary spherocytosis, with an optimal cut-off value of 47.83% decreased mean fluorescent intensity. …”
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HER2 expression and pathway status in male breast cancer patients: results of an integrated analysis among 6,150 patients by Boqiang Lyu, Shidi Zhao, Hui Wang, Shouping Gong, Biyuan Wang

“…A total of 6,015 MBC patients from 45 studies and 135 MBC patients with sequencing data were identified. HER2 positive rates and hazard ratios (HR) for overall survival (OS) were combined using Metaprop. …”
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Genotypes and phenotypes of neurofibromatosis type 1 patients in Japan: A Hereditary Tumor Cohort Study by Mashu Futagawa, Tetsuya Okazaki, Eiji Nakata, Chika Fukano, Risa Osumi, Fumino Kato, Yusaku Urakawa, Hideki Yamamoto, Toshifumi Ozaki, Akira Hirasawa

“…Therefore, in this study, we aimed to elucidate the detailed genetic and clinical characteristics of NF1 in a hereditary tumor cohort. We performed sequencing and copy number assays in a clinical laboratory and analyzed the clinical data of 44 patients with suspected NF1. …”
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Comparative Mitogenomics in the Genus <i>Chlorophorus</i> (Coleoptera: Cerambycidae) and Its Phylogenetic Implications by Zhengju Fu, Lu Chen, Lichao Tian, Zongqing Wang, Zhu Li

“…To assess the monophyly and subgeneric system of this genus, we newly obtained mitochondrial genomic data from 21 species of <i>Chlorophorus</i> via high-throughput sequencing and reconstructed the phylogeny of this genus using ML and BI methods. …”
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CircRNA-Disease Associations Prediction Based on Metapath2vec++ and Matrix Factorization by Yuchen Zhang, Xiujuan Lei, Zengqiang Fang, Yi Pan

“…Although increasing numbers of circRNAs are discovered using high-throughput sequencing technologies, these techniques are still time-consuming and costly. …”
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Comparison of Airborne Bacterial Populations Determined by Passive and Active Air Sampling at puy de Dôme, France by Kevin P. Dillon, Romie Tignat-Perrier, Muriel Joly, Sydonia N. C. M. Grogan, Catherine Larose, Pierre Amato, Gediminas Mainelis

“…The diversity of the airborne bacteria captured by both samplers across six weekly sampling periods was examined by 16S rRNA gene amplicon sequencing. The dominant phyla observed by both samplers were similar and included Firmicutes, Proteobacteria, and Actinobacteriota. …”
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