bluuebunny/crossref_metadata_2025_split huggingface dataset:
Survival of
Burkholderia pseudomallei
on Environmental Surfaces
Authors: Shams Alicia M. , Rose Laura J. , Hodges Lisa , Arduino Matthew J. 
Published: October 2007

ABSTRACT

The survival of the biothreat agent
Burkholderia pseudomallei
on the surfaces of four materials was measured by culture and esterase activity analyses. The culture results demonstrated that this organism persisted for <24 h to <7 days depending on the material, bacterial isolate, and suspension medium. The persistence determined by analysis of esterase activity, as measured with a ScanRDI solid-phase cytometer, was always longer than the persistence determined by culture analysis.
Reconstitution of Glyphosate Resistance from a Split 5-Enolpyruvyl Shikimate-3-Phosphate Synthase Gene in
Escherichia coli
and Transgenic Tobacco
Authors: Dun Bao-Qing , Wang Xu-Jing , Lu Wei , Zhao Zhong-Lin , Hou Song-Na , Zhang Bao-Ming , Li Gui-Ying , Evans Thomas C. , Xu Ming-Qun , Lin Min 
Published: October 2007

ABSTRACT

A highly
N
-phosphonomethylglycine (glyphosate)-resistant
Pseudomonas fluorescens
G2 5-enolpyruvyl shikimate-3-phosphate synthase (EPSPS) was mapped to identify potential split sites using a transposon-based linker-scanning procedure. Intein-mediated protein complementation was used to reconstitute glyphosate resistance from the genetically divided G2 EPSPS gene in
Escherichia coli
strain ER2799 and transgenic tobacco.
Antibiotic Resistance in Food-Borne Bacterial Contaminants in Vietnam
Authors: Van Thi Thu Hao , Moutafis George , Tran Linh Thuoc , Coloe Peter J. 
Published: October 2007

ABSTRACT

This study was conducted to examine the rate of contamination and the molecular characteristics of enteric bacteria isolated from a selection of food sources in Vietnam. One hundred eighty raw food samples were tested; 60.8% of meat samples and 18.0% of shellfish samples were contaminated with
Salmonella
spp., and more than 90% of all food sources contained
Escherichia coli
. The isolates were screened for antibiotic resistance against 15 antibiotics, and 50.5% of
Salmonella
isolates and 83.8% of
E. coli
isolates were resistant to at least one antibiotic. Isolates were examined for the presence of mobile genetic elements conferring antibiotic resistance. Fifty-seven percent of
E. coli
and 13% of
Salmonella
isolates were found to contain integrons, and some isolates contained two integrons. Sequencing results revealed that the integrons harbored various gene cassettes, including
aadA1
,
aadA2
, and
aadA5
(resistance to streptomycin and spectinomycin),
aacA4
(resistance to aminoglycosides), the dihydrofolate reductase gene cassettes
dhfrXII
,
dfrA1
, and
dhfrA17
(trimethoprim resistance), the beta-lactamase gene
bla
PSE1
(ampicillin resistance), and
catB3
(chloramphenicol resistance). Plasmids were also detected in all 23 antibiotic-resistant
Salmonella
isolates and in 33
E. coli
isolates. Thirty-five percent of the
Salmonella
isolates and 76% of the
E. coli
isolates contained plasmids of more than 95 kb, and some of the isolates contained two large plasmids. Conjugation experiments showed the successful transfer of all or part of the antibiotic resistance phenotypes among the
Salmonella
and
E. coli
food isolates. Our results show that enteric bacteria in raw food samples from Vietnam contain a pool of mobile genetic elements and that the transfer of antibiotic resistance can readily occur between similar bacteria.
Ni Uptake and Limitation in MarineSynechococcusStrains
Authors: Dupont Christopher L. , Barbeau Katherine , Palenik Brian 
Published: October 2007

ABSTRACTNi accumulation and utilization were studied in two strains of marineSynechococcus, isolated from both coastal (CC9311; clade I) and open-ocean (WH8102; clade III) environments, for which complete genome sequences are available. Both strains have genes encoding an Ni-containing urease and when grown on urea without Ni become Ni-N colimited. The Ni requirements of these strains also depend upon the genomic complement of genes encoding superoxide dismutase (SOD). WH8102, with a gene encoding only an Ni-SOD, has a novel obligate requirement for Ni, regardless of the N source. Reduced SOD activity in Ni-depleted cultures of WH8102 supports the link of this strain's Ni requirement to Ni-SOD. The genome of CC9311 contains a gene for a Cu/Zn-SOD in addition to a predicted pair of Ni-SODs, yet this strain cannot grow without Ni on NO3−and can grow only slowly on NH4+without Ni, implying that the Cu/Zn-SOD cannot completely replace Ni-SOD in marine cyanobacteria. CC9311 does have a greater tolerance for Ni starvation. Both strains increase their Ni uptake capabilities and actively bioconcentrate Ni in response to decreasing extracellular and intracellular Ni. The changes in Ni uptake rates were more pronounced in WH8102 than in CC9311 and for growth on urea or nitrate than for growth on ammonia. These results, combined with an analysis of fully sequenced marine cyanobacterial genomes, suggest that the growth of many marineSynechococcusand allProchlorococcusstrains is dependent upon Ni.
Association of
Vibrio cholerae
O1 El Tor and O139 Bengal with the Copepods
Acartia tonsa
and
Eurytemora affinis
Authors: Rawlings Tonya K. , Ruiz Gregory M. , Colwell Rita R. 
Published: October 2007

ABSTRACT

The association of
Vibrio cholerae
with zooplankton has been suggested as an important factor in transmission of human epidemic cholera, and the ability to colonize zooplankton surfaces may play a role in the temporal variation and predominance of the two different serogroups (
V. cholerae
O1 El Tor and O139) in the aquatic environment. To date, interactions between specific serogroups and species of plankton remain poorly understood. Laboratory microcosm experiments were carried out to compare quantitatively the colonization of two copepod species,
Acartia tonsa
and
Eurytemora affinis
, by each of the epidemic serogroups.
V. cholerae
O1 consistently achieved higher abundances than
V. cholerae
O139 in colonizing adults of each copepod species as well as the multiple life stages of
E. affinis
. This difference in colonization may be significant in the general predominance of
V. cholerae
O1 in cholera epidemics in rural Bangladesh where water supplies are taken directly from the environment.
Multilocus Characterization Scheme for Shiga Toxin-Encoding Bacteriophages
Authors: Smith Darren L. , Wareing Brian M. , Fogg Paul C. M. , Riley Laura M. , Spencer Matthew , Cox Michael J. , Saunders Jon R. , McCarthy Alan J. , Allison Heather E. 
Published: October 2007

ABSTRACT

Shiga toxin-producing
Escherichia coli
(STEC) strains are food-borne pathogens whose ability to produce Shiga toxin (Stx) is due to integration of Stx-encoding lambdoid bacteriophages. These Stx phages are both genetically and morphologically heterogeneous, and here we report the design and validation of a PCR-based multilocus typing scheme. PCR primer sets were designed for database variants of a range of key lambdoid bacteriophage genes and applied to control phages and 70
stx
+
phage preparations induced from a collection of STEC isolates. The genetic diversity residing within these populations could be described, and observations were made on the heterogeneity of individual gene targets, including the unexpected predominance of short-tailed phages with a highly conserved tail spike protein gene. Purified Stx phages can be profiled using this scheme, and the lambdoid phage-borne genes in induced STEC preparations can be identified as well as those residing in the noninducible prophage complement. The ultimate goal is to enable robust and realistically applicable epidemiological studies of Stx phages and their traits. The impact of Stx phage on STEC epidemiology is currently unknown.
Improved Succinic Acid Production in the Anaerobic Culture of an
Escherichia coli pflB ldhA
Double Mutant as a Result of Enhanced Anaplerotic Activities in the Preceding Aerobic Culture
Authors: Wu Hui , Li Zhi-min , Zhou Li , Ye Qin 
Published: October 2007

ABSTRACT

Escherichia coli
NZN111 is a
pflB ldhA
double mutant which loses its ability to ferment glucose anaerobically due to redox imbalance. In this study, two-stage culture of NZN111 was carried out for succinic acid production. It was found that when NZN111 was aerobically cultured on acetate, it regained the ability to ferment glucose with succinic acid as the major product in subsequent anaerobic culture. In two-stage culture carried out in flasks, succinic acid was produced at a level of 11.26 g/liter from 13.4 g/liter of glucose with a succinic acid yield of 1.28 mol/mol glucose and a productivity of 1.13 g/liter·h in the anaerobic stage. Analyses of key enzyme activities revealed that the activities of isocitrate lyase, malate dehydrogenase, malic enzyme, and phosphoenolpyruvate (PEP) carboxykinase were greatly enhanced while those of pyruvate kinase and PEP carboxylase were reduced in the acetate-grown cells. The two-stage culture was also performed in a 5-liter fermentor without separating the acetate-grown NZN111 cells from spent medium. The overall yield and concentration of succinic acid reached 1.13 mol/mol glucose and 28.2 g/liter, respectively, but the productivity of succinic acid in the anaerobic stage dropped to 0.7 g/liter·h due to cell autolysis and reduced anaplerotic activities. The results indicate the great potential to take advantage of cellular regulation mechanisms for improvement of succinic acid production by a metabolically engineered
E. coli
strain.
CpxRA Regulates Mutualism and Pathogenesis in
Xenorhabdus nematophila
Authors: Herbert Erin E. , Cowles Kimberly N. , Goodrich-Blair Heidi 
Published: October 2007

ABSTRACT

The CpxRA signal transduction system, which in
Escherichia coli
regulates surface structure assembly and envelope maintenance, is involved in the pathogenic and mutualistic interactions of the entomopathogenic bacterium
Xenorhabdus nematophila
. When Δ
cpxR1
cells were injected into
Manduca sexta
insects, the time required to kill 50% of the insects was twofold longer than the time observed for wild-type cells and the Δ
cpxR1
cells ultimately killed 16% fewer insects than wild-type cells killed. During mutualistic colonization of
Steinernema carpocapsae
nematodes, the Δ
cpxR1
mutant achieved colonization levels that were only 38% of the wild-type levels. Δ
cpxR1
cells exhibited an extended lag phase when they were grown in liquid LB or hemolymph, formed irregular colonies on solid medium, and had a filamentous cell morphology. A mutant with a
cpxRp-lacZ
fusion had peaks of expression in the log and stationary phases that were conversely influenced by CpxR; the Δ
cpxR1
mutant produced 130 and 17% of the wild-type β-galactosidase activity in the log and stationary phases, respectively. CpxR positively influences motility and secreted lipase activity, as well as transcription of genes necessary for mutualistic colonization of nematodes. CpxR negatively influences the production of secreted hemolysin, protease, and antibiotic activities, as well as the expression of
mrxA
, encoding the pilin subunit. Thus,
X. nematophila
CpxRA controls expression of envelope-localized and secreted products, and its activity is necessary for both mutualistic and pathogenic functions.
Survival of Indicator and Pathogenic Bacteria in Bovine Feces on Pasture
Authors: Sinton Lester W. , Braithwaite Robin R. , Hall Carollyn H. , Mackenzie Margaret L. 
Published: October 2007

ABSTRACT

The survival of enteric bacteria was measured in bovine feces on pasture. In each season, 11 cow pats were prepared from a mixture of fresh dairy cattle feces and sampled for up to 150 days. Four pats were analyzed for
Escherichia coli
, fecal streptococci, and enterococci, and four inoculated pats were analyzed for
Campylobacter jejuni
and
Salmonella enterica
. Two pats were placed on drainage collectors, and another pat was fitted with a temperature probe. In the first 1 to 3 weeks, there were increases (up to 1.5 orders of magnitude) in the counts of enterococci (in four seasons),
E. coli
(three seasons), fecal streptococci (three seasons), and
S. enterica
(two seasons), but there was no increase in the counts of
C. jejuni
. Thereafter, the counts decreased, giving an average ranking of the times necessary for 90% inactivation of
C. jejuni
(6.2 days from deposition) < fecal streptococci (35 days) <
S. enterica
(38 days) <
E. coli
(48 days) < enterococci (56 days). The pat temperature probably influenced bacterial growth, but the pattern of increases and decreases was primarily determined by desiccation; growth occurred when the water content was greater than 80%, but at a water content of 70 to 75% counts decreased.
E. coli
and enterococcus regrowth appeared to result from pat rehydration. Of 20 monthly leaching losses of
E. coli
, 16 were <10% of the total counts in the pat, and 12 were <1%. Drainage losses of
C. jejuni
(generally <1%) were detected for only 1 to 2 months. Although enterococci exhibited the best survival rate, higher final counts suggested that
E. coli
is the more practical indicator of bovine fecal pollution.
Conserved Processes and Lineage-Specific Proteins in Fungal Cell Wall Evolution
Authors: Coronado Juan E. , Mneimneh Saad , Epstein Susan L. , Qiu Wei-Gang , Lipke Peter N. 
Published: October 2007

ABSTRACT

The cell wall is a defining organelle that differentiates fungi from its sister clades in the opisthokont superkingdom. With a sensitive technique to align low-complexity protein sequences, we have identified 187 cell wall-related proteins in
Saccharomyces cerevisiae
and determined the presence or absence of homologs in 17 other fungal genomes. There were both conserved and lineage-specific cell wall proteins, and the degree of conservation was strongly correlated with protein function. Some functional classes were poorly conserved and lineage specific: adhesins, structural wall glycoprotein components, and unannotated open reading frames. These proteins are primarily those that are constituents of the walls themselves. On the other hand, glycosyl hydrolases and transferases, proteases, lipases, proteins in the glycosyl phosphatidyl-inositol-protein synthesis pathway, and chaperones were strongly conserved. Many of these proteins are also conserved in other eukaryotes and are associated with wall synthesis in plants. This gene conservation, along with known similarities in wall architecture, implies that the basic architecture of fungal walls is ancestral to the divergence of the ascomycetes and basidiomycetes. The contrasting lineage specificity of wall resident proteins implies diversification. Therefore, fungal cell walls consist of rapidly diversifying proteins that are assembled by the products of an ancestral and conserved set of genes.
Regulation of Ammonia Homeostasis by the Ammonium Transporter AmtA in
Dictyostelium discoideum
Authors: Yoshino Ryuji , Morio Takahiro , Yamada Yoko , Kuwayama Hidekazu , Sameshima Masazumi , Tanaka Yoshimasa , Sesaki Hiromi , Iijima Miho 
Published: October 2007

ABSTRACT

Ammonia has been shown to function as a morphogen at multiple steps during the development of the cellular slime mold
Dictyostelium discoideum
; however, it is largely unknown how intracellular ammonia levels are controlled. In the
Dictyostelium
genome, there are five genes that encode putative ammonium transporters:
amtA
,
amtB
,
amtC
,
rhgA
, and
rhgB
. Here, we show that AmtA regulates ammonia homeostasis during growth and development. We found that cells lacking
amtA
had increased levels of ammonia/ammonium, whereas their extracellular ammonia/ammonium levels were highly decreased. These results suggest that AmtA mediates the excretion of ammonium. In support of a role for AmtA in ammonia homeostasis, AmtA mRNA is expressed throughout the life cycle, and its expression level increases during development. Importantly, AmtA-mediated ammonia homeostasis is critical for many developmental processes.
amtA
−
cells are more sensitive to NH
4
Cl than wild-type cells in inhibition of chemotaxis toward cyclic AMP and of formation of multicellular aggregates. Furthermore, even in the absence of exogenously added ammonia, we found that
amtA
−
cells produced many small fruiting bodies and that the viability and germination of
amtA
−
spores were dramatically compromised. Taken together, our data clearly demonstrate that AmtA regulates ammonia homeostasis and plays important roles in multiple developmental processes in
Dictyostelium
.
Schizosaccharomyces pombe
Sst4p, a Conserved Vps27/Hrs Homolog, Functions Downstream of Phosphatidylinositol 3-Kinase Pik3p To Mediate Proper Spore Formation
Authors: Onishi Masayuki , Iida Michihiro , Koga Takako , Yamada Sadayuki , Hirata Aiko , Iwaki Tomoko , Takegawa Kaoru , Fukui Yasuhisa , Tachikawa Hiroyuki 
Published: October 2007

ABSTRACT

Sporulation of the fission yeast
Schizosaccharomyces pombe
is a developmental process that generates gametes and that includes the formation of spore envelope precursors called the forespore membranes. Assembly and development of forespore membranes require vesicular trafficking from other intracellular membrane compartments. We have shown that phosphatidylinositol 3-kinase (PtdIns 3-kinase) is required for efficient and proper development of forespore membranes. The role of a FYVE domain protein, Sst4p, a homolog of Vps27p/Hrs, as a downstream factor for PtdIns 3-kinase in sporulation was investigated.
sst4
Δ asci formed spores with oval-shaped morphology and with reduced viability compared to that of the wild-type spores. The extension of forespore membranes was inefficient, and bubble-like structures emerged from the leading edges of the forespore membranes. Sst4p localization was examined using fluorescent protein fusions and was found to be adjacent to the forespore membranes during sporulation. The localization and function of Sst4p were dependent on its FYVE domain and on PtdIns 3-kinase. Sst4p colocalized and interacted with Hse1p, a homolog of
Saccharomyces cerevisiae
Hse1p and of mammalian STAM. Mutations in all three UIM domains of the Sst4p/Hse1p complex resulted in formation of spores with abnormal morphology. These results suggest that Sst4p is a downstream factor of PtdIns 3-kinase and functions in forespore membrane formation.
Spatial Differentiation in the Vegetative Mycelium of
Aspergillus niger
Authors: Levin Ana M. , de Vries Ronald P. , Conesa Ana , de Bekker Charissa , Talon Manuel , Menke Hildegard H. , van Peij Noel N. M. E. , Wösten Han A. B. 
Published: October 2007

ABSTRACT

Fungal mycelia are exposed to heterogenic substrates. The substrate in the central part of the colony has been (partly) degraded, whereas it is still unexplored at the periphery of the mycelium. We here assessed whether substrate heterogeneity is a main determinant of spatial gene expression in colonies of
Aspergillus niger
. This question was addressed by analyzing whole-genome gene expression in five concentric zones of 7-day-old maltose- and xylose-grown colonies. Expression profiles at the periphery and the center were clearly different. More than 25% of the active genes showed twofold differences in expression between the inner and outermost zones of the colony. Moreover, 9% of the genes were expressed in only one of the five concentric zones, showing that a considerable part of the genome is active in a restricted part of the colony only. Statistical analysis of expression profiles of colonies that had either been or not been transferred to fresh xylose-containing medium showed that differential expression in a colony is due to the heterogeneity of the medium (e.g., genes involved in secretion, genes encoding proteases, and genes involved in xylose metabolism) as well as to medium-independent mechanisms (e.g., genes involved in nitrate metabolism and genes involved in cell wall synthesis and modification). Thus, we conclude that the mycelia of 7-day-old colonies of
A. niger
are highly differentiated. This conclusion is also indicated by the fact that distinct zones of the colony grow and secrete proteins, even after transfer to fresh medium.
Establishment of the Ambient pH Signaling Complex in
Aspergillus nidulans
: PalI Assists Plasma Membrane Localization of PalH
Authors: Calcagno-Pizarelli Ana M. , Negrete-Urtasun Susana , Denison Steven H. , Rudnicka Joanna D. , Bussink Henk-Jan , Múnera-Huertas Tatiana , Stanton Ljiljana , Hervás-Aguilar América , Espeso Eduardo A. , Tilburn Joan , Arst Herbert N. , Peñalva Miguel A. 
Published: October 2007

ABSTRACT

The
Aspergillus nidulans
ambient pH signaling pathway involves two transmembrane domain (TMD)-containing proteins, PalH and PalI. We provide in silico and mutational evidence suggesting that PalI is a three TMD (3-TMD) protein with an N-terminal signal peptide, and we show that PalI localizes to the plasma membrane. PalI is not essential for the proteolytic conversion of the PacC translation product into the processed 27-kDa form, but its absence markedly reduces the accumulation of the 53-kDa intermediate after cells are shifted to an alkaline pH. PalI and its homologues contain a predicted luminal, conserved Gly-Cys-containing motif that distantly resembles a Gly-rich dimerization domain. The Gly44Arg and Gly47Asp substitutions within this motif lead to loss of function. The Gly47Asp substitution prevents plasma membrane localization of PalI-green fluorescent protein (GFP) and leads to its missorting into the multivesicular body pathway. Overexpression of the likely ambient alkaline pH receptor, the 7-TMD protein PalH, partially suppresses the null
palI32
mutation. Although some PalH-GFP localizes to the plasma membrane, it predominates in internal membranes. However, the coexpression of PalI to stoichiometrically similar levels results in the strong predominance of PalH-GFP in the plasma membrane. Thus, one role for PalI, but possibly not the only role, is to assist with plasma membrane localization of PalH. These data, considered along with previous reports for both
Saccharomyces cerevisiae
and
A. nidulans
, strongly support the prevailing model of pH signaling involving two spatially segregated complexes: a plasma membrane complex containing PalH, PalI, and the arrestin-like protein PalF and an endosomal membrane complex containing PalA and PalB, to which PacC is recruited for its proteolytic activation.
Architecture of the Sporulation-Specific
Cdc14
Promoter from the Oomycete
Phytophthora infestans
Authors: Ah-Fong Audrey M. V. , Xiang Qijun , Judelson Howard S. 
Published: October 2007

ABSTRACT

The
Cdc14
gene of
Phytophthora infestans
is transcribed specifically during sporulation, with no mRNA detectable in vegetative hyphae, and is required for sporangium development. To unravel the mechanisms regulating its transcription, mutated
Cdc14
promoters plus chimeras of selected
Cdc14
sequences and a minimal promoter were tested in stable transformants. This revealed that a tandem repeat of three copies of the motif CTYAAC, located between 67 and 90 nucleotides (nt) upstream of the major transcription start site, is sufficient to determine sporulation-specific expression. All three repeats need to be present for activity, suggesting that they bind a transcription factor through a cooperative mechanism. Electrophoretic mobility shift assays indicated that the CTYAAC repeats are specifically bound by a protein in nuclear extracts. Evidence was also obtained for a second region within the promoter that activates
Cdc14
transcription during sporulation which does not involve those repeats. The CTYAAC motif also affects the specificity of transcription initiation. Wild-type
Cdc14
is transcribed from a major start site and minor site(s) located about 100 nt upstream of the major site. However, stepwise mutations through the CTYAAC triad caused a graded shift to the upstream sites, as did mutating bases surrounding the major start site; transcripts initiated from the upstream site remained sporulation specific. Replacing the
Cdc14
initiation region with the Inr-like region of the constitutive
Piexo1
gene had no apparent effect on the pattern of transcription. Therefore, this study reports the first motif determining sporulation-induced transcription in oomycetes and helps define oomycete core promoters.