High throughput sequencing

Invertebrates constitute the majority of animal species on Earth, including most disease-causing agents or vectors, with more diverse viromes when compared to vertebrates. Recent advancements in high-throughput sequencing have significantly expanded our understanding of invertebrate viruses, yet this knowledge remains biased toward a few well-studied animal lineages. In this study, we analyze invertebrate DNA and RNA viromes for 31 phyla using 417 publicly available RNA-Seq data sets from diverse environments in the marine-terrestrial and marine-freshwater gradients...

Immunoglobulin is an essential component of the body's defense against pathogens, aiding in the recognition and clearance of foreign antigens. Research concerning immunoglobulin gene and its diversity of expression across different breeds within the same species is relatively scarce. In this study, we employed RACE (Rapid Amplification of cDNA Ends) technology, prepared DNA libraries, performed high-throughput sequencing, and conducted related bioinformatics analysis to analyze the differences in immunoglobulin gene diversity and expression at different periods in Hy-line brown hens, Lueyang black-bone chickens, and Beijing-You chickens...

Given the dense population on university campuses, indoor and outdoor airborne bacterial contamination may lead to the rapid spread of diseases in a university environment. However, there are few studies of the characteristics of airborne and pathogenic bacterial communities in different sites on a university campus. In this study, we collected particulate matter samples from indoor and outdoor locations at a university in Bengbu City, Anhui Province, China, and analyzed the community characteristics of airborne and pathogenic bacteria using a high-throughput sequencing technique...

Global climate change has altered the frequency of soil freeze-thaw cycles, but the response of soil microorganisms to different elevation gradients during the early freeze-thaw period remains unclear. So far, the influence of the altitudinal gradient on the microbial community and metabolic characteristics in the early freeze-thaw period of the Qinghai Lake Basin remains unclear. To this end, we collected soil at different elevations in the early freeze-thaw period of the Qinghai Lake Basin and investigated the influence of the elevation gradient on soil microbial community characteristics and soil metabolic processes as well as the corresponding environmental driving mechanism by high-throughput sequencing and LC-MS (Liquid Chromatograph-Mass Spectrometer) nontargeted metabolite determination...

Kinetoplastid pathogens including Trypanosoma brucei , T. cruzi , and Leishmania species, are early diverged, eukaryotic, unicellular parasites. Functional understanding of many proteins from these pathogens has been hampered by limited sequence homology to proteins from other model organisms. Here we describe the development of a high-throughput deep mutational scanning approach in T. brucei that facilitates rapid and unbiased assessment of the impacts of many possible amino acid substitutions within a protein on cell fitness, as measured by relative cell growth...

The microbiota, also referred to as the microbial community, is a crucial component of the human microenvironment. It is located predominantly in various organs, including the intestines, skin, oral cavity, respiratory tract, and reproductive tract. The microbiota maintains a symbiotic relationship with the human body, influencing physiological and pathological functions to a significant degree. There is increasing evidence linking the microbial flora to human cancers. In contrast to the traditional belief that the urethra and urine of normal individuals are sterile, recent advancements in high-throughput sequencing technology and bacterial cultivation methods have led to the discovery of specific microbial communities in the urethras of healthy individuals...

Human leukocyte antigen (HLA) genes play pivotal roles in numerous immunological applications. Given the immense number of polymorphisms, achieving accurate high-throughput HLA typing remains challenging. This study aimed to harness the human pan-genome reference consortium (HPRC) resources as a potential benchmark for HLA reference materials. We meticulously annotated specific four field-resolution alleles for 11 HLA genes (HLA -A , -B , -C , -DPA1 , -DPB1 , -DQA1 , -DQB1 , -DRB1 , -DRB3 , -DRB4 and -DRB5 ) from 44 high-quality HPRC personal genome assemblies...

This study utilized high-throughput sequencing and SEM observation to elucidate the microbial composition of a Tibetan herder's homemade kefir grain named TKG-Y. Subsequently, S. warneri KYS-164 was isolated from TKG-Y, which can produce mixed protein substances with antibacterial activity, namely bacteriocin-like inhibitory substances (BLIS). BLIS can significantly reduce the growth rate of Escherichia coli 366-a, Staphylococcus aureus CICC 10384 and mixed strains at low concentrations (1 × MIC). The presence of the warnericin-centered gene cluster in KYS-164 may explain the antibacterial properties of the BLIS...

Wide variation in amenability to transformation and regeneration (TR) among many plant species and genotypes presents a challenge to the use of genetic engineering in research and breeding. To help understand the causes of this variation, we performed association mapping and network analysis using a population of 1204 wild trees of Populus trichocarpa (black cottonwood). To enable precise and high-throughput phenotyping of callus and shoot TR, we developed a computer vision system that cross-referenced complementary red, green, and blue (RGB) and fluorescent-hyperspectral images...

The molecular basis of orchid flower development involves a specific regulatory program in which MADS-box transcription factors play a central role. The recent 'perianth code' model hypothesizes that two types of higher-order heterotetrameric complexes, namely SP complex and L complex, play pivotal roles in the orchid perianth organ formation. Therefore, we explored their roles and searched for other components of the regulatory network.Through the combined analysis for transposase-accessible chromatin with high-throughput sequencing and RNA sequencing of the lip-like petal and lip from Phalaenopsis equestris var...

Cat scratch disease (CSD) is caused by Bartonella henselae (B. henselae) and presents as lymphadenopathy following close contact with cats. However, in context of the global COVID-19 pandemic, clinical manifestations of CSD may vary, posing new challenges for healthcare professionals. Here we describe a case of a 54-year-old male with painful left upper arm mass, which gradually resolved until he was infected with COVID-19. The mass then rapidly progressed before admission. Meanwhile, pulmonary symptoms including pleural effusion emerged simultaneously...

To obtain a multifunctional bacterium that can effectively degrade polyethylene (PE) and sulfonamide antibiotics (SAs), PE and SAs were selected as the primary research objects. Multifunctional degrading bacteria were isolated and screened from an environment in which plastics and antibiotics have existed for a long time. An efficient degrading strain, Raoultella sp., was screened by measuring the degradation performance of PE and SAs. We analyzed the changes in the microbial community of indigenous bacteria using 16S rRNA...

It is a great challenge to restore northern mines after mining and achieve optimal results due to the extremely harsh environment and climate, as in Qinghe County of Xinjiang Province, China. Qinghe County has a climate of drought, cold, strong winds, and high altitude. After sand and iron mining, the soil in this area contains a large amount of sand and gravel with extremely low organic matter, nitrogen deficiency, and a high pH of 9.26. Our preliminary studies disclosed that only three plants, including Caligonum junceum, Atraphaxis virgata, and Melilotus albus Medic, can grow naturally in this environment without any artificial management...

The escalating crisis of antimicrobial resistance (AMR) underscores the urgent need for novel antimicrobials. One promising strategy is the exploration of structural diversity, as diverse structures can lead to diverse biological activities and mechanisms of action. This review delves into the role of structural diversity in antimicrobial discovery, highlighting its influence on factors such as target selectivity, binding affinity, pharmacokinetic properties, and the ability to overcome resistance mechanisms...

Understanding the microbial community structure in soil contaminated with heavy metals (HMs) is a precondition to conduct bioremediation in mine soil. Samples were collected from a typical lead-zinc (Pb-Zn) mine to assess the microbial community structure of the HMs concentrated in the soil. The goal was to analyze the bacterial and fungal community structures and their interactions using the 16S rRNA genes and internal transcribed spacer high-throughput sequencing. Analyses at different sampling sites showed that contamination with HMs significantly reduced the bacterial richness and diversity but increased that of the fungi...

Acute ischemic stroke (AIS), commonly known as stroke, is a debilitating condition characterized by the interruption of blood flow to the brain, resulting in tissue damage and neurological deficits. Early diagnosis is crucial for effective intervention and management, as timely treatment can significantly improve patient outcomes. Therefore, novel methods for the early diagnosis of AIS are urgently needed. Several studies have shown that bioactive molecules contained in extracellular vesicles, especially circRNAs, could be ideal markers for the diagnosis of many diseases...

Decay of mRNAs can be triggered by ribosome slowdown at stretches of rare codons or positively charged amino acids. However, the full diversity of sequences that trigger co-translational mRNA decay is poorly understood. To comprehensively identify sequence motifs that trigger mRNA decay, we use a massively parallel reporter assay to measure the effect of all possible combinations of codon pairs on mRNA levels in S. cerevisiae. In addition to known mRNA-destabilizing sequences, we identify several dipeptide repeats whose translation reduces mRNA levels...

Esophageal cancer (EC) is a common form of malignant tumor in the digestive system that is classified into two types: Esophageal squamous cell carcinomas (ESCC) and esophageal adenocarcinoma. ESCC is known for its early onset of symptoms, which can be difficult to identify, as well as its rapid progression and tendency to develop drug resistance to chemotherapy and radiotherapy. These factors contribute to the high incidence of disease and low cure rate. Therefore, a diagnostic biomarker and therapeutic target need to be identified for ESCC...

OBJECTIVES: The protective effects and related mechanisms of Jing-Si herbal tea (JSHT) were investigated in cellular damage mediated by pro-inflammatory cytokines, including interleukin (IL)-1β, IL-6, and tumor necrosis factor-α, on normal human lung fibroblast by multiomic platform analysis. MATERIALS AND METHODS: The in silico high-throughput target was analyzed using pharmacophore models by BIOVIA Discovery Studio 2022 with ingenuity pathway analysis software...

Single-cell genomics has revolutionized tissue analysis by revealing the genetic program of individual cells. The key aspect of the technology is the use of barcoded beads to unambiguously tag sequences originating from a single cell. The generation of unique barcodes on beads is mainly achieved by split-pooling methods, which are labor-intensive due to repeated washing steps. Towards the automation of the split-pooling method, we developed a simple method to magnetize hydrogel beads. We show that these hydrogel beads provide increased yields and washing efficiencies for purification procedures...