Catalogue Search | MBRL
Are you sure you want to remove the book from the shelf?
{{itemTitle}}
5,854
result(s) for
"Cole, Jeff"
Sort by:
Soil HONO emissions at high moisture content are driven by microbial nitrate reduction to nitrite: tackling the HONO puzzle
Nitrous acid (HONO) is a precursor of the hydroxyl radical (OH), a key oxidant in the degradation of most air pollutants. Field measurements indicate a large unknown source of HONO during the day time. Release of nitrous acid (HONO) from soil has been suggested as a major source of atmospheric HONO. We hypothesize that nitrite produced by biological nitrate reduction in oxygen-limited microzones in wet soils is a source of such HONO. Indeed, we found that various contrasting soil samples emitted HONO at high water-holding capacity (75–140%), demonstrating this to be a widespread phenomenon. Supplemental nitrate stimulated HONO emissions, whereas ethanol (70% v/v) treatment to minimize microbial activities reduced HONO emissions by 80%, suggesting that nitrate-dependent biotic processes are the sources of HONO. High-throughput Illumina sequencing of 16S rRNA as well as functional gene transcripts associated with nitrate and nitrite reduction indicated that HONO emissions from soil samples were associated with nitrate reduction activities of diverse
Proteobacteria
. Incubation of pure cultures of bacterial nitrate reducers and gene-expression analyses, as well as the analyses of mutant strains deficient in nitrite reductases, showed positive correlations of HONO emissions with the capability of microbes to reduce nitrate to nitrite. Thus, we suggest biological nitrate reduction in oxygen-limited microzones as a hitherto unknown source of atmospheric HONO, affecting biogeochemical nitrogen cycling, atmospheric chemistry, and global modeling.
Journal Article
Nitrate, bacteria and human health
Nitrate is generally considered a water pollutant and an undesirable fertilizer residue in the food chain. Research in the 1970s indicated that, by reducing nitrate to nitrite, commensal bacteria might be involved in the pathogenesis of gastric cancers and other malignancies, as nitrite can enhance the generation of carcinogenic N-nitrosamines. More recent studies indicate that the bacterial metabolism of nitrate to nitrite and the subsequent formation of biologically active nitrogen oxides could be beneficial. Here, we will consider the evidence that nitrate-reducing commensals have a true symbiotic role in mammals and facilitate a previously unrecognized but potentially important aspect of the nitrogen cycle.
Journal Article
Loss of YhcB results in dysregulation of coordinated peptidoglycan, LPS and phospholipid synthesis during Escherichia coli cell growth
The cell envelope is essential for viability in all domains of life. It retains enzymes and substrates within a confined space while providing a protective barrier to the external environment. Destabilising the envelope of bacterial pathogens is a common strategy employed by antimicrobial treatment. However, even in one of the best studied organisms, Escherichia coli , there remain gaps in our understanding of how the synthesis of the successive layers of the cell envelope are coordinated during growth and cell division. Here, we used a whole-genome phenotypic screen to identify mutants with a defective cell envelope. We report that loss of yhcB , a conserved gene of unknown function, results in loss of envelope stability, increased cell permeability and dysregulated control of cell size. Using whole genome transposon mutagenesis strategies, we report the comprehensive genetic interaction network of yhcB , revealing all genes with a synthetic negative and a synthetic positive relationship. These genes include those previously reported to have a role in cell envelope biogenesis. Surprisingly, we identified genes previously annotated as essential that became non-essential in a Δ yhcB background. Subsequent analyses suggest that YhcB functions at the junction of several envelope biosynthetic pathways coordinating the spatiotemporal growth of the cell, highlighting YhcB as an as yet unexplored antimicrobial target.
Journal Article
Glycine acylation and trafficking of a new class of bacterial lipoprotein by a composite secretion system
Protein acylation is critical for many cellular functions across all domains of life. In bacteria, lipoproteins have important roles in virulence and are targets for the development of antimicrobials and vaccines. Bacterial lipoproteins are secreted from the cytosol via the Sec pathway and acylated on an N-terminal cysteine residue through the action of three enzymes. In Gram-negative bacteria, the Lol pathway transports lipoproteins to the outer membrane. Here, we demonstrate that the Aat secretion system is a composite system sharing similarity with elements of a type I secretion systems and the Lol pathway. During secretion, the AatD subunit acylates the substrate CexE on a highly conserved N-terminal glycine residue. Mutations disrupting glycine acylation interfere with membrane incorporation and trafficking. Our data reveal CexE as the first member of a new class of glycine-acylated lipoprotein, while Aat represents a new secretion system that displays the substrate lipoprotein on the cell surface.
Journal Article
Transposon mutagenesis screen in Klebsiella pneumoniae identifies genetic determinants required for growth in human urine and serum
Klebsiella pneumoniae is a global public health concern due to the rising myriad of hypervirulent and multidrug-resistant clones both alarmingly associated with high mortality. The molecular mechanisms underpinning these recalcitrant K. pneumoniae infection, and how virulence is coupled with the emergence of lineages resistant to nearly all present-day clinically important antimicrobials, are unclear. In this study, we performed a genome-wide screen in K. pneumoniae ECL8, a member of the endemic K2-ST375 pathotype most often reported in Asia, to define genes essential for growth in a nutrient-rich laboratory medium (Luria-Bertani [LB] medium), human urine, and serum. Through transposon directed insertion-site sequencing (TraDIS), a total of 427 genes were identified as essential for growth on LB agar, whereas transposon insertions in 11 and 144 genes decreased fitness for growth in either urine or serum, respectively. These studies not only provide further knowledge on the genetics of this pathogen but also provide a strong impetus for discovering new antimicrobial targets to improve current therapeutic options for K. pneumoniae infections.
Journal Article
Population dynamics and spatial ecology of a declining desert rodent, Pseudomys australis: the importance of refuges for persistence
Desert rodents exhibit irruptive (boom–bust) population dynamics in response to pulses of primary productivity. Such unpredictable population dynamics are a challenge for monitoring population trends and managing populations, particularly for species in decline. We studied the population dynamics and occurrence of populations of the vulnerable plains mouse, Pseudomys australis (42-g body mass), during the low (bust) phase of the cycle in the Simpson Desert, Australia, to examine the use of refuges by the species and the predation pressure experienced from native and introduced predators. Specifically we investigated landscape-scale occurrence; body mass, reproduction, and population size; and presence of native and introduced predators. Our results demonstrate that P. australis contracted to discrete areas of the landscape (refuges) during the low phase and that these areas occupied a small proportion (∼17%) of the range occupied during population peaks. Animals in refuge populations had comparable body mass, occurred at similar densities to populations during the boom phase, and continued to reproduce during dry conditions. Such refuges represented a significant concentration of biomass to predators in a resource-poor environment. Native predators were rare during the low phase, suggesting that refuges naturally experienced low predation levels. Two introduced predators, feral house cats and red foxes, persisted during the low phase and exploited refuge populations of P. australis, thus representing a significant threat to population persistence. We advocate a novel approach to management of rodents in arid systems that involves identifying the discrete parts of the landscape that function as drought refuges and then focusing threat management there. The relatively small size of these refuges increases the likelihood of cost-effective management.
Journal Article
Comparative analysis of two Neisseria gonorrhoeae genome sequences reveals evidence of mobilization of Correia Repeat Enclosed Elements and their role in regulation
Background
The Correia Repeat Enclosed Element (CREE) of the
Neisseria
spp., with its inverted repeat and conserved core structure, can generate a promoter sequence at either or both ends, can bind IHF, and can bind RNase III and either be cleaved by it or protected by it. As such, the presence of this element can directly control the expression of adjacent genes. Previous work has shown differences in regulation of gene expression between neisserial strains and species due to the presence of a CREE. These interruptions perhaps remove the expression of CREE-associated genes from ancestral neisserial regulatory networks.
Results
Analysis of the chromosomal locations of the CREE in
Neisseria gonorrhoeae
strain FA1090 and
N. gonorrhoeae
strain NCCP11945 has revealed that most of the over 120 copies of the element are conserved in location between these genome sequences. However, there are some notable exceptions, including differences in the presence and sequence of CREE 5' of copies of the opacity protein gene
opa
, differences in the potential to bind IHF, and differences in the potential to be cleaved by RNase III.
Conclusion
The presence of CREE insertions in one strain relative to the other, CREE within a prophage region, and CREE disrupting coding sequences, provide strong evidence of mobility of this element in
N. gonorrhoeae
. Due to the previously demonstrated role of these elements in altering transcriptional control and the findings from comparing the two gonococcal genome sequences, it is suggested that regulatory differences orchestrated by CREE contribute to the differences between strains and also between the closely related yet clinically distinct species
N. gonorrhoeae
,
Neisseria meningitidis
, and
Neisseria lactamica
.
Journal Article
Weather Support to Deicing Decision Making (WSDDM)
This paper describes a winter weather nowcasting system called Weather Support to Deicing Decision Making (WSDDM), designed to provide airline, airport, and air traffic users with winter weather information relevant to their operations. The information is provided on an easy to use graphical display and characterizes airport icing conditions for nonmeteorologists. The system has been developed and refined over a series of winter-long airport demonstrations at Denver’s Stapleton International Airport, Chicago’s O’Hare International Airport, and New York’s LaGuardia Airport. The WSDDM system utilizes commercially available weather information in the form of Next Generation Weather Radar WSR-88D radar reflectivity data depicted as color coded images on a window of the display and Aviation Routine Weather Report (METAR) surface weather reports from Automated Surface Observating System stations and observers. METAR information includes wind speed and direction, air temperature, and precipitation type/rate, which are routinely updated on an hourly basis or more frequently if conditions are changing. Recent studies have shown that the liquid equivalent snowfall rate is the most important factor in determining the holdover time of a deicing fluid. However, the current operational snowfall intensity reported in METARs is based on visibility, which has been shown to give misleading information on liquid equivalent rates in many cases due to the wide variation in density and shape of snow. The particular hazard has been identified ashigh visibility–high snowfallconditions. The WSDDM system addresses this potentially hazardous condition through the deployment of snow gauges at an airport. These snow gauges report real-time estimates of the liquid equivalent snowfall rate once every minute to WSDDM users. The WSDDM system also provides 30-min nowcasts of liquid equivalent snowfall rate through the use of a real-time calibration of radar reflectivity and snow gauge snowfall rate. This paper discusses the development of the system, including the development of new wind shields for snow gauges to improve catch efficiency, as well as the development of the above mentioned real-time method to convert radar reflectivity to snowfall rate on the ground using snow gauges. In addition, we discuss results from a user evaluation of the system, as well as results from an efficiency and safety benefits study of the system.
Journal Article