bluuebunny/crossref_metadata_2025_split huggingface dataset:
Removal and Transfer of Viruses on Food Contact Surfaces by Cleaning Cloths
Authors: Gibson Kristen E. , Crandall Philip G. , Ricke Steven C. 
Published: February 2012

ABSTRACT

Contamination of food contact surfaces with pathogens is considered an important vehicle for the indirect transmission of food-borne diseases. Five different cleaning cloths were assessed for the ability to remove viruses from food contact surfaces (stainless steel surface and nonporous solid surface) and to transfer viruses back to these surfaces. Cleaning cloths evaluated include two different cellulose/cotton cloths, one microfiber cloth, one nonwoven cloth, and one cotton terry bar towel. Four viral surrogates (murine norovirus [MNV], feline calicivirus [FCV], bacteriophages PRD1 and MS2) were included. Removal of FCV from stainless steel was significantly greater (
P
≤ 0.05) than that from nonporous solid surface, and overall removal of MNV from both surfaces was significantly less (
P
≤ 0.05) than that of FCV and PRD1. Additionally, the terry towel removed significantly fewer total viruses (
P
≤ 0.05) than the microfiber and one of the cotton/cellulose cloths. The cleaning cloth experiments were repeated with human norovirus. For transfer of viruses from cloth to surface, both cellulose/cotton cloths and microfiber transferred an average of 3.4 and 8.5 total PFU, respectively, to both surfaces, and the amounts transferred were significantly different (
P
≤ 0.05) from those for the nonwoven cloth and terry towel (309 and 331 total PFU, respectively). There was no statistically significant difference (
P
> 0.05) in the amount of virus transfer between surfaces. These data indicate that while the cleaning cloths assessed here can remove viruses from surfaces, some cloths may also transfer a significant amount of viruses back to food contact surfaces.
Glyoxylate Metabolism Is a Key Feature of the Metabolic Degradation of 1,4-Dioxane by Pseudonocardia dioxanivorans Strain CB1190
Authors: Grostern Ariel , Sales Christopher M. , Zhuang Wei-Qin , Erbilgin Onur , Alvarez-Cohen Lisa 
Published: February 2012

ABSTRACTThe groundwater contaminant 1,4-dioxane (dioxane) is transformed by several monooxygenase-expressing microorganisms, but only a few of these, includingPseudonocardia dioxanivoransstrain CB1190, can metabolize the compound as a sole carbon and energy source. However, nothing is yet known about the genetic basis of dioxane metabolism. In this study, we used a microarray to study differential expression of genes in strain CB1190 grown on dioxane, glycolate (a previously identified intermediate of dioxane degradation), or pyruvate. Of eight multicomponent monooxygenase gene clusters carried by the strain CB1190 genome, only the monooxygenase gene cluster located on plasmid pPSED02 was upregulated with dioxane relative to pyruvate. Plasmid-borne genes for putative aldehyde dehydrogenases, an aldehyde reductase, and an alcohol oxidoreductase were also induced during growth with dioxane. With both dioxane and glycolate, a chromosomal gene cluster encoding a putative glycolate oxidase was upregulated, as were chromosomal genes related to glyoxylate metabolism through the glyoxylate carboligase pathway. Glyoxylate carboligase activity in cell extracts from cells pregrown with dioxane and inRhodococcus jostiistrain RHA1 cells expressing the putative strain CB1190 glyoxylate carboligase gene further demonstrated the role of glyoxylate metabolism in the degradation of dioxane. Finally, we used13C-labeled dioxane amino acid isotopomer analysis to provide additional evidence that metabolites of dioxane enter central metabolism as three-carbon compounds, likely as phosphoglycerate. The routing of dioxane metabolites via the glyoxylate carboligase pathway helps to explain how dioxane is metabolized as a sole carbon and energy source for strain CB1190.
Microbial Functional Gene Diversity with a Shift of Subsurface Redox Conditions during
In Situ
Uranium Reduction
Authors: Liang Yuting , Van Nostrand Joy D. , N′Guessan Lucie A. , Peacock Aaron D. , Deng Ye , Long Philip E. , Resch C. Tom , Wu Liyou , He Zhili , Li Guanghe , Hazen Terry C. , Lovley Derek R. , Zhou Jizhong 
Published: February 2012

ABSTRACT

To better understand the microbial functional diversity changes with subsurface redox conditions during
in situ
uranium bioremediation, key functional genes were studied with GeoChip, a comprehensive functional gene microarray, in field experiments at a uranium mill tailings remedial action (UMTRA) site (Rifle, CO). The results indicated that functional microbial communities altered with a shift in the dominant metabolic process, as documented by hierarchical cluster and ordination analyses of all detected functional genes. The abundance of
dsrAB
genes (dissimilatory sulfite reductase genes) and methane generation-related
mcr
genes (methyl coenzyme M reductase coding genes) increased when redox conditions shifted from Fe-reducing to sulfate-reducing conditions. The cytochrome genes detected were primarily from
Geobacter
sp. and decreased with lower subsurface redox conditions. Statistical analysis of environmental parameters and functional genes indicated that acetate, U(VI), and redox potential (E
h
) were the most significant geochemical variables linked to microbial functional gene structures, and changes in microbial functional diversity were strongly related to the dominant terminal electron-accepting process following acetate addition. The study indicates that the microbial functional genes clearly reflect the
in situ
redox conditions and the dominant microbial processes, which in turn influence uranium bioreduction. Microbial functional genes thus could be very useful for tracking microbial community structure and dynamics during bioremediation.
Prevalence, Enumeration, Serotypes, and Antimicrobial Resistance Phenotypes of Salmonella enterica Isolates from Carcasses at Two Large United States Pork Processing Plants
Authors: Schmidt John W. , Brichta-Harhay Dayna M. , Kalchayanand Norasak , Bosilevac Joseph M. , Shackelford Steven D. , Wheeler Tommy L. , Koohmaraie Mohammad 
Published: February 2012

ABSTRACT

The objective of this study was to characterize
Salmonella enterica
contamination on carcasses in two large U.S. commercial pork processing plants. The carcasses were sampled at three points, before scalding (prescald), after dehairing/polishing but before evisceration (preevisceration), and after chilling (chilled final). The overall prevalences of
Salmonella
on carcasses at these three sampling points, prescald, preevisceration, and after chilling, were 91.2%, 19.1%, and 3.7%, respectively. At one of the two plants, the prevalence of
Salmonella
was significantly higher (
P
< 0.01) for each of the carcass sampling points. The prevalences of carcasses with enumerable
Salmonella
at prescald, preevisceration, and after chilling were 37.7%, 4.8%, and 0.6%, respectively. A total of 294 prescald carcasses had
Salmonella
loads of >1.9 log CFU/100 cm
2
, but these carcasses were not equally distributed between the two plants, as 234 occurred at the plant with higher
Salmonella
prevalences. Forty-one serotypes were identified on prescald carcasses with
Salmonella enterica
serotypes Derby, Typhimurium, and Anatum predominating.
S. enterica
serotypes Typhimurium and London were the most common of the 24 serotypes isolated from preevisceration carcasses. The
Salmonella
serotypes Johannesburg and Typhimurium were the most frequently isolated serotypes of the 9 serotypes identified from chilled final carcasses. Antimicrobial susceptibility was determined for selected isolates from each carcass sampling point. Multiple drug resistance (MDR), defined as resistance to three or more classes of antimicrobial agents, was identified for 71.2%, 47.8%, and 77.5% of the tested isolates from prescald, preevisceration, and chilled final carcasses, respectively. The results of this study indicate that the interventions used by pork processing plants greatly reduce the prevalence of
Salmonella
on carcasses, but MDR
Salmonella
was isolated from 3.2% of the final carcasses sampled.
Presence and Functionality of Mating Type Genes in the Supposedly Asexual Filamentous Fungus Aspergillus oryzae
Authors: Wada Ryuta , Maruyama Jun-ichi , Yamaguchi Haruka , Yamamoto Nanase , Wagu Yutaka , Paoletti Mathieu , Archer David B. , Dyer Paul S. , Kitamoto Katsuhiko 
Published: February 2012

ABSTRACT

The potential for sexual reproduction in
Aspergillus oryzae
was assessed by investigating the presence and functionality of
MAT
genes. Previous genome studies had identified a
MAT1-1
gene in the reference strain RIB40. We now report the existence of a complementary
MAT1-2
gene and the sequencing of an idiomorphic region from
A. oryzae
strain AO6. This allowed the development of a PCR diagnostic assay, which detected isolates of the
MAT1-1
and
MAT1-2
genotypes among 180 strains assayed, including industrial
tane-koji
isolates. Strains used for sake and miso production showed a near-1:1 ratio of the MAT1-1 and MAT1-2 mating types, whereas strains used for soy sauce production showed a significant bias toward the MAT1-2 mating type. MAT1-1 and MAT1-2 isogenic strains were then created by genetic manipulation of the resident idiomorph, and gene expression was compared by DNA microarray and quantitative real-time PCR (qRT-PCR) methodologies under conditions in which
MAT
genes were expressed. Thirty-three genes were found to be upregulated more than 10-fold in either the MAT1-1 host strain or the MAT1-2 gene replacement strain relative to each other, showing that both the
MAT1-1
and
MAT1-2
genes functionally regulate gene expression in
A. oryzae
in a mating type-dependent manner, the first such report for a supposedly asexual fungus.
MAT1-1
expression specifically upregulated an α-pheromone precursor gene, but the functions of most of the genes affected were unknown. The results are consistent with a heterothallic breeding system in
A. oryzae
, and prospects for the discovery of a sexual cycle are discussed.
Oxidative Stress Tolerance, Adenylate Cyclase, and Autophagy Are Key Players in the Chronological Life Span of Saccharomyces cerevisiae during Winemaking
Authors: Orozco Helena , Matallana Emilia , Aranda Agustín 
Published: February 2012

ABSTRACT

Most grape juice fermentation takes place when yeast cells are in a nondividing state called the stationary phase. Under such circumstances, we aimed to identify the genetic determinants controlling longevity, known as the chronological life span. We identified commercial strains with both short (EC1118) and long (CSM) life spans in laboratory growth medium and compared them under diverse conditions. Strain CSM shows better tolerance to stresses, including oxidative stress, in the stationary phase. This is reflected during winemaking, when this strain has an increased maximum life span. Compared to EC1118, CSM overexpresses a mitochondrial rhodanese gene-like gene,
RDL2
, whose deletion leads to increased reactive oxygen species production at the end of fermentation and a correlative loss of viability at this point. EC1118 shows faster growth and higher expression of glycolytic genes, and this is related to greater PKA activity due to the upregulation of the adenylate cyclase gene. This phenotype has been linked to the presence of a δ element in its promoter, whose removal increases the life span. Finally, EC1118 exhibits a higher level of protein degradation by autophagy, which might help achieve fast growth at the expense of cellular structures and may be relevant for long-term survival under winemaking conditions.
Characterization of Biphenyl Dioxygenase Sequences and Activities Encoded by the Metagenomes of Highly Polychlorobiphenyl-Contaminated Soils
Authors: Standfuß-Gabisch Christine , Al-Halbouni Djamila , Hofer Bernd 
Published: February 2012

ABSTRACT

Total extracted DNA from two heavily polychlorobiphenyl-contaminated soils was analyzed with respect to biphenyl dioxygenase sequences and activities. This was done by PCR amplification and cloning of a DNA segment encoding the active site of the enzyme. The translated sequences obtained fell into three similarity clusters (I to III). Sequence identities were high within but moderate or low between the clusters. Members of clusters I and II showed high sequence similarities with well-known biphenyl dioxygenases. Cluster III showed low (43%) sequence identity with a biphenyl dioxygenase from
Rhodococcus jostii
RHA1. Amplicons from the three clusters were used to reconstitute and express complete biphenyl dioxygenase operons. In most cases, the resulting hybrid dioxygenases were detected in cell extracts of the recombinant hosts. At least 83% of these enzymes were catalytically active. Several amino acid exchanges were identified that critically affected activity. Chlorobiphenyl turnover by the enzymes containing the prototype sequences of clusters I and II was characterized with 10 congeners that were major, minor, or not constituents of the contaminated soils. No direct correlations were observed between on-site concentrations and rates of productive dioxygenations of these chlorobiphenyls. The prototype enzymes displayed markedly different substrate and product ranges. The cluster II dioxygenase possessed a broader substrate spectrum toward the assayed congeners, whereas the cluster I enzyme was superior in the attack of
ortho
-chlorinated aromatic rings. These results demonstrate the feasibility of the applied approach to functionally characterize dioxygenase activities of soil metagenomes via amplification of incomplete genes.
Bacterial Dimethylsulfoniopropionate Degradation Genes in the Oligotrophic North Pacific Subtropical Gyre
Authors: Varaljay Vanessa A. , Gifford Scott M. , Wilson Samuel T. , Sharma Shalabh , Karl David M. , Moran Mary Ann 
Published: February 2012

ABSTRACT

Dimethylsulfoniopropionate (DMSP) is an organic sulfur compound that is rapidly metabolized by marine bacteria either by cleavage to dimethylsulfide (DMS) or demethylation to 3-methiolpropionate. The abundance and diversity of genes encoding bacterial DMS production (
dddP
) and demethylation (
dmdA
) were measured in the North Pacific subtropical gyre (NPSG) between May 2008 and February 2009 at Station ALOHA (22°45′N, 158°00′W) at two depths: 25 m and the deep chlorophyll maximum (DCM; ∼100 m). The highest abundance of
dmdA
genes was in May 2008 at 25 m, with ∼16.5% of cells harboring a gene in one of the eight subclades surveyed, while the highest abundance of
dddP
genes was in July 2008 at 25 m, with ∼2% of cells harboring a gene. The
dmdA
gene pool was consistently dominated by homologs from SAR11 subclades, which was supported by findings in metagenomic data sets derived from Station ALOHA. Expression of the SAR11
dmdA
genes was low, with typical transcript:gene ratios between 1:350 and 1:1,400. The abundance of DMSP genes was statistically different between 25 m and the DCM and correlated with a number of environmental variables, including primary production, photosynthetically active radiation, particulate DMSP, and DMS concentrations. At 25 m,
dddP
abundance was positively correlated with pigments that are diagnostic of diatoms; at the DCM,
dmdA
abundance was positively correlated with temperature. Based on gene abundance, we hypothesize that SAR11 bacterioplankton dominate DMSP cycling in the oligotrophic NPSG, with lesser but consistent involvement of other members of the bacterioplankton community.
Reduction of Salmonella enterica Serovar Enteritidis Colonization in 20-Day-Old Broiler Chickens by the Plant-Derived Compounds
trans
-Cinnamaldehyde and Eugenol
Authors: Kollanoor-Johny Anup , Mattson Tyler , Baskaran Sangeetha Ananda , Amalaradjou Mary Anne , Babapoor Sankhiros , March Benjamin , Valipe Satyender , Darre Michael , Hoagland Thomas , Schreiber David , Khan Mazhar I. , Donoghue Ann , Donoghue Dan , Venkitanarayanan Kumar 
Published: February 2012

ABSTRACT

The efficacies of
trans
-cinnamaldehyde (TC) and eugenol (EG) for reducing
Salmonella enterica
serovar Enteritidis colonization in broiler chickens were investigated. In three experiments for each compound, 1-day-old chicks (
n
= 75/experiment) were randomly assigned to five treatment groups (
n
= 15/treatment group): negative control (-ve
S
. Enteritidis, -ve TC, or EG), compound control (-ve
S
. Enteritidis, +ve 0.75% [vol/wt] TC or 1% [vol/wt] EG), positive control (+ve
S
. Enteritidis, -ve TC, or EG), low-dose treatment (+ve
S
. Enteritidis, +ve 0.5% TC, or 0.75% EG), and high-dose treatment (+ve
S
. Enteritidis, +ve 0.75% TC, or 1% EG). On day 0, birds were tested for the presence of any inherent
Salmonella
(
n
= 5/experiment). On day 8, birds were inoculated with ∼8.0 log
10
CFU
S
. Enteritidis, and cecal colonization by
S
. Enteritidis was ascertained (
n
= 10 chicks/experiment) after 24 h (day 9). Six birds from each treatment group were euthanized on days 7 and 10 after inoculation, and cecal
S
. Enteritidis numbers were determined. TC at 0.5 or 0.75% and EG at 0.75 or 1% consistently reduced (
P
< 0.05)
S
. Enteritidis in the cecum (≥3 log
10
CFU/g) after 10 days of infection in all experiments. Feed intake and body weight were not different for TC treatments (
P
> 0.05); however, EG supplementation led to significantly lower (
P
< 0.05) body weights. Follow-up
in vitro
experiments revealed that the subinhibitory concentrations (SICs, the concentrations that did not inhibit
Salmonella
growth) of TC and EG reduced the motility and invasive abilities of
S
. Enteritidis and downregulated expression of the motility genes
flhC
and
motA
and invasion genes
hilA
,
hilD
, and
invF
. The results suggest that supplementation with TC and EG through feed can reduce
S
. Enteritidis colonization in chickens.
Influence of Air Quality on the Composition of Microbial Pathogens in Fresh Rainwater
Authors: Kaushik Rajni , Balasubramanian Rajasekhar , de la Cruz Armah A. 
Published: February 2012

ABSTRACT

In this study, the microbiological quality of fresh rainwater was assessed from 50 rain events under tropical weather conditions for a year. The levels of four major opportunistic waterborne pathogens, namely,
Escherichia coli
,
Klebsiella pneumoniae
,
Pseudomonas aeruginosa
, and
Aeromonas hydrophila
, in rainwater samples were quantified by using a robust and sensitive quantitative PCR (qPCR) method. Of the 50 rainwater samples, 25 were found to be positive for at least one pathogen: 21 for
E. coli
, 16 for
P. aeruginosa
, 6 for
K. pneumoniae
, and 1 for
A. hydrophila
. In addition to the microbiological assessment of rainwater samples, we also studied the influence of prevailing air quality on the microbial quality of rainwater over the sampling period. A significant change in the diversity and relative abundance of the basic microbial indicator organisms in rainwater was observed during a major regional air pollution episode in Southeast Asia due to biomass-burning emissions.
The Bacterial Community in the Gut of the Cockroach Shelfordella lateralis Reflects the Close Evolutionary Relatedness of Cockroaches and Termites
Authors: Schauer Christine , Thompson Claire L. , Brune Andreas 
Published: February 2012

ABSTRACT

Termites and cockroaches are closely related, with molecular phylogenetic analyses even placing termites within the radiation of cockroaches. The intestinal tract of wood-feeding termites harbors a remarkably diverse microbial community that is essential for the digestion of lignocellulose. However, surprisingly little is known about the gut microbiota of their closest relatives, the omnivorous cockroaches. Here, we present a combined characterization of physiological parameters, metabolic activities, and bacterial microbiota in the gut of
Shelfordella lateralis
, a representative of the cockroach family Blattidae, the sister group of termites. We compared the bacterial communities within each gut compartment using terminal-restriction fragment length polymorphism (T-RFLP) analysis and made a 16S rRNA gene clone library of the microbiota in the colon—the dilated part of the hindgut with the highest density and diversity of bacteria. The colonic community was dominated by members of the
Bacteroidetes
,
Firmicutes
(mainly
Clostridia
), and some
Deltaproteobacteria. Spirochaetes
and
Fibrobacteres
, which are abundant members of termite gut communities, were conspicuously absent. Nevertheless, detailed phylogenetic analysis revealed that many of the clones from the cockroach colon clustered with sequences previously obtained from the termite gut, which indicated that the composition of the bacterial community reflects at least in part the phylogeny of the host.
New Complementation Constructs for Inducible and Constitutive Gene Expression in Neisseria gonorrhoeae and Neisseria meningitidis
Authors: Ramsey Meghan E. , Hackett Kathleen T. , Kotha Chaitra , Dillard Joseph P. 
Published: February 2012

ABSTRACT

We have created new complementation constructs for use in
Neisseria gonorrhoeae
and
Neisseria meningitidis
. The constructs contain regions of homology with the chromosome and direct the insertion of a gene of interest into the intergenic region between the genes
iga
and
trpB
. In order to increase the available options for gene expression in
Neisseria
, we designed the constructs to contain one of three different promoters. One of the constructs contains the isopropyl-β-
d
-thiogalactopyranoside-inducible
lac
promoter, which has been widely used in
Neisseria
. We also designed a construct that contains the strong, constitutive promoter from the gonococcal
opaB
gene. The third construct contains a tetracycline-inducible promoter, a novel use of this promoter in
Neisseria
. We demonstrate that anhydrotetracycline can be used to induce gene expression in the pathogenic
Neisseria
at very low concentrations and without negatively affecting the growth of the organisms. We use these constructs to complement an arginine auxotrophy in
N. gonorrhoeae
as well as to express a translational fusion of alkaline phosphatase with TraW. TraW is a component of the gonococcal type IV secretion system, and we demonstrate that TraW localizes to the periplasm.
Effects of Sporulation Conditions on the Germination and Germination Protein Levels of Bacillus subtilis Spores
Authors: Ramirez-Peralta Arturo , Zhang Pengfei , Li Yong-qing , Setlow Peter 
Published: February 2012

ABSTRACT

Bacillus subtilis
spores prepared in rich medium germinated faster with nutrient germinants than poor-medium spores as populations in liquid and multiple individual spores on a microscope slide. Poor-medium spores had longer average lag times between mixing of spores with nutrient germinants and initiation of Ca-dipicolinic acid (CaDPA) release. Rich-medium spores made at 37°C germinated slightly faster with nutrient germinants than 23°C spores in liquid, but not when spores germinated on a slide. The difference in germination characteristics of these spore populations in liquid was paralleled by changes in expression levels of a transcriptional
lacZ
fusion to the
gerA
operon, encoding a germinant receptor (GR). Levels of GR subunits were 3- to 8-fold lower in poor-medium spores than rich-medium spores and 1.6- to 2-fold lower in 23°C spores than 37°C spores, and levels of the auxiliary germination protein GerD were 3.5- to 4-fold lower in poor medium and 23°C spores. In contrast, levels of another likely germination protein, SpoVAD, were similar in all these spores. These different spores germinated similarly with CaDPA, and poor-medium and 23°C spores germinated faster than rich-medium and 37°C spores, respectively, with dodecylamine. Since spore germination with CaDPA and dodecylamine does not require GerD or GRs, these results indicate that determinants of rates of nutrient germination of spores prepared differently are primarily the levels of the GRs that bind nutrient germinants and trigger germination and secondarily the levels of GerD.