9,329 results match your criteria inferred dna

Hydrologic and nutrient-driven regime shifts of cyanobacterial and eukaryotic algal communities in a large shallow lake: Evidence from empirical state indicator and ecological network analyses.

Sci Total Environ 2021 Apr 12;783:147059. Epub 2021 Apr 12.

State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.

The detection and prediction of lake ecosystem responses to environmental changes are pressing scientific challenge of major global relevance. Specifically, an understanding of lake ecosystem stability over long-term scales is urgently needed to identify impending ecosystem regime shifts induced by human activities and improve lake ecosystem protection. This study investigated regime shifts in cyanobacterial and eukaryotic algal communities in a large shallow lake over a century in response to nutrient enrichment and hydrologic regulation using evidence from empirical state indicators and ecological network analyses of sedimentary-inferred communities. Read More

View Article and Full-Text PDF

Long-term storage of feces at -80 °C versus -20 °C is negligible for 16S rRNA amplicon profiling of the equine bacterial microbiome.

PeerJ 2021 9;9:e10837. Epub 2021 Mar 9.

Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada.

The development of next-generation sequencing technologies has spurred a surge of research on bacterial microbiome diversity and function. But despite the rapid growth of the field, many uncertainties remain regarding the impact of differing methodologies on downstream results. Sample storage temperature is conventionally thought to be among the most important factors for ensuring reproducibility across marker gene studies, but to date much of the research on this topic has focused on short-term storage in the context of clinical applications. Read More

View Article and Full-Text PDF

Following Trypanosoma cruzi RPA-DNA Interaction Using Fluorescent In Situ Hybridization Coupled with Immunofluorescence (FISH/IF).

Methods Mol Biol 2021 ;2281:209-215

Laboratório de Ciclo Celular and Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, SP, Brazil.

Fluorescent in situ hybridization coupled with immunofluorescence (FISH/IF) is an assay that has been widely used to study DNA-protein interactions. The technique is based on the use of a fluorescent nucleic acid probe and fluorescent antibodies to reveal the localization of a DNA sequence and a specific protein in the cell. The interaction can be inferred by the quantification of the co-localization between the protein and the DNA. Read More

View Article and Full-Text PDF
January 2021

Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators.

Nat Plants 2021 Apr 12. Epub 2021 Apr 12.

Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.

Gene regulation is a dynamic process in which transcription factors (TFs) play an important role in controlling spatiotemporal gene expression. To enhance our global understanding of regulatory interactions in Arabidopsis thaliana, different regulatory input networks capturing complementary information about DNA motifs, open chromatin, TF-binding and expression-based regulatory interactions were combined using a supervised learning approach, resulting in an integrated gene regulatory network (iGRN) covering 1,491 TFs and 31,393 target genes (1.7 million interactions). Read More

View Article and Full-Text PDF

Exploring a Region on Chromosome 8p23.1 Displaying Positive Selection Signals in Brazilian Admixed Populations: Additional Insights Into Predisposition to Obesity and Related Disorders.

Front Genet 2021 25;12:636542. Epub 2021 Mar 25.

Department of Medical Genetics and Genomic Medicine, Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), University of Campinas - UNICAMP, Campinas, Brazil.

We recently reported a deviation of local ancestry on the chromosome (ch) 8p23.1, which led to positive selection signals in a Brazilian population sample. The deviation suggested that the genetic variability of candidate genes located on ch 8p23. Read More

View Article and Full-Text PDF

Morphological and molecular characterization of n. sp. (Nematoda: Heteroderidae) from Gran Canaria, Canary Islands.

J Nematol 2020 24;52. Epub 2020 Nov 24.

Nematology Research Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.

n. sp. from the coastal dunes of Gran Canaria, Canary Islands, is described. Read More

View Article and Full-Text PDF
November 2020

An order independent algorithm for inferring gene regulatory network using quantile value for conditional independence tests.

Sci Rep 2021 Apr 7;11(1):7605. Epub 2021 Apr 7.

Department of Computer and Data Sciences, Faculty of Mathematical Sciences, Shahid Beheshti University, Tehran, Iran.

In recent years, due to the difficulty and inefficiency of experimental methods, numerous computational methods have been introduced for inferring the structure of Gene Regulatory Networks (GRNs). The Path Consistency (PC) algorithm is one of the popular methods to infer the structure of GRNs. However, this group of methods still has limitations and there is a potential for improvements in this field. Read More

View Article and Full-Text PDF

Migration through a major Andean ecogeographic disruption as a driver of genetic and phenotypic diversity in a wild tomato species.

Mol Biol Evol 2021 Apr 3. Epub 2021 Apr 3.

Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA.

Evolutionary dynamics at the population level play a central role in creating the diversity of life on our planet. In this study, we sought to understand the origins of such population-level variation in mating systems and defensive acylsugar chemistry in Solanum habrochaites-a wild tomato species found in diverse Andean habitats in Ecuador and Peru. Using Restriction-site-Associated-DNA-Sequencing (RAD-seq) of 50 S. Read More

View Article and Full-Text PDF

Genetic structure of the endangered Irrawaddy dolphin (Orcaella brevirostris) in the Gulf of Thailand.

Genet Mol Biol 2021 2;44(2):e20200365. Epub 2021 Apr 2.

Third Institute of Oceanography, Ministry of Natural Resources, Laboratory of Marine Biology and Ecology, Xiamen, China.

The Irrawaddy dolphin (Orcaella brevirostris) is an endangered, small cetacean species which is widely distributed in rivers, estuaries, and coastal waters throughout the tropical and subtropical Indo-Pacific. Despite the extensive distribution of this species, little is known of individual movements or genetic exchange among regions in Thailand. Here, we evaluate the genetic diversity and genetic structure of O. Read More

View Article and Full-Text PDF

An Information Theoretical Multilayer Network Approach to Breast Cancer Transcriptional Regulation.

Front Genet 2021 18;12:617512. Epub 2021 Mar 18.

Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.

Breast cancer is a complex, highly heterogeneous disease at multiple levels ranging from its genetic origins and molecular processes to clinical manifestations. This heterogeneity has given rise to the so-called intrinsic or molecular breast cancer subtypes. Aside from classification, these subtypes have set a basis for differential prognosis and treatment. Read More

View Article and Full-Text PDF

Inference of DNA methylation patterns in molluscs.

Philos Trans R Soc Lond B Biol Sci 2021 May 5;376(1825):20200166. Epub 2021 Apr 5.

LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany.

Mollusca are the second largest and arguably most diverse phylum of the animal kingdom. This is in sharp contrast to our very limited knowledge concerning epigenetic mechanisms including DNA methylation in this invertebrate group. Here, we inferred DNA methylation patterns by analysing the normalized dinucleotide CG content in protein-coding sequences and identified DNA methyltransferases (DNMT1 and 3) in published transcriptomes and genomes of 140 species across all eight classes of molluscs. Read More

View Article and Full-Text PDF

Distribution of CRISPR Types in Fluoroquinolone-Resistant Isolates.

Pathogens 2021 Mar 16;10(3). Epub 2021 Mar 16.

Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA.

To aid development of phage therapy against , we investigated the distribution of the clustered regularly interspaced short palindromic repeats (CRISPR) systems in fluoroquinolone (FQ)-resistant . A total of 100 FQ-resistant strains from different sources were analyzed by PCR and DNA sequencing to determine resistance-conferring mutation in the gene and the presence of various CRISPR systems. All but one isolate harbored 1-5 point mutations in and the most common mutation was the Thr86Ile change. Read More

View Article and Full-Text PDF

Phylogeny, Global Biogeography and Pleomorphism of .

Microorganisms 2021 Mar 29;9(4). Epub 2021 Mar 29.

Westerdijk Fungal Biodiversity Institute, 3508 AD Utrecht, The Netherlands.

() is a neglected, phialidic dematiaceous hyphomycete with striking phenotypic heterogeneity among its species. Little is known about its global biogeography due to its extreme scarcity and lack of records verified by molecular data. Phylogenetic analyses of six nuclear loci, supported by phenotypic data, revealed as highly polyphyletic, with species distributed among three distantly related lineages in Sordariomycetes. Read More

View Article and Full-Text PDF

The Genome Stability Maintenance DNA Helicase DDX11 and Its Role in Cancer.

Genes (Basel) 2021 Mar 10;12(3). Epub 2021 Mar 10.

Istituto di Biochimica e Biologia Cellulare-CNR, Via P. Castellino, 111, 80131 Naples, Italy.

DDX11/ChlR1 is a super-family two iron-sulfur cluster containing DNA helicase with roles in DNA replication and sister chromatid cohesion establishment, and general chromosome architecture. Bi-allelic mutations of the DDX11 gene cause a rare hereditary disease, named Warsaw breakage syndrome, characterized by a complex spectrum of clinical manifestations (pre- and post-natal growth defects, microcephaly, intellectual disability, heart anomalies and sister chromatid cohesion loss at cellular level) in accordance with the multifaceted, not yet fully understood, physiological functions of this DNA helicase. In the last few years, a possible role of DDX11 in the onset and progression of many cancers is emerging. Read More

View Article and Full-Text PDF

Lake Ecosystem Robustness and Resilience Inferred from a Climate-Stressed Protistan Plankton Network.

Microorganisms 2021 Mar 6;9(3). Epub 2021 Mar 6.

Department of Ecology, University of Kaiserslautern, D-67633 Kaiserslautern, Germany.

Network analyses of biological communities allow for identifying potential consequences of climate change on the resilience of ecosystems and their robustness to resist stressors. Using DNA metabarcoding datasets from a three-year-sampling (73 samples), we constructed the protistan plankton co-occurrence network of Lake Zurich, a model lake ecosystem subjected to climate change. Despite several documentations of dramatic lake warming in Lake Zurich, our study provides an unprecedented perspective by linking changes in biotic association patterns to climate stress. Read More

View Article and Full-Text PDF

Mitochondrial genome characterization of (Orthoptera: Gryllidae) and its phylogenetic implications.

Mitochondrial DNA B Resour 2021 Mar 19;6(3):1056-1058. Epub 2021 Mar 19.

School of Preclinical Medicine, Wannan Medical College, Wuhu, China.

is a cricket widely distributed throughout the world. In this study, we reported the first complete mitogenome sequence of Genus and inferred its phylogeny. The mitogenome of was 16,369 bp and consisted of a control region and a typical set of 37 genes. Read More

View Article and Full-Text PDF

First report of the mitogenome of (Diptera, Tachinidae) from Beijing, China.

Mitochondrial DNA B Resour 2021 Mar 17;6(3):862-864. Epub 2021 Mar 17.

School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.

(Mesnil, 1967) (Diptera, Tachinidae) is a parasitic fly species and of great ecological importance in natural systems as parasitoids of herbivorous insects. The mitogenome of . was sequenced and analyzed here for the first time. Read More

View Article and Full-Text PDF

Effects of sheared chromatin length on ChIP-seq quality and sensitivity.

G3 (Bethesda) 2021 Mar 31. Epub 2021 Mar 31.

Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.

Chromatin immunoprecipitation followed by massively parallel, high throughput sequencing (ChIP-seq) is the method of choice for genome-wide identification of DNA segments bound by specific transcription factors or in chromatin with particular histone modifications. However, the quality of ChIP-seq datasets varies widely, with a substantial fraction being of intermediate to poor quality. Thus, it is important to discern and control the factors that contribute to variation in ChIP-seq. Read More

View Article and Full-Text PDF

Plastome phylogenomics of the East Asian endemic genus .

Plant Divers 2021 Feb 29;43(1):35-42. Epub 2020 May 29.

CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.

is a dioecious genus endemic to East Asia that consists of two extant species: and . Although the genus is morphologically distinct, its phylogenetic position remains controversial. In this study, we investigated the phylogenetic relationships between and related taxa by sequencing the whole plastome DNA sequences for both extant species of and comparing them to published plastomes within Sapindales. Read More

View Article and Full-Text PDF
February 2021

Molecular Evolution and Organization of Ribosomal DNA in the Hawkweed Tribe Hieraciinae (Cichorieae, Asteraceae).

Front Plant Sci 2021 12;12:647375. Epub 2021 Mar 12.

Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia.

Molecular evolution of ribosomal DNA can be highly dynamic. Hundreds to thousands of copies in the genome are subject to concerted evolution, which homogenizes sequence variants to different degrees. If well homogenized, sequences are suitable for phylogeny reconstruction; if not, sequence polymorphism has to be handled appropriately. Read More

View Article and Full-Text PDF

Class II HLA Variants Associate with Risk of Pegaspargase Hypersensitivity.

Clin Pharmacol Ther 2021 Mar 26. Epub 2021 Mar 26.

Departments of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis.

We conducted the first HLA allele and genome wide association study to identify loci associated with hypersensitivity reactions exclusively to the PEGylated preparation of asparaginase (pegaspargase) in racially diverse cohorts of pediatric leukemia patients: St. Jude Children's Research Hospital's Total XVI (TXVI, n = 598), Children's Oncology Group AALL0232 (n = 2472) and AALL0434 (n = 1189). Germline DNA was genotyped using arrays. Read More

View Article and Full-Text PDF

First Report of Moldy Core of Sweet Tango Apples from New Zealand Caused by Alternaria arborescens.

Plant Dis 2021 Mar 24. Epub 2021 Mar 24.

Agriculture and Agri-Food Canada, 4902 Victoria Avenue North, Vineland Station, ON L0R 2E0, Canada, Vineland, Ontario, Canada;

Moldy core is a fungal disease of apple fruits that is characterized by mycelial growth in the seed locules and is sometimes accompanied by penetration of the immediate surrounding flesh. The disease can go undetected until the fruit is cut open, as no external symptoms appear on the fruit. Alternaria, Aspergillus, Cladosporium, Coniothyrium, Epicoccum, Phoma and Stemphylium are some of the common pathogens associated with moldy core (Serdani et al. Read More

View Article and Full-Text PDF

Modeling Radiation-Induced Neoplastic Cell Transformation In Vitro and Tumor Induction In Vivo with the Local Effect Model.

Radiat Res 2021 Mar 24. Epub 2021 Mar 24.

GSI Helmholtz Centre for Heavy Ion Research, Department of Biophysics, Darmstadt, Germany.

Ionizing radiation induces DNA damage to cycling cells which, if left unrepaired or misrepaired, can cause cell inactivation or heritable, viable mutations. The latter can lead to cell transformation, which is thought to be an initial step of cancer formation. Consequently, the study of radiation-induced cell transformation promises to offer insights into the general properties of radiation carcinogenesis. Read More

View Article and Full-Text PDF

Polymorphisms of T- cell leukemia 1A gene loci are not related to the development of adjuvant letrozole-induced adverse events in breast cancer.

PLoS One 2021 24;16(3):e0247989. Epub 2021 Mar 24.

Department of Pharmacology, Centre for Advanced Research in Pharmacogenomics, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, India.

Letrozole, an aromatase inhibitor (AI), is the first-line adjuvant drug for treating hormone receptor-positive (HR+) breast cancer in postmenopausal women. However, harmful adverse events (AEs) and significant differences in drug response among individuals remain a significant problem in clinical application. Current evidence suggests that the observed individual variation in the treatment outcomes of AI is conferred by genetic variants. Read More

View Article and Full-Text PDF

Mitochondrial functional resilience after TFAM ablation in the adult heart.

Am J Physiol Cell Physiol 2021 Mar 24. Epub 2021 Mar 24.

Division of Pediatric Cardiology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA (N.G., J.N.P. J.Q.K.), United States.

The nuclear genome-encoded mitochondrial DNA (mtDNA) transcription factor A (TFAM) is indispensable for mitochondrial energy production in the developing and postnatal heart; a similar role for TFAM is inferred in adult heart. Here, we provide evidence that challenges this long-standing paradigm. Unexpectedly, conditionalTfam ablation in vivo in adult mouse cardiomyocytes resulted in a prolonged period of functional resilience characterized by preserved mtDNA content, mitochondrial function, and cardiac function, despite mitochondrial structural alterations and decreased transcript abundance. Read More

View Article and Full-Text PDF

Molecular evidence for deeper diversity in Australian Tanypodinae (Chironomidae): Yarrhpelopia and related new taxa.

Zootaxa 2021 Mar 24;4949(1):zootaxa.4949.1.1. Epub 2021 Mar 24.

Evolution and Ecology, Research School of Biological Sciences, The Australian National University, Canberra, ACT 2600, Australia..

The diversity and endemism of Australian Tanypodinae (Diptera: Chironomidae) has been unclear from morphological comparisons with well-grounded northern hemisphere taxonomy. As part of a comprehensive study, here we focus on one of the few described endemic genera, Yarrhpelopia Cranston. Extensive and intensive new sampling and newly-acquired molecular data provides clarity for the type species, Yarrhpelopia norrisi Cranston and allows recognition of congeners and potential sister group(s). Read More

View Article and Full-Text PDF

First Report of Round Spot Disease of Zanthoxylum armatum DC Caused by Fusarium fujikuroi in China.

Plant Dis 2021 Mar 23. Epub 2021 Mar 23.

chengdu, China;

Zanthoxylum armatum DC, a deciduous tree in Rutaceae, has significant economic value as an important food condiment, spice, and medicine (Cao et al. 2019). Recently, an unknown round leaf spot disease has been found on Z. Read More

View Article and Full-Text PDF

IL-6 and IL-10 in the serum and exfoliated cervical cells of patients infected with high-risk human papillomavirus.

PLoS One 2021 22;16(3):e0248639. Epub 2021 Mar 22.

Multicentric Program of Post-Graduation in Biochemistry and Molecular Biology of the Institute of Biosciences, UFMS, Campo Grande, MS, Brazil.

Persistent infection by high-risk human papillomavirus (HR-HPV) is the main cause of cervical cancer and its precursor lesions. While some cytokines help immune cells in virus clearance, others contribute to the persistence of infection and neoplastic progression. Here, the levels of interferon (IFN)-γ, tumor necrosis factor (TNF)-α, interleukin (IL)-10, IL-6, IL-4, and IL-2 were quantified in the serum and exfoliated cervical cells (ECCs) of patients with HR-HPV, and the presence of IL-6+ cells was investigated in uterine cervix biopsies. Read More

View Article and Full-Text PDF

Evolution and biogeography of Memecylon.

Am J Bot 2021 Mar 21. Epub 2021 Mar 21.

Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA.

Premise: The woody plant group Memecylon (Melastomataceae) is a large clade occupying diverse forest habitats in the Old World tropics and exhibiting high regional endemism. Its phylogenetic relationships have been previously studied using ribosomal DNA with extensive sampling from Africa and Madagascar. However, divergence times, biogeography, and character evolution of Memecylon remain uninvestigated. Read More

View Article and Full-Text PDF

Analysis of different size fractions provides a more complete perspective of viral diversity in a freshwater embayment.

Appl Environ Microbiol 2021 Mar 19. Epub 2021 Mar 19.

Department of Physical and Environmental Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada

Inspired by recent discoveries of the prevalence of large viruses in the environment, we re-assessed the longstanding approach of filtering water through small pore-size filters to separate viruses from cells before metagenomic analysis. We collected samples from three sites in Hamilton Harbour, an embayment of Lake Ontario, and studied 6 datasets derived from < 0.45 μm and > 0. Read More

View Article and Full-Text PDF