Genetics and Genomics Commons^™

Predicting Disease-Related Genes Using Integrated Biomedical Networks, Jiajie Peng, Kun Bai, Xuequn Shang, Guohua Wang, Hansheng Xue, Shuilin Jin, Liang Cheng, Yadong Wang, Jin Chen

Institute for Biomedical Informatics Faculty Publications

Background: Identifying the genes associated to human diseases is crucial for disease diagnosis and drug design. Computational approaches, esp. the network-based approaches, have been recently developed to identify disease-related genes effectively from the existing biomedical networks. Meanwhile, the advance in biotechnology enables researchers to produce multi-omics data, enriching our understanding on human diseases, and revealing the complex relationships between genes and diseases. However, none of the existing computational approaches is able to integrate the huge amount of omics data into a weighted integrated network and utilize it to enhance disease related gene discovery.

Results: We propose a new network-based disease …

The Subject Librarian Newsletter, Biology, Spring 2017, Sandy Avila

Libraries' Newsletters

No abstract provided.

High Throughput In Vivo Functional Validation Of Candidate Congenital Heart Disease Genes In Drosophila., Jun-Yi Zhu, Yulong Fu, Margaret Nettleton, Adam Richman, Zhe Han

Pediatrics Faculty Publications

Genomic sequencing has implicated large numbers of genes and de novo mutations as potential disease risk factors. A high throughput in vivo model system is needed to validate gene associations with pathology. We developed a Drosophila-based functional system to screen candidate disease genes identified from Congenital Heart Disease (CHD) patients. 134 genes were tested in the Drosophila heart using RNAi-based gene silencing. Quantitative analyses of multiple cardiac phenotypes demonstrated essential structural, functional, and developmental roles for more than 70 genes, including a subgroup encoding histone H3K4 modifying proteins. We also demonstrated the use of Drosophila to evaluate cardiac phenotypes resulting …

Restoration Of The Iconic Pando Aspen Clone: Emerging Evidence Of Recovery, Paul C. Rogers, Jody A. Gale

Aspen Bibliography

Quaking aspen (Populus tremuloides Michx.) is being stressed across the America West from a variety of sources including drought, herbivory, fire suppression, development, and past management practices. Rich assemblages of plants and animals that utilize aspen forests, as well as economic values of tourism, grazing, hunting, and water conservation, make aspen ecosystems among the most valuable vegetation types in this region. The 43-ha Pando clone near Fish Lake, Utah, is an iconic example of an aspen community undergoing rapid decline due to overstory mortality and chronic recruitment failure. As part of a larger project to restore Pando, we fenced, …

Penetrance Estimates For Incidental Genomic Findings In Acmg-59, James A. Diao

Yale Day of Data

The dropping costs and rising popularity of next-generation sequencing has introduced the possibility of personalizing medical treatments and screening for genetic diseases. Still, the clinical community’s understanding remains incomplete, with limited consensus on the proper interpretation for many genetic variants. Thus, the standard procedure when returning sequencing results has been to report findings only in genes related to the diagnostic indication, and not incidental findings in other genes. To balance the threat of false positives with the medical benefits of true findings, the American College on Medical Genetics and Genomics (ACMG) recommends an exception: that clinical sequencing laboratories seek and …

Familial Lung Cancer: A Brief History From The Earliest Work To The Most Recent Studies, Anthony Musolf, Claire Simpson, Mariza De Andrade, Diptasri Mandal, Colette Gaba, Ping Yang, Yafang Li

Dartmouth Scholarship

Lung cancer is the deadliest cancer in the United States, killing roughly one of four cancer patients in 2016. While it is well-established that lung cancer is caused primarily by environmental effects (particularly tobacco smoking), there is evidence for genetic susceptibility. Lung cancer has been shown to aggregate in families, and segregation analyses have hypothesized a major susceptibility locus for the disease. Genetic association studies have provided strong evidence for common risk variants of small-to-moderate effect. Rare and highly penetrant alleles have been identified by linkage studies, including on 6q23–25. Though not common, some germline mutations have also been identified …

Association Of Body Mass Index With Dna Methylation And Gene Expression In Blood Cells And Relations To Cardiometabolic Disease: A Mendelian Randomization Approach, Michael M. Mendelson, Riccardo E. Marioni, Roby Joehanes, Chunyu Liu, Åsa K. Hedman, Stella Aslibekyan, Ellen W. Demerath, Weihua Guan, Degui Zhi, Chen Yao, Tianxiao Huan, Christine Willinger, Brian Chen, Paul Courchesne, Michael Multhaup, Marguerite R. Irvin, Ariella Cohain, Eric E. Schadt, Megan L. Grove, Jan Bressler, Kari North, Johan Sundström, Stefan Gustafsson, Sonia Shah, Allan F. Mcrae, Sarah E. Harris, Jude Gibson, Paul Redmond, Janie Corley, Lee Murphy, Donna K. Arnett

Epidemiology and Environmental Health Faculty Publications

Background

The link between DNA methylation, obesity, and adiposity-related diseases in the general population remains uncertain.

Methods and Findings

We conducted an association study of body mass index (BMI) and differential methylation for over 400,000 CpGs assayed by microarray in whole-blood-derived DNA from 3,743 participants in the Framingham Heart Study and the Lothian Birth Cohorts, with independent replication in three external cohorts of 4,055 participants. We examined variations in whole blood gene expression and conducted Mendelian randomization analyses to investigate the functional and clinical relevance of the findings. We identified novel and previously reported BMI-related differential methylation at 83 CpGs …

Radiation Induced Apoptosis Of Murine Bone Marrow Cells Is Independent Of Early Growth Response 1 (Egr1), Karine Z. Oben, Beth W. Gachuki, Sara S. Alhakeem, Mary Kathryn Mckenna, Ying Liang, Daret K. St. Clair, Vivek M. Rangnekar, Subbarao Bondada

Microbiology, Immunology, and Molecular Genetics Faculty Publications

An understanding of how each individual 5q chromosome critical deleted region (CDR) gene contributes to malignant transformation would foster the development of much needed targeted therapies for the treatment of therapy related myeloid neoplasms (t-MNs). Early Growth Response 1 (EGR1) is a key transcriptional regulator of myeloid differentiation located within the 5q chromosome CDR that has been shown to regulate HSC (hematopoietic stem cell) quiescence as well as the master regulator of apoptosis—p53. Since resistance to apoptosis is a hallmark of malignant transformation, we investigated the role of EGR1 in apoptosis of bone marrow cells; a cell population from which …

Genome Analysis Of Clostridium Difficile Pcr Ribotype 014 Lineage In Australian Pigs And Humans Reveals A Diverse Genetic Repertoire And Signatures Of Long-Range Interspecies Transmission, Daniel R. Knight, Michael M. Squire, Deirdre A. Collins, Thomas V. Riley

Research outputs 2014 to 2021

Clostridium difficile PCR ribotype (RT) 014 is well-established in both human and porcine populations in Australia, raising the possibility that C. difficile infection (CDI) may have a zoonotic or foodborne etiology. Here, whole genome sequencing and high-resolution core genome phylogenetics were performed on a contemporaneous collection of 40 Australian RT014 isolates of human and porcine origin. Phylogenies based on MLST (7 loci, STs 2, 13, and 49) and core orthologous genes (1260 loci) showed clustering of human and porcine strains indicative of very recent shared ancestry. Core genome single nucleotide variant (SNV) analysis found 42 % of human strains showed …

Human-Nonhuman Chimeras, Ontology, And Dignity: A Constructivist Approach To The Ethics Of Conducting Research On Cross-Species Hybrids, Jonathan M. Vajda

The Hilltop Review

Developments in biological technology in the last few decades highlight the surprising and ever-expanding practical benefits of stem cells. With this progress, the possibility of combining human and nonhuman organisms is a reality, with ethical boundaries that are not readily obvious. These inter-species hybrids are of a larger class of biological entities called “chimeras.” As the concept of a human-nonhuman creature is conjured in our minds, either incredulous wonder or grotesque horror is likely to follow. This paper seeks to mitigate those worries and demotivate reasonable concerns raised against chimera research, all the while pressing current ethical positions toward their …

A Comparative Genomic Analysis Of Putative Pathogenicity Genes In The Host-Specific Sibling Species Colletotrichum Graminicola And Colletotrichum Sublineola, Ester A. S. Buiate, Katia Viana Xavier, Neil Moore, Maria F. Torres, Mark L. Farman, Christopher L. Schardl, Lisa J. Vaillancourt

Plant Pathology Faculty Publications

Background: Colletotrichum graminicola and C. sublineola cause anthracnose leaf and stalk diseases of maize and sorghum, respectively. In spite of their close evolutionary relationship, the two species are completely host-specific. Host specificity is often attributed to pathogen virulence factors, including specialized secondary metabolites (SSM), and small-secreted protein (SSP) effectors. Genes relevant to these categories were manually annotated in two co-occurring, contemporaneous strains of C. graminicola and C. sublineola. A comparative genomic and phylogenetic analysis was performed to address the evolutionary relationships among these and other divergent gene families in the two strains.

Results: Inoculation of maize with C. sublineola …

Inferring Condition-Specific Targets Of Human Tf-Tf Complexes Using Chip-Seq Data, Chia-Chun Yang, Min-Hsuan Chen, Sheng-Yi Lin, Erik H. Andrews, Chao Cheng, Jeremy J.W Chen

Dartmouth Scholarship

Background:

Transcription factors (TFs) often interact with one another to form TF complexes that bind DNA and regulate gene expression. Many databases are created to describe known TF complexes identified by either mammalian two-hybrid experiments or data mining. Lately, a wealth of ChIP-seq data on human TFs under different experiment conditions are available, making it possible to investigate condition-specific (cell type and/or physiologic state) TF complexes and their target genes.

Results:

Here, we developed a systematic pipeline to infer Condition-Specific Targets of human TF-TF complexes (called the CST pipeline) by integrating ChIP-seq data and TF motifs. In total, we predicted …

Organelle_Pba, A Pipeline For Assembling Chloroplast And Mitochondrial Genomes From Pacbio Dna Sequencing Data, Aboozar Soorni, David Haak, David Zaitlin, Aureliano Bombarely

Kentucky Tobacco Research and Development Center Faculty Publications

Background: The development of long-read sequencing technologies, such as single-molecule real-time (SMRT) sequencing by PacBio, has produced a revolution in the sequencing of small genomes. Sequencing organelle genomes using PacBio long-read data is a cost effective, straightforward approach. Nevertheless, the availability of simple-to-use software to perform the assembly from raw reads is limited at present.

Results: We present Organelle-PBA, a Perl program designed specifically for the assembly of chloroplast and mitochondrial genomes. For chloroplast genomes, the program selects the chloroplast reads from a whole genome sequencing pool, maps the reads to a reference sequence from a closely related species, and …

Predictive Screening Of M1 And M2 Macrophages Reveals The Immunomodulatory Effectiveness Of Post Spinal Cord Injury Azithromycin Treatment, John C. Gensel, Timothy J. Kopper, Bei Zhang, Michael B. Orr, William M. Bailey

Spinal Cord and Brain Injury Research Center Faculty Publications

Spinal cord injury (SCI) triggers a heterogeneous macrophage response that when experimentally polarized toward alternative forms of activation (M2 macrophages) promotes tissue and functional recovery. There are limited pharmacological therapies that can drive this reparative inflammatory state. In the current study, we used in vitrosystems to comprehensively defined markers of macrophages with known pathological (M1) and reparative (M2) properties in SCI. We then used these markers to objectively define the macrophage activation states after SCI in response to delayed azithromycin treatment. Mice were subjected to moderate-severe thoracic contusion SCI. Azithromycin or vehicle was administered beginning 30 minutes post-SCI and …

Genome Editing Of Wnt-1, A Gene Associated With Segmentation, Via Crispr/Cas9 In The Pine Caterpillar Moth, Dendrolimus Punctatus, Huihui Liu, Qun Liu, Xuguo Zhou, Yongping Huang, Zhen Zhang

Entomology Faculty Publications

The pine caterpillar moth, Dendrolimus punctatus, is a devastating forest pest. Genetic manipulation of this insect pest is limited due to the lack of genomic and functional genomic toolsets. Recently, CRISPR/Cas9 technology has been demonstrated to be a promising approach to modify the genome. To investigate gene functions during the embryogenesis, we introduced CRISPR/Cas9 system in D. punctatus to precisely and effectively manipulate gene expressions inmutant embryos. Compared to controls, knocking out of DpWnt-1, a gene well known for its role in the early body planning, led to high embryonic mortality. Among these mutants, 32.9% of the embryos …

Inhibition Of Mammalian Glycoprotein Ykl-40 Identification Of The Physiological Ligand, Abhishek A. Kognole, Christina M. Payne

Chemical and Materials Engineering Faculty Publications

YKL-40 is a mammalian glycoprotein associated with progression, severity, and prognosis of chronic inflammatory diseases and a multitude of cancers. Despite this well documented association, identification of the lectin′s physiological ligand and, accordingly, biological function has proven experimentally difficult. YKL-40 has been shown to bind chito-oligosaccharides; however, the production of chitin by the human body has not yet been documented. Possible alternative ligands include proteoglycans, polysaccharides, and fibers like collagen, all of which makeup the extracellular matrix. It is likely that YKL-40 is interacting with these alternative polysaccharides or proteins within the body, extending its function to cell biological roles …

Differential Methylation Between Ethnic Sub-Groups Reflects The Effect Of Genetic Ancestry And Environmental Exposures, Joshua M. Galanter, Christopher R. Gignoux, Sam S. Oh, Dara Torgerson, Maria Pino-Yanes, Neeta Thakur, Celeste Eng, Donglei Hu, Scott Huntsman, Harold J. Farber, Pedro C. Avila, Emerita Brigino-Buenaventura, Michael A. Lenoir, Kelly Meade, Denise Serebrisky, William Rodriguez-Cintron, Rajesh Kumar, Jose R. Rodrıguez-Cintron, Max A. Seibold, Luisa N. Borrell, Esteban G. Burchard, Noah Zaitlen

Publications and Research

Populations are often divided categorically into distinct racial/ethnic groups based on social rather than biological constructs. Genetic ancestry has been suggested as an alternative to this categorization. Herein, we typed over 450,000 CpG sites in whole blood of 573 individuals of diverse Hispanic origin who also had high-density genotype data. We found that both self- identified ethnicity and genetically determined ancestry were each significantly associated with methylation levels at 916 and 194 CpGs, respectively, and that shared genomic ancestry accounted for a median of 75.7% (IQR 45.8% to 92%) of the variance in methylation associated with ethnicity. There was a …

The Family Rhabdoviridae: Mono- And Bipartite Negative-Sense Rna Viruses With Diverse Genome Organization And Common Evolutionary Origins, Ralf G. Dietzgen, Hideki Kondo, Michael M. Goodin, Gael Kurath, Nikos Vasilakis

Plant Pathology Faculty Publications

The family Rhabdoviridae consists of mostly enveloped, bullet-shaped or bacilliform viruses with a negative-sense, single-stranded RNA genome that infect vertebrates, invertebrates or plants. This ecological diversity is reflected by the diversity and complexity of their genomes. Five canonical structural protein genes are conserved in all rhabdoviruses, but may be overprinted, overlapped or interspersed with several novel and diverse accessory genes. This review gives an overview of the characteristics and diversity of rhabdoviruses, their taxonomic classification, replication mechanism, properties of classical rhabdoviruses such as rabies virus and rhabdoviruses with complex genomes, rhabdoviruses infecting aquatic species, and plant rhabdoviruses with both mono- …

Structure Of The Chlorovirus Pbcv-1 Major Capsid Glycoprotein Determined By Combining Crystallographic And Carbohydrate Molecular Modeling Approaches, Cristina De Castro, Thomas Klose, Immacolata Speciale, Rosa Lanzetta, Antonio Molinaro, James L. Van Etten, Michael G. Rossmann

James Van Etten Publications

The glycans of the major capsid protein (Vp54) of Paramecium bursaria chlorella virus (PBCV-1) were recently described and found to be unusual. This prompted a reexamination of the previously reported Vp54 X-ray structure. A detailed description of the complete glycoprotein was achieved by combining crystallographic data with molecular modeling. The crystallographic data identified most of the monosaccharides located close to the protein backbone, but failed to detect those further from the glycosylation sites. Molecular modeling complemented this model by adding the missing monosaccharides and examined the conformational preference of the whole molecule, alone or within the crystallographic environment. Thus, combining …

Hepatocellular Cancer Genome And Transcriptome Analysis Validates Clinically Significant Mutational Signatures With The Tgf-𝛃 Pathway, Shuyun Rao, Jian Chen, Kazufumi Ohshiro, Shoujun Gu, Sobia Zaidi, Wilma S. Jogunoori, Jon White, Nagarajan Pattabiraman, Raja Mazumder, Anelia Horvath, Ray-Chang Wu, Shulin Li, Chuxia Deng, Bibhuti Mishra, Rehan Akbanni, The Tcga Cancer Network, Lopa Mishra

Hepatobiliary Cancers: Pathobiology and Translational Advances

No abstract provided.

Oncogenic Nelfe Enhances Myc-Induced Hepatocellular Carcinogenesis, Hien Dang, Atsushi Takai, Marshonna Forgues, Yosawat Pomyen, Haiwei Mou, Wen Xue, Debashish Ray, Kevn Ha, Quiad Morris, Timothy Hughes, Xin Wei Wang

Hepatobiliary Cancers: Pathobiology and Translational Advances

No abstract provided.

Scanning Labyrinthulomycete Genomes For Yeast Transcription Factor Binding Site Motifs, Jackie L. Collier, Joshua Rest

Interdisciplinary Research Data

To develop broadly useful methods for the genetic manipulation of Labyrinthulomycetes (a diverse group of ubiquitous osmoheterotrophic marine protists), it is essential to understand the similarities and differences in regulation of gene expression among them. Toward this end we have used FIMO from the MEME suite (http://meme-suite.org/doc/fimo.html) to identify potential transcription factor binding sites in each of the three available genome sequences: Aplanochytrium kerguelense PBS07, Schizochytrium aggregatum ATCC 28209, and Aurantiochytrium limacinum ATCC MYA-1381

Distribution Bias Analysis Of Germline And Somatic Single-Nucleotide Variations That Impact Protein Functional Site And Neighboring Amino Acids, Y Pan, C Yan, Y Hu, Y Fan, Qing Pan, Q Wan, J Torcivia-Rodriguez, Raja Mazumder

Biochemistry and Molecular Medicine Faculty Publications

Single nucleotide variations (SNVs) can result in loss or gain of protein functional sites. We analyzed the effects of SNVs on enzyme active sites, ligand binding sites, and various types of post translational modification (PTM) sites. We found that, for most types of protein functional sites, the SNV pattern differs between germline and somatic mutations as well as between synonymous and non-synonymous mutations. From a total of 51,138 protein functional site affecting SNVs (pfsSNVs), a pan-cancer analysis revealed 142 somatic pfsSNVs in five or more cancer types. By leveraging patient information for somatic pfsSNVs, we identified 17 loss of functional …

Fit For Genomic And Proteomic Purposes: Sampling The Fitness Of Nucleic Acid And Protein Derivatives From Formalin Fixed Paraffin Embedded Tissue., Anna Yakovleva, Jordan L Plieskatt, Sarah Jensen, Razan Humeida, Jonathan Lang, Guangzhao Li, Paige Bracci, Sylvia Silver, Jeffrey Michael Bethony

Microbiology, Immunology, and Tropical Medicine Faculty Publications

The demand for nucleic acid and protein derivatives from formalin-fixed paraffin-embedded (FFPE) tissue has greatly increased due to advances in extraction and purification methods, making these derivatives available for numerous genomic and proteomic platforms. Previously, DNA, RNA, microRNA (miRNA), or protein derived from FFPE tissue blocks were considered “unfit” for such platforms, as the process of tissue immobilization by FFPE resulted in cross-linked, fragmented, and chemically modified macromolecules. We conducted a systematic examination of nucleic acids and proteins co-extracted from 118 FFPE blocks sampled from the AIDS and Cancer Specimen Resource (ACSR) at The George Washington University after stratification by …

Human Ipsc-Derived Cerebellar Neurons From A Patient With Ataxia-Telangiectasia Reveal Disrupted Gene Regulatory Networks, Sam Nayler, Joseph Powell, Darya Vanichkina, Othmar Korn, Christine Wells, Ryan J. Taft, +Several Additional Authors

Genomics and Precision Medicine Faculty Publications

Ataxia-telangiectasia (A-T) is a rare genetic disorder caused by loss of function of the ataxia-telangiectasia-mutated kinase and is characterized by a predisposition to cancer, pulmonary disease, immune deficiency and progressive degeneration of the cerebellum. As animal models do not faithfully recapitulate the neurological aspects, it remains unclear whether cerebellar degeneration is a neurodevelopmental or neurodegenerative phenotype. To address the necessity for a human model, we first assessed a previously published protocol for the ability to generate cerebellar neuronal cells, finding it gave rise to a population of precursors highly enriched for markers of the early hindbrain such as EN1 and …

Mrub_1873, Mrub_1872, Mrub_1871 Genes Are Predicted Orthologs Of The B2285, B2284, And B2283 Genes Respectively, Found In Escherichia Coli Coding For Nadh Ubiquinone Oxidoreductase Complex Subunits E, F, And G., Hannah Lohmeier, Dr. Lori R. Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_1873, Mrub_1872, and Mrub_1871.We predict that Mrub_1873 (DNA coordinates 1933743..1934309 on the reverse strand), Mrub_1872 (DNA coordinates 1932430..1933746 on the reverse strand), and Mrub_1871 (DNA coordinates 1930055..1932421 on the reverse strand) are subunits of the NADH ubiquinone oxidoreductase complex (00190). The complex catalyzes both the transfer of protons across the cytoplasmic membrane and the transfer of electrons to ubiquinone during …

Mrub_2294, Mrub_2293, And Mrub_1942 Genes Are Orthologs Of E. Coli B2476, B1131, And B4006 Genes, Respectively, Lindsay Popp, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

No abstract provided.

Annotation And Identification Of Several Glycerolipid Metabolic Related Ortholog Genes; Mrub_0437, Mrub_1813 And Mrub_2759 In The Organism Meithermus Ruber And Their Predicted Respective Orthologs B3926, B4042 And Bo514 Found In E.Coli., Abdul Rahman Abdul Kader, Dr. Lori R. Scott

Meiothermus ruber Genome Analysis Project

We predict Mrub_0437 encodes the enzyme glycerol kinase (DNA coordinates [417621..419183), which is an intermediary step of the glycerolipid metabolic pathway (KEGG map00561), It catalyzes the conversion of glycerol to sn-Glycerol-3-phosphate. The E. coli K12 MG1655 ortholog is predicted to be b3926.

We predict Mrub_1813 encodes the enzyme diacylglycerol kinase (DNA coordinates [1864659..1865063), which is an intermediary step of the glycerolipid metabolic pathway (KEGG map00561), It catalyzes the conversion of 1,2-diacyl-sn-glycerol to 1,2-diacyl-sn-glycerol 3-phosphate. The E. coli K12 MG1655 ortholog is predicted to be b4042.

We predict Mrub_2759 encodes the enzyme glycerol kinase (DNA coordinates [2799712..2800665), which is an intermediary …

Serine Biosynthesis And Glycine Biosynthesis/Degradation: Mrub_0173 Is Orthologous To E. Coli B2913 (Sera); Mrub_0125 Is Orthologous To E. Coli B4388 (Serb); Mrub_2910 Is Orthologous To E. Coli B2551 (Glya)., Megan M. Janssen, Dr. Lori R. Scott

Meiothermus ruber Genome Analysis Project

ABSTRACT. This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_0173, Mrub_0125, and Mrub_ 2910. We predict that Mrub_0173 encodes the enzyme phosphoglycerate dehydrogenase (DNA coordinates 152982 ... 154347), which is the 1st step of the serine biosynthesis pathway (KEGG map number 00680). It catalyzes the conversion of NAD+ + 3-phospho-D-glycerate → NADH H+ + 3-phospho-hydroxypyruvate. The E. coli K12 MG1655 ortholog is predicted to be b2913, which has …

Mrub_3029, Mrub_2052, Are Predicted Orthologs Of B_0688, B_0394, While Mrub_0759 And Mrub_2365 Are Not Predicted Orthologs Of B_1309, In Escherichia Coli, Which Code For Enzymes Involved In Starch And Sucrose Metabolism, Max A. Benstine, Dr. Lori R. Scott

Meiothermus ruber Genome Analysis Project

We predict that Mrub__[0759] encodes the enzyme [Meiothermus ruber Fruktokinase] (DNA coordinates [741282..742202 on the forward strand] which is the 00500 step of the Starch and Sucrose Metabolism pathway (KEGG map number [2.7.1.4]). It catalyzes the conversion of [ATP + D-fructoseADP + D-fructose 6-phosphate]. The E. coli K12 MG1655 ortholog is predicted to be b1309, which has the gene identifier [ycjM] We predict that Mrub__[ 2365] encodes the enzyme [Meiothermus ruber Fruktokinase] (DNA coordinates [2417118..2418059 on the forward strand], which is the [00500] step of the [Starch and Sucrose Metabolism] pathway (KEGG map number [2.7.1.4]). It catalyzes the …