Life Sciences Commons^™

Genetic Effect Of The Dwarfing Genes On Some Culm Characteristics Associatcd With Lodging Resistance In Bread Wheat, Md. Mahbub Hasan

Md. Mahbub Hasan

Due to the challenge of screening traits related to lodging resistance under natural field conditions, selection for lodging resistant varieties in wheat breeding programs is difficult. The identification of easily measurable culm anatomical traits related to lodging resistance would simplify the selection process. The present study was conducted to determine the effect of dwarfing genes on culm anatomical traits related to lodging resistance in our of basal internode 1. Field and laboratory study was conducted in Shahjalal University of Science and Technology, Sylhet, Bangladesh with eight wheat genotypes having Rhr1, Rht2 dwarfing genes in them and a local land race …

Francisella Tularensis Type A Strains Cause The Rapid Encystment Of Acanthamoeba Castellanii And Survive In Amoebal Cysts For Three Weeks Postinfection, Jeffrey J. Margolis, Sahar H. El-Etr, Denise Monack, Richard A. Robinson, Marissa Cohen, Emily Moore, Amy Rasley

Jeffrey Margolis

Proteogenomic Monitoring Of Geobacter Physiology During Stimulated Uranium Bioremdiation, Michael J. Wilkins, Nathan C. Verberkmes, Kenneth H. Williams, Stephen J. Callister, Paula J. Mouser, Hila Elifantz, A. Lucie N'Guessan, Brian C. Thomas, Carrie D. Nicora, Manesh B. Shah, Paul Abraham, Mary S. Lipton, Derek Lovley, Robert L. Hettich, Philip E. Long, Jillian F. Banfield

Derek Lovley

Implementation of uranium bioremediation requires methods for monitoring the membership and activities of the subsurface microbial communities that are responsible for reduction of soluble U(VI) to insoluble U(IV). Here, we report a proteomics-based approach for simultaneously documenting the strain membership and microbial physiology of the dominant Geobacter community members during in situ acetate amendment of the U-contaminated Rifle, CO, aquifer. Three planktonic Geobacter-dominated samples were obtained from two wells down-gradient of acetate addition. Over 2,500 proteins from each of these samples were identified by matching liquid chromatography-tandem mass spectrometry spectra to peptides predicted from seven isolate Geobacter genomes. Genome-specific peptides …

Archaeal Populations In Biological Soil Crusts From Arid Lands In North America, Tanya Soule, Ian J. Anderson, Shannon L. Johnson, Scott T. Bates, Ferran Garcia-Pichel

Tanya Soule

Archaea are common and abundant members of biological soil crust communities across large-scale biogeographic provinces of arid North America. Regardless of microbial community development, archaeal populations averaged 2 × 107 16S rRNA gene copies per gram of soil, representing around 5% of the prokaryotic (total calculated bacterial and archaeal) numbers assessed by quantitative-PCR. In contrast, archaeal diversity, determined by denaturing gradient gel electrophoresis fingerprinting and clone libraries of 16S rRNA genes, was very restricted. Only six different phylotypes (all Crenarchaea) were detected, three of which were very dominant. Some phylotypes were widespread, while others were typical of Southern desert areas.

Tracking Insertion Mutants Within Libraries By Deep Sequencing And A Genome-Wide Screen For Haemophilus Genes Required In The Lung, Jeffrey D. Gawronski, Sandy M. S. Wong, Georgia Giannoukos, Doyle V. Ward, Brian J. Akerley

Brian J. Akerley

Rapid genome-wide identification of genes required for infection would expedite studies of bacterial pathogens. We developed genome-scale "negative selection" technology that combines high-density transposon mutagenesis and massively parallel sequencing of transposon/chromosome junctions in a mutant library to identify mutants lost from the library after exposure to a selective condition of interest. This approach was applied to comprehensively identify Haemophilus influenzae genes required to delay bacterial clearance in a murine pulmonary model. Mutations in 136 genes resulted in defects in vivo, and quantitative estimates of fitness generated by this technique were in agreement with independent validation experiments using individual mutant strains. …

A Comparative Genomics Approach To Understanding The Biosynthesis Of The Sunscreen Scytonemin In Cyanobacteria, Tanya Soule, Kendra Palmer, Qunjie Gao, Ruth M. Potrafka, Valerie Stout, Ferran Garcia-Pichel

Tanya Soule

Background The extracellular sunscreen scytonemin is the most common and widespread indole-alkaloid among cyanobacteria. Previous research using the cyanobacterium Nostoc punctiforme ATCC 29133 revealed a unique 18-gene cluster (NpR1276 to NpR1259 in the N. punctiforme genome) involved in the biosynthesis of scytonemin. We provide further genomic characterization of these genes in N. punctiforme and extend it to homologous regions in other cyanobacteria.

Results Six putative genes in the scytonemin gene cluster (NpR1276 to NpR1271 in the N. punctiforme genome), with no previously known protein function and annotated in this study as scyA to scyF, are likely involved in the assembly …

Identification Of Synechococcus Sp. Iu 625 Phycocyanin Gene And Bioinformatic Analyses Of Cyanobacterial Phycocyanin., Tin-Chun Chu, Aline Oliveira, Arti Rana, Lee Lee

Tin-Chun Chu, Ph.D.

No abstract provided.

Gene Expression Patterns Associated With The Biosynthesis Of The Sunscreen Scytonemin In Nostoc Punctiforme Atcc 29133 In Response To Uva Radiation, Tanya Soule, Ferran Garcia-Pichel, Valerie Stout

Tanya Soule

Under exposure to UV radiation, some cyanobacteria synthesize sunscreen compounds. Scytonemin is a heterocyclic indole-alkaloid sunscreen, the synthesis of which is induced upon exposure to UVA (long-wavelength UV) radiation. We previously identified and characterized an 18-gene cluster associated with scytonemin biosynthesis in the cyanobacterium Nostoc punctiforme ATCC 29133; we now report on the expression response of these genes to a step-up shift in UVA exposure. Using quantitative PCR on cDNAs from the N. punctiforme transcriptome and primers targeting each of the 18 genes in the cluster, we followed their differential expression in parallel subcultures incubated with and without UVA. All …

Discovery Of Dual Function Acridones As A New Antimalarial Chemotype, Jane X. Kelly, Martin J. Smilkstein, Reto Brun, Sergio Wittlin, Roland A. Cooper, Kristin D. Lane, Aaron Janowsky, Robert A. Johnson, Rozalia A. Dodean, Rolf Winter, David J. Hinrichs, Michael K. Riscoe

Roland A. Cooper

Metabolic Variability In Seafloor Brines Revealed By Carbon And Sulphur Dynamics, Samantha B. Joye, Vladimir A. Samarkin, Beth! N. Orcutt, Ian R. Macdonald, Kai-Uwe Hinrichs, Marcus Elvert, Andreas P. Teske, Karen Lloyd, Mark A. Lever, Joseph P. Montoya, Christof D. Meile

Karen Lloyd

Brine fluids that upwell from deep, hot reservoirs below the sea bed supply the sea floor with energy-rich substrates and nutrients that are used by diverse microbial ecosystems. Contemporary hypersaline environments formed by brine seeps may provide insights into the metabolism and distribution of microorganisms on the early Earth or on extraterrestrial bodies. Here we use geochemical and genetic analyses to characterize microbial community composition and metabolism in two seafloor brines in the Gulf of Mexico: an active mud volcano and a quiescent brine pool. Both brine environments are anoxic and hypersaline. However, rates of sulphate reduction and acetate production …

The Generation Of Influenza-Specific Humoral Responses Is Impaired In St6gal I-Deficient Mice., Thandi M. Onami, J Zeng, H. M. Joo, B. Rajini, J. P. Wrammert, M. Y. Sangster

Thandi M. Onami

Posttranslational modification of proteins, such as glycosylation, can impact cell signaling and function. ST6Gal I, a glycosyltransferase expressed by B cells, catalyzes the addition of alpha-2,6 sialic acid to galactose, a modification found on N-linked glycoproteins such as CD22, a negative regulator of B cell activation. We show that SNA lectin, which binds alpha-2,6 sialic acid linked to galactose, shows high binding on plasma blasts and germinal center B cells following viral infection, suggesting ST6Gal I expression remains high on activated B cells in vivo. To understand the relevance of this modification on the antiviral B cell immune response, we …

Interregional Comparison Of Karst Disturbance: West-Central Florida And Southeast Italy, Leslie North

Leslie North

Chapter 20:The Impact Of Probiotics On Maternal And Child Health: Clinical Evidence., Kingsley Anukam, Gregor Reid

Kingsley C Anukam

Key Points • Alleviating the problems of maternal and child health in countries with large malnourished and/or HIV-infected populations, will require multidimensional approaches including holistic and pharmaceutical interventions. • Urogenital infections have a major role in preterm labor and the well-being of newborns. • Probiotics show potential in reducing the risk of recurrence of urinary tract infection (UTI). • There is some evidence to suggest that probiotics can have a role to play in bacterial vaginosis (BV) and maternal health. • The role of probiotics in a number of newborn, and childhood diseases is reviewed in this chapter.

Coupling A Genome-Scale Metabolic Model With A Reactive Transport Model To Describe In Situ Uranium Bioremediation, Derek Lovley, Timothy D. Scheibe, Radhakrishnan Mahadeven, Yilin Fang, Srinath Garg, Philip E. Long

Derek Lovley

The increasing availability of the genome sequences of microorganisms involved in important bioremediation processes makes it feasible to consider developing genome-scale models that can aid in predicting the likely outcome of potential subsurface bioremediation strategies. Previous studies of the in situ bioremediation of uranium-contaminated groundwater have demonstrated that Geobacter species are often the dominant members of the groundwater community during active bioremediation and the primary organisms catalysing U(VI) reduction. Therefore, a genome-scale, constraint-based model of the metabolism of Geobacter sulfurreducens was coupled with the reactive transport model HYDROGEOCHEM in an attempt to model in situ uranium bioremediation. In order to …

Future Shock From The Microbe Electric (In Crystal Ball), Derek Lovley

Derek Lovley

No abstract provided.

Genome-Scale Constraint-Based Modeling Of Geobacter Metallireducens, Derek Lovley, Jun Sun, Bahareh Sayyar, Jessica E. Butler, Priti Pharkya, Tom R. Fahland, Iman Famili, Christophe H. Schillng

Derek Lovley

Background: Geobacter metallireducens was the first organism that can be grown in pure culture to completely oxidize organic compounds with Fe(III) oxide serving as electron acceptor. Geobacter species, including G. sulfurreducens and G. metallireducens, are used for bioremediation and electricity generation from waste organic matter and renewable biomass. The constraint-based modeling approach enables the development of genome-scale in silico models that can predict the behavior of complex biological systems and their responses to the environments. Such a modeling approach was applied to provide physiological and ecological insights on the metabolism of G. metallireducens.

Results: The genome-scale metabolic model of G. …

Evaluation Of Glyphosate-Tolerant Soybean Cultivars For Resistance To Bacterial Pustule, Lopa Goradia, Glen Hartman, Steven L. Daniel

Steven L. Daniel

Xanthomonas axonopodis pv. glycines causes bacterial pustule of soybean, which is a common disease in many soybean-growing areas of the world and is controlled by a single recessive gene (rxp gene) commonly found in many conventional glyphosate-sensitive soybean cultivars. Since glyphosate-tolerant cultivars are commonly planted today, there has been no information about whether these new cultivars have bacterial pustule resistance. The goal of this study was to screen glyphosate-tolerant soybean cultivars for resistance to X. axonopodis pv. glycines. Three experiments were completed to evaluate resistance. In experiment 1, 525 commercial glyphosate-tolerant cultivars from 2001 were inoculated with X. axonopodis pv. …

First Report Of Sweet Wormwood Leaf Blight Disease In India, Kunal Mandal

Kunal Mandal

Artemisia annua is an important drug plant yielding antimalarial compounds. It was found to be infected by Alternaria alternata in India. The pathogen reduces active leaf area and is also known to produce mycotoxins. Hence, the disease demands serious attention to ensure the availability of a safe drug.

The Evolution Of Reduced Microbial Killing, Jan A.C. Vriezen Dr., Michael Valliere, Margaret A. Riley Dr.

Jan A.C. Vriezen Dr.

Bacteria engage in a never-ending arms race in which they compete for limited resources and niche space. The outcome of this intense interaction is the evolution of a powerful arsenal of biological weapons. Perhaps the most studied of these are colicins, plasmid-based toxins produced by and active against Escherichia coli. The present study was designed to explore the molecular responses of a colicin-producing strain during serial transfer evolution. What evolutionary changes occur when colicins are produced with no target present? Can killing ability be maintained in the absence of a target? To address these, and other, questions, colicinogenic strains and …

Effect Of Aqueous Extract Of Aegle Marmelos Fruit On Adherence And Β-Lactam Resistance Of Enteropathogenic Escherichia Coli By Down Regulating Outer Membrane Protein C, Murali Malliga Raman

Murali Malliga Raman

Problem statement: Enteropathogenic Escherichia Coli (EPEC) continue to be a major health problem, leading to death due to diarrhea, predominantly in children below the age of five. Due to evolution of multi drug resistance in EPEC and side effects caused to host by antibiotics necessitated a search for alternative medicines from medicinal plants. One such medicinal plant used since ancient times to cure diarrhea is Aegle marmelos. This study was done to investigate the effect of aqueous extract of Aegle marmelos fruit (AEAM) on outer membrane protein C (OmpC) of EPEC, which plays a key role in adherence and antibiotic …

Furfural Inhibits Growth By Limiting Sulfur Assimilation In Ethanologenic Escherichia Coli Strain Ly180, Elliot N. Miller, Laura R. Jarboe, Peter C. Turner, Prita Pharkya, Lorraine P. Yomano, Sean W. York, David Nunn, K. T. Shanmugan, Lonnie O. Ingram

Laura R. Jarboe

A wide variety of commercial products can be potentially made from monomeric sugars produced by the dilute acid hydrolysis of lignocellulosic biomass. However, this process is accompanied by side products such as furfural that hinder microbial growth and fermentation. To investigate the mechanism of furfural inhibition, mRNA microarrays of an ethanologenic strain of Escherichia coli (LY180) were compared immediately prior to and 15 min after a moderate furfural challenge. Expression of genes and regulators associated with the biosynthesis of cysteine and methionine was increased by furfural, consistent with a limitation of these critical metabolites. This was in contrast to a …

Silencing Of Nadph-Dependent Oxidoreductase Genes (Yqhd And Dkga) In Furfural-Resistant Ethanologenic Escherichia Coli, Elliot N. Miller, Laura R. Jarboe, L. P. Yomano, S. W. York, K. T. Shanmugam, L. O. Ingram

Laura R. Jarboe

Low concentrations of furfural are formed as a side product during the dilute acid hydrolysis of hemicellulose. Growth is inhibited by exposure to furfural but resumes after the complete reduction of furfural to the less toxic furfuryl alcohol. Growth-based selection was used to isolate a furfural-resistant mutant of ethanologenic Escherichia coli LY180, designated strain EMFR9. Based on mRNA expression levels in the parent and mutant in response to furfural challenge, genes encoding 12 oxidoreductases were found to vary by more than twofold (eight were higher in EMFR9; four were higher in the parent). All 12 genes were cloned. When expressed …

Genome-Scale Comparison And Constraint-Based Metabolic Reconstruction Of The Facilitative Anaerobic Fe(Iii)-Reducer Rhodoferax Ferrireducens, Derek Lovley, Carla Risso, Jun Sun, Kai Zhuang, Radhakrishnan Mahadevan, Robert Deboy, Wael Ismail, Susmita Shrivastava, Heather Huot, Sagar Kothari, Sean Daughtry, Olivia Bui, Christophe H. Schilling, Barbara A. Methѐ

Derek Lovley

Background Rhodoferax ferrireducens is a metabolically versatile, Fe(III)-reducing, subsurface microorganism that is likely to play an important role in the carbon and metal cycles in the subsurface. It also has the unique ability to convert sugars to electricity, oxidizing the sugars to carbon dioxide with quantitative electron transfer to graphite electrodes in microbial fuel cells. In order to expand our limited knowledge about R. ferrireducens, the complete genome sequence of this organism was further annotated and then the physiology of R. ferrireducens was investigated with a constraint-based, genome-scale in silico metabolic model and laboratory studies. Results The iterative modeling and …

Evolution From A Respiratory Ancestor To Fill Syntrophic And Fermentative Niches: Comparative Genomics Of Six Geobacteraceae Species, Derek Lovley, Jessica E. Butler, Nelson D. Young

Derek Lovley

Background The anaerobic degradation of organic matter in natural environments, and the biotechnical use of anaerobes in energy production and remediation of subsurface environments, both require the cooperative activity of a diversity of microorganisms in different metabolic niches. The Geobacteraceae family contains members with three important anaerobic metabolisms: fermentation, syntrophic degradation of fermentation intermediates, and anaerobic respiration. Results In order to learn more about the evolution of anaerobic microbial communities, the genome sequences of six Geobacteraceae species were analyzed. The results indicate that the last common Geobacteraceae ancestor contained sufficient genes for anaerobic respiration, completely oxidizing organic compounds with the …

The Genome Sequence Of Geobacter Metallireducens: Features Of Metabolism, Physiology And Regulation Common And Dissimilar To Geobacter Sulfurreducens, Derek Lovley, Muktak Aklujkar, Julia Krushkal, Genevieve Dibartolo, Alla Lapidus, Miriam L. Land

Derek Lovley

BACKGROUND: The genome sequence of Geobacter metallireducens is the second to be completed from the metal-respiring genus Geobacter, and is compared in this report to that of Geobacter sulfurreducens in order to understand their metabolic, physiological and regulatory similarities and differences. RESULTS: The experimentally observed greater metabolic versatility of G. metallireducens versus G. sulfurreducens is borne out by the presence of more numerous genes for metabolism of organic acids including acetate, propionate, and pyruvate. Although G. metallireducens lacks a dicarboxylic acid transporter, it has acquired a second putative succinate dehydrogenase/fumarate reductase complex, suggesting that respiration of fumarate was important until …

Anode Biofilm Transcriptomics Reveals Outer Surface Components Essential For High Density Current Production In Geobacter Sulfurreducens Fuel Cells, Derek Lovley, Kelly P. Nevin, Byoung-Chan Kim, Richard H. Glaven, Jessica P. Johnson, Trevor L. Woodard, Barbara A. Methѐ, Raymond J. Didonato Jr., Sean F. Covalla, Ashley E. Franks, Anna Liu

Derek Lovley

The mechanisms by which Geobacter sulfurreducens transfers electrons through relatively thick (>50 µm) biofilms to electrodes acting as a sole electron acceptor were investigated. Biofilms of Geobacter sulfurreducens were grown either in flow-through systems with graphite anodes as the electron acceptor or on the same graphite surface, but with fumarate as the sole electron acceptor. Fumarate-grown biofilms were not immediately capable of significant current production, suggesting substantial physiological differences from current-producing biofilms. Microarray analysis revealed 13 genes in current-harvesting biofilms that had significantly higher transcript levels. The greatest increases were for pilA, the gene immediately downstream of pilA, and …

Novel Strategy For Three-Dimensional Real-Time Imaging Of Microbial Fuel Cell Communities: Monitoring The Inhibitory Effects Of Proton Accumulation Within The Anode Biofilm, Derek Lovley, Ashley E. Franks, Kelly P. Nevin, Hongfei Jia, Mounir Izallalen, Trevor L. Woodard

Derek Lovley

Harvesting electricity from the environment, organic wastes, or renewable biomass with microbial fuel cells (MFCs) is an appealing strategy, but the destructive sampling required to investigate the anode-associated biofilms has hampered research designed to better understand and optimize microbe–anode interactions. Therefore, a MFC that permits real-time imaging of the anode biofilm with confocal scanning laser microscopy was developed. In this new MFC Geobacter sulfurreducens, an organism closely related to those often found on MFC anodes and capable of high current densities, produced current comparable to that previously reported with other MFC designs. G. sulfurreducens engineered to produce the fluorescent protein …

Genome-Wide Analysis Of The Rpon Regulon In Geobacter Sulfurreducens, Derek Lovley, Ching Leang, Julia Krushkal, Toshiyuki Ueki, Marko Puljic, Jun Sun, Katy Juárez, Chinthia Núñez, Gemma Reguera, Raymond Didonato, Bradley Postier, Ronald M. Adkins

Derek Lovley

Background The role of the RNA polymerase sigma factor RpoN in regulation of gene expression in Geobacter sulfurreducens was investigated to better understand transcriptional regulatory networks as part of an effort to develop regulatory modules for genome-scale in silico models, which can predict the physiological responses of Geobacter species during groundwater bioremediation or electricity production. Results An rpoN deletion mutant could not be obtained under all conditions tested. In order to investigate the regulon of the G. sulfurreducens RpoN, an RpoN over-expression strain was made in which an extra copy of the rpoN gene was under the control of a …

Anode Biofilm Transcriptomics Reveals Outer Surface Components Essential For High Density Current Production In Geobacter Sulfurreducens Fuel Cells, Derek Lovley, Kelly P. Nevin, Byoung-Chan Kim, Richard H. Glaven, Jessica P. Johnson, Trevor L. Woodard, Barbara A. Methѐ, Raymond J. Didonato Jr., Sean F. Covalla, Ashley E. Franks, Anna Liu

Kelly Nevin

The mechanisms by which Geobacter sulfurreducens transfers electrons through relatively thick (>50 µm) biofilms to electrodes acting as a sole electron acceptor were investigated. Biofilms of Geobacter sulfurreducens were grown either in flow-through systems with graphite anodes as the electron acceptor or on the same graphite surface, but with fumarate as the sole electron acceptor. Fumarate-grown biofilms were not immediately capable of significant current production, suggesting substantial physiological differences from current-producing biofilms. Microarray analysis revealed 13 genes in current-harvesting biofilms that had significantly higher transcript levels. The greatest increases were for pilA, the gene immediately downstream of pilA, and …

Bioinformatic Analysis Of Gene Regulation In Geobacter Sulfurreducens, Derek Lovley, Julia Krushkal, Yanhua Qu, Peter Brown, Sreedhar Sontineni, Toshiyuki Ueki, Katy Juarez, Ching Leang, Enrique Merino, Jeanette Peeples, Jose F. Barbe, Ronald M. Adkins

Derek Lovley

Background Geobacteraceae are a family of microorganisms from the delta subdivision of Proteobacteria. They have potential for environmental bioremediation and electricity generation. In this presentation, we describe our recent bioinformatic analyses of gene regulation in Geobacter sulfurreducens, a model representative of this family. Results and conclusion We have developed an online database, GSEL (Geobacter Sequence Elements), which compiles regulatory information for G. sulfurreducens. We have recently completed the development of a new, significantly expanded and updated, relational version 2 of the GSEL database and its accompanying online query system, which compiles manually curated information on operon organization and transcription regulatory …