Tài liệu miễn phí Sinh học
Download Tài liệu học tập miễn phí Sinh học
Quantitative proteomics of the tobacco pollen tube secretome identifies novel pollen tube guidance proteins important for fertilization
As in animals, cell–cell communication plays a pivotal role in male–female recognition during plant sexual reproduction. Prelaid peptides secreted from the female reproductive tissues guide pollen tubes towards ovules for fertilization. However, the elaborate mechanisms for this dialogue have remained elusive, particularly from the male perspective.
4/6/2023 7:15:48 AM +00:00
Design and computational analysis of single-cell RNA-sequencing experiments
In this article, we highlight the computational methods available for the design and analysis of scRNA-seq experiments, their advantages and disadvantages in various settings, the open questions for which novel methods are needed, and expected future developments in this exciting area.
4/6/2023 7:15:41 AM +00:00
Systematic identification of genetic influences on methylation across the human life course
The influence of genetic variation on complex diseases is potentially mediated through a range of highly dynamic epigenetic processes exhibiting temporal variation during development and later life. Here we present a catalogue of the genetic influences on DNA methylation (methylation quantitative trait loci (mQTL)) at five different life stages in human blood: children at birth, childhood, adolescence and their mothers during pregnancy and middle age.
4/6/2023 7:15:35 AM +00:00
ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data
A cell’s epigenome arises from interactions among regulatory factors—transcription factors and histone modifications—co-localized at particular genomic regions. We developed a novel statistical method, ChromNet, to infer a network of these interactions, the chromatin network, by inferring conditional-dependence relationships among a large number of ChIP-seq data sets.
4/6/2023 7:15:27 AM +00:00
JBrowse: A dynamic web platform for genome visualization and analysis
JBrowse is a fast and full-featured genome browser built with JavaScript and HTML5. It is easily embedded into websites or apps but can also be served as a standalone web page. Results: Overall improvements to speed and scalability are accompanied by specific enhancements that support complex interactive queries on large track sets. Analysis functions can readily be added using the plugin framework; most visual aspects of tracks can also be customized, along with clicks, mouseovers, menus, and popup boxes.
4/6/2023 7:15:16 AM +00:00
4D nucleomes in single cells: What can computational modeling reveal about spatial chromatin conformation?
Genome-wide sequencing technologies enable investigations of the structural properties of the genome in various spatial dimensions. Here, we review computational techniques developed to model the three-dimensional genome in single cells versus ensembles of cells and assess their underlying assumptions.
4/6/2023 7:15:08 AM +00:00
Talking about cross-talk: The immune system and the microbiome
The first Next Gen Immunology EMBO conference, held at the Weizmann Institute of Science in mid-February, touched upon a broad set of topics from host genetics to transcriptomics and microbiome analysis. It specifically demonstrated the intimate cross-talk between the microbiome and the immune system and called for a similarly close interdisciplinary collaboration between microbiologists and immunologists.
4/6/2023 7:14:58 AM +00:00
Single-CpG resolution mapping of 5-hydroxymethylcytosine by chemical labeling and exonuclease digestion identifies evolutionarily unconserved CpGs as TET targets
Conventional techniques for single-base resolution mapping of epigenetic modifications of DNA such as 5-hydroxymethylcytosine (5hmC) rely on the sequencing of bisulfite-modified DNA. Here we present an alternative approach called SCL-exo which combines selective chemical labeling (SCL) of 5hmC in genomic DNA with exonuclease (exo) digestion of the bead-trapped modified DNA molecules.
4/6/2023 7:14:51 AM +00:00
EAGER: Efficient ancient genome reconstruction
The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process. Results: Here we introduce EAGER, a time-efficient pipeline, which greatly simplifies the analysis of large-scale genomic data sets. EAGER provides features to preprocess, map, authenticate, and assess the quality of ancient DNA samples. Additionally, EAGER comprises tools to genotype samples to discover, filter, and analyze variants.
4/6/2023 7:14:44 AM +00:00
The real cost of sequencing: Scaling computation to keep pace with data generation
As the cost of sequencing continues to decrease and the amount of sequence data generated grows, new paradigms for data storage and analysis are increasingly important. The relative scaling behavior of these evolving technologies will impact genomics research moving forward.
4/6/2023 7:14:38 AM +00:00
Neglected tropical diseases in the genomics era: Re-evaluating the impact of new drugs and mass drug administration
Simon Croft answers Genome Biology’s questions on ways to approach neglected tropical diseases in the genomics era, including re-evaluating the impact of new drugs and mass drug administration.
4/6/2023 7:14:32 AM +00:00
CRISPR library designer (CLD): Software for multispecies design of single guide RNA libraries
Genetic screens using CRISPR/Cas9 are a powerful method for the functional analysis of genomes. Results: Here we describe CRISPR library designer (CLD), an integrated bioinformatics application for the design of custom single guide RNA (sgRNA) libraries for all organisms with annotated genomes.
4/6/2023 7:14:25 AM +00:00
There is no human interactome
Protein complexes are dynamic. A new analysis of two quantitative proteomic datasets reveals cell type-specific changes in the stoichiometry of complexes, which often involve paralog switching.
4/6/2023 7:14:14 AM +00:00
Spatiotemporal variation of mammalian protein complex stoichiometries
Recent large-scale studies revealed cell-type specific proteomes. However, protein complexes, the basic functional modules of a cell, have been so far mostly considered as static entities with well-defined structures. The co-expression of their members has not been systematically charted at the protein level.
4/6/2023 7:14:08 AM +00:00
A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways
We present a generative model, Lux, to quantify DNA methylation modifications from any combination of bisulfite sequencing approaches, including reduced, oxidative, TET-assisted, chemical-modification assisted, and methylaseassisted bisulfite sequencing data.
4/6/2023 7:14:01 AM +00:00
Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models
The three-dimensional (3D) organization of chromosomes can be probed using methods like Capture-C. However, it is unclear how such population-level data relate to the organization within a single cell, and the mechanisms leading to the observed interactions are still largely obscure. We present a polymer modeling scheme based on the assumption that chromosome architecture is maintained by protein bridges, which form chromatin loops.
4/6/2023 7:13:49 AM +00:00
Evolution of plant genome architecture
We have witnessed an explosion in our understanding of the evolution and structure of plant genomes in recent years. Here, we highlight three important emergent realizations: (1) that the evolutionary history of all plant genomes contains multiple, cyclical episodes of whole-genome doubling that were followed by myriad fractionation processes; (2) that the vast majority of the variation in genome size reflects the dynamics of proliferation and loss of lineage-specific transposable elements;...
4/6/2023 7:13:39 AM +00:00
Genomic approaches for understanding dengue: Insights from the virus, vector, and host
The incidence and geographic range of dengue have increased dramatically in recent decades. Climate change, rapid urbanization and increased global travel have facilitated the spread of both efficient mosquito vectors and the four dengue virus serotypes between population centers.
4/6/2023 7:13:28 AM +00:00
When (distant) relatives stay too long: Implications for cancer medicine
The extent of intratumor heterogeneity and how treatment affects clonal evolution of cancer is an emerging theme in the field of cancer biology. In the era of targeted therapy, the presence of pre-existing treatmentresistant subclones within the tumor is a critical barrier to achieving durable responses.
4/6/2023 7:13:21 AM +00:00
Smash and DASH with Cas9
DeRisi and colleagues present a creative application for Cas9 in vitro, using it to deplete unwanted sequence from DNA libraries. It seems plausible that the in vitro use of CRISPR/Cas9 has unrealized potential to revolutionize the practice of molecular biology well beyond genome editing.
4/6/2023 7:13:15 AM +00:00
Depletion of Abundant Sequences by Hybridization (DASH): Using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications
Next-generation sequencing has generated a need for a broadly applicable method to remove unwanted highabundance species prior to sequencing. We introduce DASH (Depletion of Abundant Sequences by Hybridization). Sequencing libraries are ‘DASHed’ with recombinant Cas9 protein complexed with a library of guide RNAs targeting unwanted species for cleavage, thus preventing them from consuming sequencing space.
4/6/2023 7:13:06 AM +00:00
Multiple testing correction in linear mixed models
Multiple hypothesis testing is a major issue in genome-wide association studies (GWAS), which often analyze millions of markers. The permutation test is considered to be the gold standard in multiple testing correction as it accurately takes into account the correlation structure of the genome.
4/6/2023 7:12:59 AM +00:00
Comparative transcriptomics reveals the conserved building blocks involved in parallel evolution of diverse phenotypic traits in ants
Reproductive division of labor in eusocial insects is a striking example of a shared genetic background giving rise to alternative phenotypes, namely queen and worker castes. Queen and worker phenotypes play major roles in the evolution of eusocial insects. Their behavior, morphology and physiology underpin many ecologically relevant colony-level traits, which evolved in parallel in multiple species.
4/6/2023 7:12:53 AM +00:00
Pro-inflammatory miR-223 mediates the cross-talk between the IL23 pathway and the intestinal barrier in inflammatory bowel disease
The IL23/Th17 pathway is essential for the onset of inflammatory bowel disease (IBD), yet the specific mechanism by which this pathway initiates the disease remains unknown. In this study, we identify the mechanisms that mediate cross-talk between the IL23 pathway and the intestinal barrier in IBD.
4/6/2023 7:12:46 AM +00:00
Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design
Genome-scale CRISPR interference (CRISPRi) has been used in human cell lines; however, the features of effective guide RNAs (gRNAs) in different organisms have not been well characterized. Here, we define rules that determine gRNA effectiveness for transcriptional repression in Saccharomyces cerevisiae.
4/6/2023 7:12:39 AM +00:00
Polycomb-mediated chromatin compaction weathers the STORM
A recent super-resolution imaging study by Boettiger et al. elegantly demonstrates that three epigenetically defined, and functionally disparate, chromatin states have distinct folding characteristics in Drosophila nuclei.
4/6/2023 7:12:33 AM +00:00
Butterfly gene flow goes berserk
A group of animals that cannot interbreed with animals from another group is often taken as the definition of a ‘true’ species. However, a suite of recent studies suggests that the rare event of hybridization, that is, the production of viable offspring by the interbreeding of individuals from two such species, can facilitate adaptation through the process of genome ‘introgression’.
4/6/2023 7:12:25 AM +00:00
GATA3-dependent cellular reprogramming requires activation-domain dependent recruitment of a chromatin remodeler
Transcription factor-dependent cellular reprogramming is integral to normal development and is central to production of induced pluripotent stem cells. This process typically requires pioneer transcription factors (TFs) to induce de novo formation of enhancers at previously closed chromatin. Mechanistic information on this process is currently sparse.
4/6/2023 7:12:18 AM +00:00
HSA: Integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure
Genome-wide 3C technologies (Hi-C) are being increasingly employed to study three-dimensional (3D) genome conformations. Existing computational approaches are unable to integrate accumulating data to facilitate studying 3D chromatin structure and function.
4/6/2023 7:12:11 AM +00:00
Modelling local gene networks increases power to detect trans-acting genetic effects on gene expression
Expression quantitative trait loci (eQTL) mapping is a widely used tool to study the genetics of gene expression. Confounding factors and the burden of multiple testing limit the ability to map distal trans eQTLs, which is important to understand downstream genetic effects on genes and pathways.
4/6/2023 7:12:05 AM +00:00