A5066167699- RNA modifications and cancer
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Cancer-related molecular mechanisms research
- CRISPR and Genetic Engineering
- Bioinformatics and Genomic Networks
- RNA regulation and disease
- Genomics and Phylogenetic Studies
- Bacterial Genetics and Biotechnology
- Gene Regulatory Network Analysis
- Genomics and Chromatin Dynamics
- Immune Cell Function and Interaction
- Animal Virus Infections Studies
- Genetics, Bioinformatics, and Biomedical Research
- Bacteriophages and microbial interactions
- Biomedical Text Mining and Ontologies
- Virus-based gene therapy research
- Gene expression and cancer classification
- Virology and Viral Diseases
- T-cell and B-cell Immunology
- Microbial Metabolic Engineering and Bioproduction
- MicroRNA in disease regulation
- interferon and immune responses
- Viral Infections and Vectors
- Retinal Imaging and Analysis
Indiana University – Purdue University Indianapolis
2016-2025
Indiana University School of Medicine
2015-2024
Indiana University Indianapolis
2023-2024
Indiana University
2015-2023
Walker (United States)
2014-2021
Indiana Clinical and Translational Sciences Institute
2021
University of Indianapolis
2014-2020
Indiana University Health
2020
Indiana University Bloomington
2014
MRC Laboratory of Molecular Biology
2007-2014
One-third of the 4,225 protein-coding genes Escherichia coli K-12 remain functionally unannotated (orphans). Many map to distant clades such as Archaea, suggesting involvement in basic prokaryotic traits, whereas others appear restricted E. coli, including pathogenic strains. To elucidate orphans' biological roles, we performed an extensive proteomic survey using affinity-tagged strains and generated comprehensive genomic context inferences derive a high-confidence compendium for virtually...
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...
Relative to the atmosphere, much of aerobic ocean is supersaturated with methane; however, source this important greenhouse gas remains enigmatic. Catabolism methylphosphonic acid by phosphorus-starved marine microbes, concomitant release methane, has been suggested explain phenomenon, yet methylphosphonate not a known natural product, nor it detected in systems. Further, its synthesis from products would require unknown biochemistry. Here we show that archaeon Nitrosopumilus maritimus...
Abstract Background RNA-binding proteins (RBPs) play important roles in cellular homeostasis by controlling gene expression at the post-transcriptional level. Results We explore of more than 800 RBPs sixteen healthy human tissues and their patterns dysregulation cancer genomes from The Cancer Genome Atlas project. show that genes encoding are consistently significantly highly expressed compared with other classes genes, including those regulatory components such as transcription factors,...
Phosphonates, molecules containing direct carbon-phosphorus bonds, compose a structurally diverse class of natural products with interesting and useful biological properties. Although their synthesis in protozoa was discovered more than 50 y ago, the extent diversity phosphonate production nature remains poorly characterized. The rearrangement phosphoenolpyruvate (PEP) to phosphonopyruvate, catalyzed by enzyme PEP mutase (PepM), is shared vast majority known biosynthetic pathways. Thus, pepM...
Taking advantage of available functional data associated with 115 transcription and 7 sigma factors, we have performed a structural analysis the regulatory network Escherichia coli. While mode interaction between factors (TFs) is predominantly positive, TFs are frequently negatively autoregulated. Furthermore, feedback loops, motifs pathways unevenly distributed in this network. Short pathways, multiple feed-forward loops negative autoregulatory interactions particularly predominant...
The modulation of mRNA levels across tissues and time is key for the establishment operation developmental programs that transform fertilized egg into a fully formed embryo. Although mechanisms leading to differential synthesis are heavily investigated, comparatively little attention given processes degradation how these relate molecular controlling development. Here we combine timed collection Drosophila embryos unfertilized eggs with genome-wide microarray technology determine patterns all...
Hundreds of RNA-binding proteins (RBPs) control diverse aspects post-transcriptional gene regulation. To identify novel and unconventional RBPs, we probed high-density protein microarrays with fluorescently labeled RNA selected 200 that reproducibly interacted different types from budding yeast Saccharomyces cerevisiae. Surprisingly, more than half these represent previously known enzymes, many them acting in metabolism, providing opportunities to directly connect intermediary metabolism...
RNA Binding Proteins (RBPs) are a class of post-transcriptional regulatory molecules which increasingly documented to be dysfunctional in cancer genomes. However, our current understanding these alterations is limited. Here, we delineate the mutational landscape ∼1300 RBPs ∼6000 Our analysis revealed that have an average ∼3 mutations per Mb across 26 types. We identified 281 enriched for (GEMs) at least one type. GEM were found undergo frequent frameshift and inframe deletions as well...
Differing from the mouse Foxp3 gene that encodes only one protein product, human FOXP3 two major isoforms through alternative splicing—a longer isoform (FOXP3 FL) containing all coding exons and a shorter lacking amino acids encoded by exon 2 ΔE2). The are naturally expressed in humans, yet their differences controlling regulatory T cell phenotype functionality remain unclear. In this study, we show patients expressing fail to maintain self-tolerance develop immunodeficiency,...
In eukaryotic organisms, gene expression requires an additional level of coordination that links transcriptional and posttranslational processes. Messenger RNAs have traditionally been viewed as passive molecules in the pathway from transcription to translation. However, it is now clear RNA-binding proteins (RBPs) play important role cellular homeostasis by controlling at posttranscriptional level. Here, we show RBPs, a class proteins, distinct dynamics compared other protein coding genes...
Archaea, which represent a large fraction of the phylogenetic diversity organisms, are prokaryotes with eukaryote-like basal transcriptional machinery. This organization makes study their DNA-binding transcription factors (TFs) and regulatory networks particularly interesting. In addition, there limited experimental data regarding TFs. this work, 3,918 TFs were identified exhaustively analyzed in 52 archaeal genomes. represented less than 5% gene products all studied species comparable...
Abstract Expression of HOX transcript antisense intergenic RNA ( HOTAIR ), a large noncoding (lincRNA), has been described as metastases-associated lincRNA in various cancers including breast, liver and colon cancer cancers. We sought to determine if expression could be used surrogate for assessing nodal metastases evaluated situ hybridization (RNA-ISH) assay tissue microarray constructed from 133 breast patients. The prognostic value was further validated cohorts using Cancer Genome Atlas...