Int J Syst Evol Microbiol
October 2024
A Gram-stain-positive, aerobic, moderate halophilic actinobacterium, designated strain YIM 96095, was isolated from a saline soil sample collected from Aiding Lake, Xinjiang, North-western China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate belonged to the family , formed a distinct subclade, and was most closely related to DSM 102030 and DSM 45697 with sequence identity values of 95.8 and 95.
View Article and Find Full Text PDFBackground: Sexual differences across molecular levels profoundly impact cancer biology and outcomes. Patient gender significantly influences drug responses, with divergent reactions between men and women to the same drugs. Despite databases on sex differences in human tissues, understanding regulations of sex disparities in cancer is limited.
View Article and Find Full Text PDFAntibodies play a pivotal role in immune defense and serve as key therapeutic agents. The process of affinity maturation, wherein antibodies evolve through somatic mutations to achieve heightened specificity and affinity to target antigens, is crucial for effective immune response. Despite their significance, assessing antibody-antigen binding affinity remains challenging due to limitations in conventional wet lab techniques.
View Article and Find Full Text PDFStemDriver is a comprehensive knowledgebase dedicated to the functional annotation of genes participating in the determination of hematopoietic stem cell fate, available at http://biomedbdc.wchscu.cn/StemDriver/.
View Article and Find Full Text PDFNucleic Acids Res
January 2024
The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, has resulted in the loss of millions of lives and severe global economic consequences. Every time SARS-CoV-2 replicates, the viruses acquire new mutations in their genomes. Mutations in SARS-CoV-2 genomes led to increased transmissibility, severe disease outcomes, evasion of the immune response, changes in clinical manifestations and reducing the efficacy of vaccines or treatments.
View Article and Find Full Text PDFSample multiplexing is often used to reduce cost and limit batch effects in single-cell RNA sequencing (scRNA-seq) experiments. A commonly used multiplexing technique involves tagging cells prior to pooling with a hashtag oligo (HTO) that can be sequenced along with the cells' RNA to determine their sample of origin. Several tools have been developed to demultiplex HTO sequencing data and assign cells to samples.
View Article and Find Full Text PDFSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of coronavirus disease 19 (COVID-19), has caused a global health crisis. Despite ongoing efforts to treat patients, there is no universal prevention or cure available. One of the feasible approaches will be identifying the key genes from SARS-CoV-2-infected cells.
View Article and Find Full Text PDFSpatial proteomics technologies have revealed an underappreciated link between the location of cells in tissue microenvironments and the underlying biology and clinical features, but there is significant lag in the development of downstream analysis methods and benchmarking tools. Here we present SPIAT (spatial image analysis of tissues), a spatial-platform agnostic toolkit with a suite of spatial analysis algorithms, and spaSim (spatial simulator), a simulator of tissue spatial data. SPIAT includes multiple colocalization, neighborhood and spatial heterogeneity metrics to characterize the spatial patterns of cells.
View Article and Find Full Text PDFThe coronavirus disease of 2019 pandemic has catalyzed the rapid development of mRNA vaccines, whereas, how to optimize the mRNA sequence of exogenous gene such as severe acute respiratory syndrome coronavirus 2 spike to fit human cells remains a critical challenge. A new algorithm, iDRO (integrated deep-learning-based mRNA optimization), is developed to optimize multiple components of mRNA sequences based on given amino acid sequences of target protein. Considering the biological constraints, we divided iDRO into two steps: open reading frame (ORF) optimization and 5' untranslated region (UTR) and 3'UTR generation.
View Article and Find Full Text PDFNucleic Acids Res
January 2023
In recent years, the explosive growth of spatial technologies has enabled the characterization of spatial heterogeneity of tissue architectures. Compared to traditional sequencing, spatial transcriptomics reserves the spatial information of each captured location and provides novel insights into diverse spatially related biological contexts. Even though two spatial transcriptomics databases exist, they provide limited analytical information.
View Article and Find Full Text PDFA Gram-negative, aerobic, nonmotile, rod-shaped and yellow-pigment-producing bacteria was isolated from Baima snow mountain of Diqing Tibetan Autonomous Prefecture in Yunnan province, south-west China and characterized using a polyphasic approach. The results of 16S rRNA gene sequence similarity analysis showed that strain YIM B04101 was closely related to the type strain of Dyadobacter koreensis DSM 19938 (97.81%) and Dyadobacter frigoris AR-3-8 (97.
View Article and Find Full Text PDFA novel moderately halophilic, Gram-stain-negative, catalase- and oxidase-positive, strictly aerobic, non-sporulating, non-motile rod, designated strain JSM 104105, was isolated from human faeces. Strain JSM 104105 was able to grow with 0.5-18% (w/v) NaCl (optimum 4-9%), at pH 6-10.
View Article and Find Full Text PDFA novel Gram-stain-positive, aerobic, cocci-shaped actinobacterium, designated YIM 75000, was isolated from a soil sample collected from a dry-hot river valley in Yunnan Province, P.R. China.
View Article and Find Full Text PDFA novel bacterium, XHU 5135, belonging to the genus , was isolated from a salt lake sample collected in Xinjiang Province, north-west PR China. The isolate was Gram-stain-negative, rod-shaped and non-motile. The strain was catalase-positive and oxidase-negative.
View Article and Find Full Text PDFInt J Syst Evol Microbiol
July 2019
A Gram-positive, aerobic, non-motile actinobacterium, designated YIM 75507, that was isolated from a soil sample collected from a dry-hot valley, was subjected to a polyphasic taxonomic study. The isolate formed branched hyphae and no fragmentation was found. Clustered spore chains were borne from aerial mycelium.
View Article and Find Full Text PDFInt J Syst Evol Microbiol
February 2019
A novel halophilic actinobacterial strain, designated YIM 96934, was isolated from a soil sample collected from the edge of a saline lake in Xinjiang, north-west China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were aerobic and Gram-stain-positive.
View Article and Find Full Text PDF