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Department of Energy Joint Genome Insti... Publications | LitMetric

961 results match your criteria: "Department of Energy Joint Genome Institute[Affiliation]"

The protein structurome of Orthornavirae and its dark matter.

mBio

December 2024

Division of Intramural Research, Computational Biology Branch, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.

Unlabelled: Metatranscriptomics is uncovering more and more diverse families of viruses with RNA genomes comprising the viral kingdom Orthornavirae in the realm Riboviria. Thorough protein annotation and comparison are essential to get insights into the functions of viral proteins and virus evolution. In addition to sequence- and hmm profile‑based methods, protein structure comparison adds a powerful tool to uncover protein functions and relationships.

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Alga-dominated geothermal spring communities in Yellowstone National Park (YNP), USA, have been the focus of many studies, however, relatively little is known about the composition and community interactions which underpin these ecosystems. Our goal was to determine, in three neighboring yet distinct environments in Lemonade Creek, YNP, how cells cope with abiotic stressors over the diurnal cycle. All three environments are colonized by two photosynthetic lineages, and , both of which are extremophilic Cyanidiophyceae red algae.

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Transcriptomic Analysis of the CAM Species Under Low- and High-Temperature Regimes.

Plants (Basel)

December 2024

Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.

Temperature stress is one of the major limiting environmental factors that negatively impact global crop yields. is an obligate crassulacean acid metabolism (CAM) plant species, exhibiting much higher water-use efficiency and tolerance to drought and heat stresses than C or C plant species. Previous studies on gene expression responses to low- or high-temperature stress have been focused on C and C plants.

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Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues.

Nat Struct Mol Biol

December 2024

Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.

While a rich set of putative cis-regulatory sequences involved in mouse fetal development have been annotated recently on the basis of chromatin accessibility and histone modification patterns, delineating their role in developmentally regulated gene expression continues to be challenging. To fill this gap, here we mapped chromatin contacts between gene promoters and distal sequences across the genome in seven mouse fetal tissues and across six developmental stages of the forebrain. We identified 248,620 long-range chromatin interactions centered at 14,138 protein-coding genes and characterized their tissue-to-tissue variations and developmental dynamics.

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Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015.

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We report the genome sequences of four sp. strains isolated from the octocoral maintained long term at an aquarium facility. Our analysis reveals the coding potential for versatile polysaccharide metabolism; Type II, III, IV, and VI secretion systems; and the biosynthesis of novel ribosomally synthesized and post-translationally modified peptides.

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An orphan gene BOOSTER enhances photosynthetic efficiency and plant productivity.

Dev Cell

November 2024

Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.

Article Synopsis
  • The text discusses how transferring DNA from organelles to the nucleus is crucial for the evolution of eukaryotes, highlighted by a study that identified a specific gene (BSTR) linked to photosynthesis in Populus trichocarpa.
  • BSTR has three exons, with two derived from endophytic sources and one including a large part of a plastid gene related to Rubisco, which is essential for photosynthesis.
  • Overexpressing BSTR in poplar and Arabidopsis plants led to significant increases in plant height (up to 200%) and biomass (up to 200%), demonstrating its potential for enhancing growth under field conditions.
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Congenital heart defects (CHD) arise in part due to inherited genetic variants that alter genes and noncoding regulatory elements in the human genome. These variants are thought to act during fetal development to influence the formation of different heart structures. However, identifying the genes, pathways, and cell types that mediate these effects has been challenging due to the immense diversity of cell types involved in heart development as well as the superimposed complexities of interpreting noncoding sequences.

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Sex chromosomes have evolved hundreds of times across the flowering plant tree of life; their recent origins in some members of this clade can shed light on the early consequences of suppressed recombination, a crucial step in sex chromosome evolution. Amborella trichopoda, the sole species of a lineage that is sister to all other extant flowering plants, is dioecious with a young ZW sex determination system. Here we present a haplotype-resolved genome assembly, including highly contiguous assemblies of the Z and W chromosomes.

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Hydrophobins from mediate fungal interactions with microplastics.

bioRxiv

November 2024

Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, DE 19716.

Microplastics present myriad ecological and human health risks including serving as a vector for pathogens in human and animal food chains. However, the specific mechanisms by which pathogenic fungi colonize these microplastics have yet to be explored. In this work, we examine the opportunistic fungal pathogen, and other common soil and marine , which we found bind microplastics tightly.

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Article Synopsis
  • - Pecan scab, caused by Venturia effusa, severely impacts pecan crops in the southeastern U.S., with resistance influenced by host genetics interacting with different disease forms.
  • - A transcriptome analysis of the 'Desirable' pecan cultivar revealed distinct gene expression patterns when exposed to both pathogenic and non-pathogenic scab isolates, particularly highlighting early defense mechanisms.
  • - The study identified key gene modules linked to defense responses, suggesting that the early activation of signal transduction and barrier formation are critical for resistance against the fungus, laying the groundwork for future resistance gene research.
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Ancient whole-genome duplications (WGDs) are believed to facilitate novelty and adaptation by providing the raw fuel for new genes. However, it is unclear how recent WGDs may contribute to evolvability within recent polyploids. Hybridization accompanying some WGDs may combine divergent gene content among diploid species.

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Genome sequence of CCS1 assembled from an ammonia-oxidizing enrichment culture.

Microbiol Resour Announc

December 2024

Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, California, USA.

We report the metagenome-assembled genome of an ammonia-oxidizing archaeon that is closely related to NF5 but shows distinct genomic features compared to strain NF5.

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Article Synopsis
  • In Finland, isolated cleft palate (CP) occurs more frequently than cleft lip with or without cleft palate (CL/P), which is the opposite trend seen in other European countries.
  • A genome-wide association study revealed a specific single nucleotide polymorphism (rs570516915) strongly linked to CP in the Finnish population, showing significant statistical results and confirmed in other cohorts.
  • The risk allele for rs570516915 disrupts a binding site for the IRF6 transcription factor, leading to decreased IRF6 expression, indicating that this genetic alteration may be a key factor in the mechanism causing CP.
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Combinatorial transcription factor binding encodes cis-regulatory wiring of mouse forebrain GABAergic neurogenesis.

Dev Cell

October 2024

Department of Neurobiology, Physiology and Behavior, and Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95618, USA. Electronic address:

Transcription factors (TFs) bind combinatorially to cis-regulatory elements, orchestrating transcriptional programs. Although studies of chromatin state and chromosomal interactions have demonstrated dynamic neurodevelopmental cis-regulatory landscapes, parallel understanding of TF interactions lags. To elucidate combinatorial TF binding driving mouse basal ganglia development, we integrated chromatin immunoprecipitation sequencing (ChIP-seq) for twelve TFs, H3K4me3-associated enhancer-promoter interactions, chromatin and gene expression data, and functional enhancer assays.

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Regulatory elements (enhancers) are major drivers of gene expression in mammals and harbor many genetic variants associated with human diseases. Here, we present an updated VISTA Enhancer Browser (https://enhancer.lbl.

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Enhancers in Plant Development, Adaptation, and Evolution.

Plant Cell Physiol

October 2024

U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Understanding plant responses to developmental and environmental cues is crucial for studying morphological divergence and local adaptation. Gene expression changes, governed by cis-regulatory modules (CRMs) including enhancers, are a major source of plant phenotypic variation. However, while genome-wide approaches have revealed thousands of putative enhancers in mammals, far fewer have been identified and functionally characterized in plants.

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Functional diversification within the heme-binding split-barrel family.

J Biol Chem

November 2024

Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, Berkeley, California, USA; The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California, USA. Electronic address:

Due to neofunctionalization, a single fold can be identified in multiple proteins that have distinct molecular functions. Depending on the time that has passed since gene duplication and the number of mutations, the sequence similarity between functionally divergent proteins can be relatively high, eroding the value of sequence similarity as the sole tool for accurately annotating the function of uncharacterized homologs. Here, we combine bioinformatic approaches with targeted experimentation to reveal a large multifunctional family of putative enzymatic and nonenzymatic proteins involved in heme metabolism.

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Approximately a quarter of the human genome consists of gene deserts, large regions devoid of genes often located adjacent to developmental genes and thought to contribute to their regulation. However, defining the regulatory functions embedded within these deserts is challenging due to their large size. Here, we explore the cis-regulatory architecture of a gene desert flanking the Shox2 gene, which encodes a transcription factor indispensable for proximal limb, craniofacial, and cardiac pacemaker development.

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Third-harmonic generation microscopy is a powerful label-free nonlinear imaging technique, providing essential information about structural characteristics of cells and tissues without requiring external labelling agents. In this work, we integrated a recently developed compact adaptive optics module into a third-harmonic generation microscope, to measure and correct for optical aberrations in complex tissues. Taking advantage of the high sensitivity of the third-harmonic generation process to material interfaces and thin membranes, along with the 1,300-nm excitation wavelength used here, our adaptive optical third-harmonic generation microscope enabled high-resolution in vivo imaging within highly scattering biological model systems.

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The McMurdo Dry Valleys (MDVs) of Antarctica are a mosaic of extreme habitats which are dominated by microbial life. The MDVs include glacial melt holes, streams, lakes, and soils, which are interconnected through the transfer of energy and flux of inorganic and organic material via wind and hydrology. For the first time, we provide new data on the viral community structure and function in the MDVs through metagenomics of the planktonic and benthic mat communities of Lakes Bonney and Fryxell.

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enhancers have distinct functions in controlling expression during cortical development.

Proc Natl Acad Sci U S A

October 2024

Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, University of California San Francisco Weill Institute for Neurosciences, University of California, San Francisco, CA 94158.

Article Synopsis
  • Transcription factor genes, crucial for cell development, have numerous enhancers that regulate their expression, particularly affecting brain development.
  • The study focused on the NR2F1 transcription factor, identifying six key enhancers linked to prenatal cortical development, some associated with mutations found in Autism Spectrum Disorder (ASD) individuals.
  • By deleting two strong enhancers, researchers discovered they have distinct but complementary roles in regional and cell layer expression in the developing cortex, highlighting their importance in fine-tuning brain development.
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Over a billion years of fungal evolution has enabled representatives of this kingdom to populate almost all parts of planet Earth and to adapt to some of its most uninhabitable environments including extremes of temperature, salinity, pH, water, light, or other sources of radiation. is an endolithic fungus that inhabits rock outcrops in Antarctica. It survives extremes of cold, humidity and solar radiation in one of the least habitable environments on Earth.

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Mutagenesis Sensitivity Mapping of Human Enhancers .

bioRxiv

September 2024

Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA.

Distant-acting enhancers are central to human development. However, our limited understanding of their functional sequence features prevents the interpretation of enhancer mutations in disease. Here, we determined the functional sensitivity to mutagenesis of human developmental enhancers .

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Cultivar Williams 82 has served as the reference genome for the soybean research community since 2008, but is known to have areas of genomic heterogeneity among different sub-lines. This work provides an updated assembly (version Wm82.a6) derived from a specific sub-line known as Wm82-ISU-01 (seeds available under USDA accession PI 704477).

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