10,385 results match your criteria time illumina


Soil fungal community structure and seasonal diversity following application of organic amendments of different quality under maize cropping in Zimbabwe.

PLoS One 2021 14;16(10):e0258227. Epub 2021 Oct 14.

Department of Soil Science & Environment, University of Zimbabwe, Mount Pleasant, Harare, Zimbabwe.

Recent advocacy for Integrated Soil Fertility Management (ISFM) in smallholder farming systems in east and southern Africa show substantial evidence of increased and sustained crop yields associated with enhanced soil productivity. However, the impact ISFM on soil fungi has received limited attention, yet fungi play key roles in crop growth. Following total soil DNA extraction with ZR soil microbe miniprep kit, illumina sequencing was used to, examine the fungal communities (ITS1F) under a maize crop following co-application of organic nutrient resources including Crotalaria juncea, cattle manure and maize stover with inorganic fertilizers at three-time periods (T1-December, T2-January, and T3-February) in Zimbabwe. Read More

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October 2021

The intestinal flora of patients with GHPA affects the growth and the expression of PD-L1 of tumor.

Cancer Immunol Immunother 2021 Oct 13. Epub 2021 Oct 13.

Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.

Context: Pituitary adenoma (PA) is a common intracranial tumor. The evidence indicates that the tumor immune microenvironment (TIME) is associated with PA and that the intestinal flora influences other tumors' growth through interacting with the TIME. However, how the intestinal microbial flora contributes to the development of PA through the immune response is unknown. Read More

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October 2021

Comparative genomic characterization of multidrug-resistant Citrobacter spp. strains in Fennec fox imported to China.

Gut Pathog 2021 Oct 13;13(1):59. Epub 2021 Oct 13.

Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.

Background: To investigate the antimicrobial profiles and genomic characteristics of MDR-Citrobacter spp. strains isolated from Fennec fox imported from Sudan to China.

Methods: Four Citrobacter spp. Read More

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October 2021

Long-read sequencing reveals the structural complexity of genomic integration of HBV DNA in hepatocellular carcinoma.

NPJ Genom Med 2021 Oct 12;6(1):84. Epub 2021 Oct 12.

Peking University Fifth School of Clinical Medicine, Beijing, China.

The integration of HBV DNA into the human genome can disrupt its structure in hepatocellular carcinoma (HCC), but the complexity of HBV genomic integration remains elusive. Here we applied long-read sequencing to precisely elucidate the HBV integration pattern in the human hepatocellular genome. The DNA library was sequenced using the long-read sequencing on GridION and PacBio Sequel II, respectively. Read More

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October 2021

Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs.

BMC Genomics 2021 Oct 12;22(1):736. Epub 2021 Oct 12.

National Engineering Laboratory for Animal Breeding, Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, China Agricultural University, Beijing, China.

Background: Reference sequences play a vital role in next-generation sequencing (NGS), impacting mapping quality during genome analyses. However, reference genomes usually do not represent the full range of genetic diversity of a species as a result of geographical divergence and independent demographic events of different populations. For the mitochondrial genome (mitogenome), which occurs in high copy numbers in cells and is strictly maternally inherited, an optimal reference sequence has the potential to make mitogenome alignment both more accurate and more efficient. Read More

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October 2021

Concatenation of paired-end reads improves taxonomic classification of amplicons for profiling microbial communities.

BMC Bioinformatics 2021 Oct 12;22(1):493. Epub 2021 Oct 12.

Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, USA.

Background: Taxonomic classification of genetic markers for microbiome analysis is affected by the numerous choices made from sample preparation to bioinformatics analysis. Paired-end read merging is routinely used to capture the entire amplicon sequence when the read ends overlap. However, the exclusion of unmerged reads from further analysis can result in underestimating the diversity in the sequenced microbial community and is influenced by bioinformatic processes such as read trimming and the choice of reference database. Read More

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October 2021

Draft genome of Semisulcospira libertina, a species of freshwater snail.

Genomics Inform 2021 Sep 30;19(3):e32. Epub 2021 Sep 30.

Department of Orthopaedic Surgery, Gyeongsang National University Hospital, Jinju 52727, Korea.

Semisulcospira libertina, a species of freshwater snail, is widespread in East Asia. It is important as a food source. Additionally, it is a vector of clonorchiasis, paragonimiasis, metagonimiasis, and other parasites. Read More

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September 2021

Data on RNA-seq analysis of Drosophila melanogaster during ageing.

Data Brief 2021 Oct 22;38:107413. Epub 2021 Sep 22.

USM-RIKEN Interdisciplinary Collaboration for Advanced Sciences, Universiti Sains Malaysia, Gelugor, Penang 11800, Malaysia.

Ageing is defined as gradual decline of physiological, cellular and molecular state of an organism with time. The age-associated cell dysfunctions usually cause chronic diseases such as diabetes, cancers and other age-related diseases. Many of the genes and pathways involved in ageing are conserved in different species. Read More

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October 2021

Moderate-Intensity Physical Exercise Affects the Exercise Performance and Gut Microbiota of Mice.

Front Cell Infect Microbiol 2021 24;11:712381. Epub 2021 Sep 24.

School of Physical Education and Sports Science, South China Normal University, Guangzhou, China.

The gut microbiota is closely associated with the health of the host and is affected by many factors, including exercise. In this study, we compared the gut microbial changes and exercise performance over a 14-week period in mice that performed exercise (NE; n = 15) and mice that did not perform exercise (NC; n = 15). Mice were subjected to stool collection and exercise tests one week prior to adaptive training and after 2, 6, 10, and 14 weeks of exercise. Read More

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September 2021

Targeted Next-Generation Sequencing of Cancer-Related Genes in a Norwegian Patient Cohort With Head and Neck Squamous Cell Carcinoma Reveals Novel Actionable Mutations and Correlations With Pathological Parameters.

Front Oncol 2021 24;11:734134. Epub 2021 Sep 24.

Department of Pathology, Haukeland University Hospital, Bergen, Norway.

Background: Targeted next-generation sequencing (NGS) is increasingly applied in clinical oncology to advance personalized treatment. Despite success in many other tumour types, use of targeted NGS panels for assisting diagnosis and treatment of head and neck squamous cell carcinomas (HNSCC) is still limited.

Aim: The focus of this study was to establish a robust NGS panel targeting most frequent cancer mutations in long-term preserved formalin-fixed paraffin-embedded (FFPE) tissue samples of HNSCC from routine diagnostics. Read More

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September 2021

Combined nanopore adaptive sequencing and enzyme-based host depletion efficiently enriched microbial sequences and identified missing respiratory pathogens.

BMC Genomics 2021 Oct 9;22(1):732. Epub 2021 Oct 9.

Center for Molecular Medicine, Pediatric Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.

Background: Enzyme-based host depletion significantly improves the sensitivity of clinical metagenomics. Recent studies found that real-time adaptive sequencing of DNA molecules was achieved using a nanopore sequencing machine, which enabled effective enrichment of microbial sequences. However, few studies have compared the enzyme-based host depletion and nanopore adaptive sequencing for microbial enrichment efficiency. Read More

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October 2021

Characterization of the early gene expression profile in Populus ussuriensis under cold stress using PacBio SMRT sequencing integrated with RNA-seq reads.

Tree Physiol 2021 Oct 9. Epub 2021 Oct 9.

State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.

Populus ussuriensis is an important and fast-growing afforestation plant species in north-eastern China. The whole-genome sequencing of P. ussuriensis has not been completed. Read More

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October 2021

Hallmarks of response, resistance, and toxicity to immune checkpoint blockade.

Cell 2021 Oct 7;184(21):5309-5337. Epub 2021 Oct 7.

Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address:

Unprecedented advances have been made in cancer treatment with the use of immune checkpoint blockade (ICB). However, responses are limited to a subset of patients, and immune-related adverse events (irAEs) can be problematic, requiring treatment discontinuation. Iterative insights into factors intrinsic and extrinsic to the host that impact ICB response and toxicity are critically needed. Read More

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October 2021

Classification of Estrogen Receptor-Positive Breast Cancer Based on Immunogenomic Profiling and Validation at Single-Cell Resolution.

Front Cell Dev Biol 2021 21;9:722841. Epub 2021 Sep 21.

Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

The aim of this paper was to identify an immunotherapy-sensitive subtype for estrogen receptor-positive breast cancer (ER+ BC) patients by exploring the relationship between cancer genetic programs and antitumor immunity via multidimensional genome-scale analyses. Multidimensional ER+ BC high-throughput data (raw count data) including gene expression profiles, copy number variation (CNV) data, single-nucleotide polymorphism mutation data, and relevant clinical information were downloaded from The Cancer Genome Atlas to explore an immune subtype sensitive to immunotherapy using the Consensus Cluster Plus algorithm based on multidimensional genome-scale analyses. One ArrayExpress dataset and eight Gene Expression Omnibus (GEO) datasets (GEO-meta dataset) as well as the Molecular Taxonomy of Breast Cancer International Consortium dataset were used as validation sets to confirm the findings regarding the immune profiles, mutational features, and survival outcomes of the three identified immune subtypes. Read More

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September 2021

SARS-CoV-2 whole-genome sequencing using reverse complement PCR: For easy, fast and accurate outbreak and variant analysis.

J Clin Virol 2021 Oct 2;144:104993. Epub 2021 Oct 2.

Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud university medical center, Nijmegen, The Netherlands.

During the course of the SARS-CoV-2 pandemic reports of mutations with effects on spreading and vaccine effectiveness emerged. Large scale mutation analysis using rapid SARS-CoV-2 Whole Genome Sequencing (WGS) is often unavailable but could support public health organizations and hospitals in monitoring transmission and rising levels of mutant strains. Here we report a novel WGS technique for SARS-CoV-2, the EasySeq™ RC-PCR SARS-CoV-2 WGS kit. Read More

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October 2021

Surveillance of : Early detection, population dynamics and quasimetagenomic sequencing during selective enrichment.

Appl Environ Microbiol 2021 Oct 6:AEM0177421. Epub 2021 Oct 6.

Nofima - Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway.

In this study we addressed different aspects regarding the implementation of quasimetagenomic sequencing as a hybrid surveillance method in combination with enrichment for early detection of in the food industry. Different experimental enrichment cultures were used, comprising seven strains of different sequence types (STs), with and without a background microbiota community. To assess whether the proportions of the different STs changed over time during enrichment, the growth and population dynamics were assessed using colony sequencing and and 16S rRNA amplicon sequencing. Read More

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October 2021

Rapid and High-Throughput Reverse Transcriptase Quantitative PCR (RT-qPCR) Assay for Identification and Differentiation between SARS-CoV-2 Variants B.1.1.7 and B.1.351.

Microbiol Spectr 2021 Oct 6:e0050621. Epub 2021 Oct 6.

Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel.

Emerging SARS-CoV-2 (SC-2) variants with increased infectivity and vaccine resistance are of major concern. Rapid identification of such variants is important for the public health decision making and to provide valuable data for epidemiological and policy decision making. We developed a multiplex reverse transcriptase quantitative PCR (RT-qPCR) assay that can specifically identify and differentiate between the emerging B. Read More

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October 2021

WNT3 hypomethylation counteracts low activity of the Wnt signaling pathway in the placenta of preeclampsia.

Cell Mol Life Sci 2021 Oct 4. Epub 2021 Oct 4.

Department of Laboratory Medicine, Third Affiliated Hospital of Zhengzhou University, 7 Kangfu Qian Street, Zhengzhou, 450052, Henan, People's Republic of China.

Preeclampsia is a hypertensive disorder of pregnancy. Many studies have shown that epigenetic mechanisms may play a role in preeclampsia. Moreover, our previous study indicated that the differentially methylated genes in preeclampsia were enriched in the Wnt/β-catenin signaling pathway. Read More

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October 2021

Barrett's Epithelium to Esophageal Adenocarcinoma: Is There a "Point of No Return"?

Front Genet 2021 17;12:706706. Epub 2021 Sep 17.

Department of Gastroenterology and Hepatology, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States.

Esophageal adenocarcinoma (EA) arises from Barrett's epithelium (BE), and chronic gastroesophageal reflux disease is considered the strongest risk factor for disease progression. All BE patients undergo acid suppressive therapy, surveillance, and BE removal by surgery or endoscopic ablation, yet the incidence of EAC continues to increase. Despite the known side effects and mortality, the one-size-fits-all approach is the standard clinical management as there are no reliable methods for risk stratification. Read More

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September 2021

Transcriptome analysis reveals important candidate gene families related to oligosaccharides biosynthesis in Morindaofficinalis.

Plant Physiol Biochem 2021 Oct 28;167:1061-1071. Epub 2021 Sep 28.

School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China. Electronic address:

Morinda officinalis How (MO) is one of the best-known traditional herbs and is widely cultivated in subtropical and tropical areas for many years, especially in southern China. Oligosaccharides are the major constituents in the roots of MO, which is well known for its therapeutic effects with anti-depression, anti-osteoporosis, memory-enhancing, ect. To date, the main gene families that regulate the biosynthetic pathway of MO oligosaccharides metabolism yet have been published. Read More

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October 2021

Performance of a scalable RNA extraction-free transcriptome profiling method for adherent cultured human cells.

Sci Rep 2021 Sep 30;11(1):19438. Epub 2021 Sep 30.

Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA.

RNA sequencing enables high-content/high-complexity measurements in small molecule screens. Whereas the costs of DNA sequencing and RNA-seq library preparation have decreased consistently, RNA extraction remains a significant bottleneck to scalability. We evaluate the performance of a bulk RNA-seq library prep protocol optimized for analysis of many samples of adherent cultured cells in parallel. Read More

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September 2021

Multicenter Analysis of Genomically Targeted Single Patient Use Requests for Pediatric Neoplasms.

J Clin Oncol 2021 Sep 30:JCO2101213. Epub 2021 Sep 30.

Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY.

Purpose: The US Food and Drug Administration-expanded access program (EAP) uses a single patient use (SPU) mechanism to provide patient access to investigational agents in situations where no satisfactory or comparable therapy is available. Genomic profiling of de novo and relapsed or refractory childhood cancer has led to increased identification of new drug targets in the last decade. The aim of this study is to examine the SPU experience for genomically targeted therapies in patients with pediatric cancer. Read More

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September 2021

The first case of Planococcus glaciei found in blood, a report from the Czech Republic.

Folia Microbiol (Praha) 2021 Sep 30. Epub 2021 Sep 30.

Czech National Collection of Type Cultures, National Institute of Public Health, Prague, Czech Republic.

The isolation of Planococcus glaciei (designed strain CNCTC 7660) from blood of a patient with appendicitis is reported. Species P. glaciei (type strain CGMCC 1. Read More

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September 2021

ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone.

BMC Biol 2021 09 29;19(1):217. Epub 2021 Sep 29.

Department of Biological Sciences, National University of Singapore, Singapore, Singapore.

Background: DNA barcodes are a useful tool for discovering, understanding, and monitoring biodiversity which are critical tasks at a time of rapid biodiversity loss. However, widespread adoption of barcodes requires cost-effective and simple barcoding methods. We here present a workflow that satisfies these conditions. Read More

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September 2021

rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects.

BMC Bioinformatics 2021 Sep 28;22(1):468. Epub 2021 Sep 28.

Department of Biomedical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium.

Background: The advent of population-scale genome projects has revolutionized our biological understanding of parasitic protozoa. However, while hundreds to thousands of nuclear genomes of parasitic protozoa have been generated and analyzed, information about the diversity, structure and evolution of their mitochondrial genomes remains fragmentary, mainly because of their extraordinary complexity. Indeed, unicellular flagellates of the order Kinetoplastida contain structurally the most complex mitochondrial genome of all eukaryotes, organized as a giant network of homogeneous maxicircles and heterogeneous minicircles. Read More

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September 2021

Diversity of endophytic bacteria in wild rice (Oryza meridionalis) and potential for promoting plant growth and degrading phthalates.

Sci Total Environ 2021 Sep 14;806(Pt 1):150310. Epub 2021 Sep 14.

Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China. Electronic address:

Phthalates (PAEs) accumulated in agricultural soils and rice have increased human exposure risks. Microbial degradation could efficiently reduce the residue of organic pollutants in soil and crop plants. Here, we hypothesized that endophytic bacteria from wild rice have the potential for degradation of PAEs and plant growth promoting. Read More

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September 2021

Evaluating for Disparities in Prenatal Genetic Counseling.

Am J Obstet Gynecol MFM 2021 Sep 25:100494. Epub 2021 Sep 25.

Department of Obstetrics and Gynecology, University of Colorado School of Medicine, 12631 E 17(th) Avenue, Aurora, Colorado 80045.

Introduction: Guidelines recommend that all pregnant women should be offered prenatal genetic counseling (PGC) which includes discussions of aneuploidy and carrier screening. Previous studies have demonstrated racial and ethnic disparities in completion of prenatal genetic testing, but few studies have evaluated for disparities in the offering of these tests. Prenatal genetic screening is a covered provision of Colorado Medicaid. Read More

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September 2021

Full-length transcriptome analysis and identification of transcript structures in Eimeria necatrix from different developmental stages by single-molecule real-time sequencing.

Parasit Vectors 2021 Sep 27;14(1):502. Epub 2021 Sep 27.

College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.

Background: Eimeria necatrix is one of the most pathogenic parasites, causing high mortality in chickens. Although its genome sequence has been published, the sequences and complete structures of its mRNA transcripts remain unclear, limiting exploration of novel biomarkers, drug targets and genetic functions in E. necatrix. Read More

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September 2021

Transcriptome analysis of heterogeneity in mouse model of metastatic breast cancer.

Breast Cancer Res 2021 09 27;23(1):93. Epub 2021 Sep 27.

Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, 92697, USA.

Background: Cancer metastasis is a complex process involving the spread of malignant cells from a primary tumor to distal organs. Understanding this cascade at a mechanistic level could provide critical new insights into the disease and potentially reveal new avenues for treatment. Transcriptome profiling of spontaneous cancer models is an attractive method to examine the dynamic changes accompanying tumor cell spread. Read More

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September 2021