Tài liệu miễn phí Sinh học
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RNA methylomes reveal the m6 A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening
Methylation of nucleotides, notably in the forms of 5-methylcytosine (5mC) in DNA and N6 - methyladenosine (m6 A) in mRNA, carries important information for gene regulation. 5mC has been elucidated to participate in the regulation of fruit ripening, whereas the function of m6 A in this process and the interplay between 5mC and m6 A remain uncharacterized.
4/6/2023 9:03:00 AM +00:00
A systematic assessment of current genome-scale metabolic reconstruction tools
Several genome-scale metabolic reconstruction software platforms have been developed and are being continuously updated. These tools have been widely applied to reconstruct metabolic models for hundreds of microorganisms ranging from important human pathogens to species of industrial relevance.
4/6/2023 9:02:47 AM +00:00
Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes
Tsetse flies (Glossina sp.) are the vectors of human and animal trypanosomiasis throughout subSaharan Africa. Tsetse flies are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood-specific diet by both sexes, and obligate bacterial symbiosis.
4/6/2023 9:02:32 AM +00:00
Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis
Chromatin provides a tunable platform for gene expression control. Besides the well-studied core nucleosome, H1 linker histones are abundant chromatin components with intrinsic potential to influence chromatin function.
4/6/2023 9:02:20 AM +00:00
Analysis of Vibrio cholerae genomes identifies new type VI secretion system gene clusters
Like many bacteria, Vibrio cholerae deploys a harpoon-like type VI secretion system (T6SS) to compete against other microbes in environmental and host settings. The T6SS punctures adjacent cells and delivers toxic effector proteins that are harmless to bacteria carrying cognate immunity factors.
4/6/2023 9:02:12 AM +00:00
BERMUDA: A novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes
To fully utilize the power of single-cell RNA sequencing (scRNA-seq) technologies for identifying cell lineages and bona fide transcriptional signals, it is necessary to combine data from multiple experiments. We present BERMUDA (Batch Effect ReMoval Using Deep Autoencoders), a novel transfer-learning-based method for batch effect correction in scRNA-seq data.
4/6/2023 9:02:04 AM +00:00
Modulating chromatin accessibility by transactivation and targeting proximal dsgRNAs enhances Cas9 editing efficiency in vivo
The CRISPR/Cas9 system is unable to edit all targetable genomic sites with full efficiency in vivo. We show that Cas9-mediated editing is more efficient in open chromatin regions than in closed chromatin regions in rice. A construct (Cas9-TV) formed by fusing a synthetic transcription activation domain to Cas9 edits target sites more efficiently, even in closed chromatin regions.
4/6/2023 9:01:57 AM +00:00
Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes
General translational cis-elements are present in the mRNAs of all genes and affect the recruitment, assembly, and progress of preinitiation complexes and the ribosome under many physiological states. These elements include mRNA folding, upstream open reading frames, specific nucleotides flanking the initiating AUG codon, protein coding sequence length, and codon usage.
4/6/2023 9:01:50 AM +00:00
Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation
We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community.
4/6/2023 9:01:42 AM +00:00
Cytoscape Automation: Empowering workflow-based network analysis
Cytoscape is one of the most successful network biology analysis and visualization tools, but because of its interactive nature, its role in creating reproducible, scalable, and novel workflows has been limited. We describe Cytoscape Automation (CA), which marries Cytoscape to highly productive workflow systems, for example, Python/R in Jupyter/RStudio.
4/6/2023 9:01:34 AM +00:00
Benchmarking of alignment-free sequence comparison methods
Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment.
4/6/2023 9:01:27 AM +00:00
RaPID: Ultra-fast, powerful, and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts
While genetic relatedness, usually manifested as segments identical by descent (IBD), is ubiquitous in modern large biobanks, current IBD detection methods are not efficient at such a scale. Here, we describe an efficient method, RaPID, for detecting IBD segments in a panel with phased haplotypes.
4/6/2023 9:01:15 AM +00:00
Screening for genes that accelerate the epigenetic aging clock in humans reveals a role for the H3K36 methyltransferase NSD1
Epigenetic clocks are mathematical models that predict the biological age of an individual using DNA methylation data and have emerged in the last few years as the most accurate biomarkers of the aging process.
4/6/2023 9:01:08 AM +00:00
HUPAN: A pan-genome analysis pipeline for human genomes
The human reference genome is still incomplete, especially for those population-specific or individual-specific regions, which may have important functions. Here, we developed a HUman Pan-genome ANalysis (HUPAN) system to build the human pan-genome.
4/6/2023 9:01:01 AM +00:00
BART-Seq: Cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis
We describe a highly sensitive, quantitative, and inexpensive technique for targeted sequencing of transcript cohorts or genomic regions from thousands of bulk samples or single cells in parallel. Multiplexing is based on a simple method that produces extensive matrices of diverse DNA barcodes attached to invariant primer sets, which are all pre-selected and optimized in silico.
4/6/2023 9:00:48 AM +00:00
Systematic underestimation of the epigenetic clock and age acceleration in older subjects
The Horvath epigenetic clock is widely used. It predicts age quite well from 353 CpG sites in the DNA methylation profile in unknown samples and has been used to calculate “age acceleration” in various tissues and environments.
4/6/2023 9:00:41 AM +00:00
A comparison of automatic cell identification methods for single-cell RNA sequencing data
Single-cell transcriptomics is rapidly advancing our understanding of the cellular composition of complex tissues and organisms. A major limitation in most analysis pipelines is the reliance on manual annotations to determine cell identities, which are time-consuming and irreproducible
4/6/2023 9:00:34 AM +00:00
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx
Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink of extinction.
4/6/2023 7:33:44 AM +00:00
Choosing panels of genomics assays using submodular optimization
Due to the high cost of sequencing-based genomics assays such as ChIP-seq and DNase-seq, the epigenomic characterization of a cell type is typically carried out using a small panel of assay types. Deciding a priori which assays to perform is, thus, a critical step in many studies. We present the submodular selection of assays (SSA), a method for choosing a diverse panel of genomic assays that leverages methods from submodular optimization.
4/6/2023 7:33:34 AM +00:00
Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface
Relatively little is known about the genomic basis and evolution of wood-feeding in beetles. We undertook genome sequencing and annotation, gene expression assays, studies of plant cell wall degrading enzymes, and other functional and comparative studies of the Asian longhorned beetle, Anoplophora glabripennis, a globally significant invasive species capable of inflicting severe feeding damage on many important tree species.
4/6/2023 7:33:27 AM +00:00
Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms
Genomes are composed of long strings of nucleotide monomers (A, C, G and T) that are either scavenged from the organism’s environment or built from metabolic precursors. The biosynthesis of each nucleotide differs in atomic requirements with different nucleotides requiring different quantities of nitrogen atoms.
4/6/2023 7:33:20 AM +00:00
Tiny microbes, enormous impacts: What matters in gut microbiome studies?
Many factors affect the microbiomes of humans, mice, and other mammals, but substantial challenges remain in determining which of these factors are of practical importance. Considering the relative effect sizes of both biological and technical covariates can help improve study design and the quality of biological conclusions. Care must be taken to avoid technical bias that can lead to incorrect biological conclusions.
4/6/2023 7:33:13 AM +00:00
A new timepiece: An epigenetic mitotic clock
The ability to accurately and efficiently detect the acceleration in the stem cell mitotic “tick rate”—a so-called mitotic clock—could be a useful tool for predicting cancer risk. A new mitotic clock and mathematical approach that incorporates DNA methylation biology common among human cell types provides a new tool for cancer epigenetics research.
4/6/2023 7:33:06 AM +00:00
Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities
Autism spectrum disorder (ASD) is a common neurodevelopmental disorder that tends to co-occur with other diseases, including asthma, inflammatory bowel disease, infections, cerebral palsy, dilated cardiomyopathy, muscular dystrophy, and schizophrenia. However, the molecular basis of this co-occurrence, and whether it is due to a shared component that influences both pathophysiology and environmental triggering of illness, has not been elucidated.
4/6/2023 7:32:56 AM +00:00
Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity
Short interspersed elements (SINEs) represent the most abundant group of non-long-terminal repeat transposable elements in mammalian genomes. In primates, Alu elements are the most prominent and homogenous representatives of SINEs. Due to their frequent insertion within or close to coding regions, SINEs have been suggested to play a crucial role during genome evolution.
4/6/2023 7:32:50 AM +00:00
Rapid gene isolation in barley and wheat by mutant chromosome sequencing
Identification of causal mutations in barley and wheat is hampered by their large genomes and suppressed recombination. To overcome these obstacles, we have developed MutChromSeq, a complexity reduction approach based on flow sorting and sequencing of mutant chromosomes, to identify induced mutations by comparison to parental chromosomes.
4/6/2023 7:32:43 AM +00:00
Closing the loop: 3C versus DNA FISH
Chromosome conformation capture (3C)-based techniques have revolutionized the field of nuclear organization, partly replacing DNA FISH as the method of choice for studying three-dimensional chromosome architecture. Although DNA FISH is commonly used for confirming 3C-based findings, the two techniques are conceptually and technically different and comparing their results is not trivial. Here, we discuss both 3C-based techniques and DNA FISH approaches to highlight their similarities and differences.
4/6/2023 7:32:37 AM +00:00
The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes
Comparisons between C3 and C4 grasses often utilize C3 species from the subfamilies Ehrhartoideae or Pooideae and C4 species from the subfamily Panicoideae, two clades that diverged over 50 million years ago.
4/6/2023 7:32:27 AM +00:00
Extensive RNA editing and splicing increase immune self-representation diversity in medullary thymic epithelial cells
In order to become functionally competent but harmless mediators of the immune system, T cells undergo a strict educational program in the thymus, where they learn to discriminate between self and non-self. This educational program is, to a large extent, mediated by medullary thymic epithelial cells that have a unique capacity to express, and subsequently present, a large fraction of body antigens.
4/6/2023 7:32:21 AM +00:00
Capture Hi-C identifies a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23
The identification of causal genes from genome-wide association studies (GWAS) is the next important step for the translation of genetic findings into biologically meaningful mechanisms of disease and potential therapeutic targets.
4/6/2023 7:32:14 AM +00:00