A5011434478- RNA and protein synthesis mechanisms
- Photosynthetic Processes and Mechanisms
- Genomics and Phylogenetic Studies
- Legume Nitrogen Fixing Symbiosis
- Bacterial Genetics and Biotechnology
- Plant Stress Responses and Tolerance
- Plant responses to water stress
- Ion channel regulation and function
- Plant nutrient uptake and metabolism
- Bayesian Methods and Mixture Models
- Material Properties and Processing
- Bioinformatics and Genomic Networks
- CRISPR and Genetic Engineering
- Gene Regulatory Network Analysis
- Caveolin-1 and cellular processes
- Microbial Metabolism and Applications
- Coastal wetland ecosystem dynamics
- Gene expression and cancer classification
- Forensic and Genetic Research
- Nicotinic Acetylcholine Receptors Study
- melanin and skin pigmentation
- Cellular transport and secretion
- Agronomic Practices and Intercropping Systems
- Plant Virus Research Studies
- Lipid Membrane Structure and Behavior
University of California, San Diego
2016-2025
Bethesda University
2008
United States Department of Justice
2008
Seattle University
2008
Pasadena City College
2008
Universidad de Salamanca
2008
Advisory Board Company (United States)
2008
University of San Francisco
2008
Science Oxford
2008
Howard Hughes Medical Institute
2008
We report the complete 6,530,228-bp genome sequence of symbiotic nitrogen fixing bacterium Rhizobium etli . Six large plasmids comprise one-third total size. The chromosome encodes most functions necessary for cell growth, whereas few essential genes or metabolic pathways are located in plasmids. Chromosomal synteny is disrupted by related to insertion sequences, phages, plasmids, and cell-surface components. Plasmids do not show synteny, their orthologs mostly shared accessory replicons...
Abstract The Transporter Classification Database (TCDB; tcdb.org) is a freely accessible reference resource, which provides functional, structural, mechanistic, medical and biotechnological information about transporters from organisms of all types. TCDB the only transport protein classification database adopted by International Union Biochemistry Molecular Biology (IUBMB) now (October 1, 2020) consists 20 653 proteins classified in 15 528 non-redundant systems with 1567 tabulated 3D...
Sensing and responding to environmental water deficiency osmotic stresses are essential for the growth, development, survival of plants. Recently, an osmolality-sensing ion channel called OSCA1 was discovered that functions in sensing hyperosmolality Arabidopsis . Here, we report cryo-electron microscopy (cryo-EM) structure function homolog from rice ( Oryza sativa ; OsOSCA1.2), leading a model how it could mediate transport pathway gating. The reveals dimer; molecular architecture each...
Abstract Although common bean (Phaseolus vulgaris) is the most important grain legume in developing world for human consumption, few genomic resources exist this species. The objectives of research were to develop expressed sequence tag (EST) and assess nodule gene expression through high-density macroarrays. We sequenced a total 21,026 ESTs derived from 5 different cDNA libraries, including nitrogen-fixing root nodules, phosphorus-deficient roots, pods, leaves Mesoamerican genotype, Negro...
Our laboratory has developed bioinformatic strategies for identifying distant phylogenetic relationships and characterizing families superfamilies of transport proteins. Results using these tools suggest that the Anoctamin Superfamily cation anion channels, as well lipid scramblases, includes three functionally characterized families: (ANO), Transmembrane Channel (TMC) Ca2+-permeable Stress-gated Cation (CSC) families; four uncharacterized proteins, which we refer to Anoctamin-like (ANO-L),...
Marine sediments are highly bioactive habitats, where sulfate-reducing bacteria contribute substantially to seabed carbon cycling by oxidizing ~77 Tmol C org year −1 . This remarkable activity is largely attributable the deltaproteobacterial family Desulfobacteraceae of complete oxidizers (to CO 2 ), which our biogeography focused meta-analysis verified as cosmopolitan. However, catabolic/regulatory networks underlying this ecophysiological feat at thermodynamic limit essentially unknown....
We present evidence supporting the notion that codon usage (CU) compatibility between foreign genes and recipient genomes is an important prerequisite to assess selective advantage of imported functions, therefore increase fixation probability horizontal gene transfer (HGT) events. This contrasts with current tendency in research predict recent HGTs prokaryotes by assuming acquired generally display poor CU. By looking at CU level (poor, typical, or rich) exhibited putative xenologs still...
The membrane attack complex/perforin (MACPF) superfamily consists of a diverse group proteins involved in bacterial pathogenesis and sporulation as well eukaryotic immunity, embryonic development, neural migration fruiting body formation. present work shows that the evolutionary relationships between members superfamily, previously suggested by comparison their tertiary structures, can also be supported analyses primary structures. includes MACPF family (TC 1.C.39), cholesterol-dependent...
Abstract Background Comparative genomics has provided valuable insights into the nature of gene sequence variation and chromosomal organization closely related bacterial species. However, questions about biological significance order conservation, or synteny, remain open. Moreover, few comprehensive studies have been reported for rhizobial genomes. Results We analyzed genomic sequences four fast growing Rhizobiales ( Sinorhizobium meliloti , Agrobacterium tumefaciens Mesorhizobium loti...
Here we provide bioinformatic evidence that the Organo-Arsenical Exporter (ArsP), Endoplasmic Reticulum Retention Receptor (KDELR), Mitochondrial Pyruvate Carrier (MPC), L-Alanine (AlaE), and Lipid-linked Sugar Translocase (LST) protein families are members of Transporter-Opsin-G Protein-coupled (TOG) Superfamily. These share domains homologous to well-established TOG superfamily members, their topologies transmembranal segments (TMSs) compatible with basic 4-TMS repeat unit characteristic...
Bdellovibrio, δ-proteobacteria, including B. bacteriovorus (Bba) and exovorus (Bex), are obligate predators of other Gram-negative bacteria. While Bba grows in the periplasm prey cell, Bex externally. We have analyzed compared transport proteins these 2 organisms based on current contents Transporter Classification Database (TCDB; www.tcdb.org). has 103 transporters more than Bex, 50% secondary carriers, 3 times as many MFS carriers. far metabolite expected from its larger genome, but there...
Sensing and responding to environmental water deficiencies is essential for the growth, development survival of plants. Recently, an osmolality-sensing ion channel called OSCA1 was discovered that functions in sensing hyperosmolarity Arabidopsis. Here, we report cryo-EM structure function from rice (Oryza stativa; OsOSCA1.2), showing how it mediates hyperosmolality permeability. The reveals a dimer, molecular architecture each subunit consists eleven transmembrane helices cytosolic soluble...
Upon discovery of the first archaeal species in 1970s, life has been subdivided into three domains: Eukarya, Archaea, and Bacteria. However, organization three-domain tree challenged following lineages such as TACK Asgard superphyla. The Superphylum emerged closest ancestor to eukaryotes, potentially improving our understanding evolution forms. We characterized transportomes their substrates within four metagenome-assembled genomes (MAGs), that is, Odin-, Thor-, Heimdall- Loki-archaeota well...
Members of the Piezo family mechanically activated cation channels are involved in multiple physiological processes higher eukaryotes, including vascular development, cell differentiation, touch perception, hearing, and more, but they also common single-celled eukaryotic microorganisms. Mutations these proteins humans associated with a variety diseases, such as colorectal adenomatous polyposis, dehydrated hereditary stomatocytosis, xerocytosis. Available 3D structures for show nine regions...
Based on mixture models, we present a Bayesian method (called BClass) to classify biological entities (e.g. genes) when variables of quite heterogeneous nature are analyzed. Various statistical distributions used model the continuous/categorical data commonly produced by genetic experiments and large-scale genomic projects. We calculate posterior probability each entry belong element (group) in mixture. In this way, an original set is transformed into purely homogeneous characteristics...
In this report we present seven lines of bioinformatic evidence supporting the conclusion that Pentameric Ligand-gated Ion Channel (pLIC) Family is a member Voltage-gated (VIC) Superfamily. our approach, used Transporter Classification Database (TCDB) as reference and applied series methods to search for similarities between pLIC family members VIC superfamily. These include: (1) sequence similarity, (2) compatibility topology hydropathy profiles, (3) shared domains, (4) conserved motifs,...
Abstract Escherichia coli is a free-living bacterium that condensates large legacy of knowledge as result years experimental work in molecular biology. It represents point departure for analyses and comparisons with the ever-increasing number finished microbial genomes. For years, we have been gathering from literature on transcriptional regulation operon organization E. K-12, organizing it relational database, RegulonDB. RegulonDB contains information 2025 % expected total sets regulatory...
Using bioinformatic approaches, we present evidence of distant relatedness among the Ephemerovirus Viroporin family, Rhabdoviridae Putative U5 Phospholemman and Small Integral Membrane Protein family. Our approach is based on transitivity property homology complemented with five validation criteria: (1) significant sequence similarity alignment coverage, (2) compatibility topology transmembrane segments, (3) overlap hydropathy profiles, (4) conservation protein domains, (5) motifs. results...