bluuebunny/crossref_metadata_2025_split huggingface dataset:
Minimum Requirements of Flagellation and Motility for Infection of Agrobacterium sp. Strain H13-3 by Flagellotropic Bacteriophage 7-7-1
Authors: Yen Jiun Y. , Broadway Katherine M. , Scharf Birgit E. 
Published: August 2012

ABSTRACT

The flagellotropic phage 7-7-1 specifically adsorbs to
Agrobacterium
sp. strain H13-3 (formerly
Rhizobium lupini
H13-3) flagella for efficient host infection. The
Agrobacterium
sp. H13-3 flagellum is complex and consists of three flagellin proteins: the primary flagellin FlaA, which is essential for motility, and the secondary flagellins FlaB and FlaD, which have minor functions in motility. Using quantitative infectivity assays, we showed that absence of FlaD had no effect on phage infection, while absence of FlaB resulted in a 2.5-fold increase in infectivity. A
flaA
deletion strain, which produces straight and severely truncated flagella, experienced a significantly reduced infectivity, similar to that of a
flaB flaD
strain, which produces a low number of straight flagella. A strain lacking all three flagellin genes is phage resistant. In addition to flagellation, flagellar rotation is required for infection. A strain that is nonmotile due to an in-frame deletion in the gene encoding the motor component MotA is resistant to phage infection. We also generated two strains with point mutations in the
motA
gene resulting in replacement of the conserved charged residue Glu98, which is important for modulation of rotary speed. A change to the neutral Gln caused the flagellar motor to rotate at a constant high speed, allowing a 2.2-fold-enhanced infectivity. A change to the positively charged Lys caused a jiggly motility phenotype with very slow flagellar rotation, which significantly reduced the efficiency of infection. In conclusion, flagellar number and length, as well as speed of flagellar rotation, are important determinants for infection by phage 7-7-1.
Ecology of Vibrio parahaemolyticus and Vibrio vulnificus in the Coastal and Estuarine Waters of Louisiana, Maryland, Mississippi, and Washington (United States)
Authors: Johnson Crystal N. , Bowers John C. , Griffitt Kimberly J. , Molina Vanessa , Clostio Rachel W. , Pei Shaofeng , Laws Edward , Paranjpye Rohinee N. , Strom Mark S. , Chen Arlene , Hasan Nur A. , Huq Anwar , Noriea Nicholas F. , Grimes D. Jay , Colwell Rita R. 
Published: August 2012

ABSTRACT

Vibrio parahaemolyticus
and
Vibrio vulnificus
, which are native to estuaries globally, are agents of seafood-borne or wound infections, both potentially fatal. Like all vibrios autochthonous to coastal regions, their abundance varies with changes in environmental parameters. Sea surface temperature (SST), sea surface height (SSH), and chlorophyll have been shown to be predictors of zooplankton and thus factors linked to vibrio populations. The contribution of salinity, conductivity, turbidity, and dissolved organic carbon to the incidence and distribution of
Vibrio
spp. has also been reported. Here, a multicoastal, 21-month study was conducted to determine relationships between environmental parameters and
V. parahaemolyticus
and
V. vulnificus
populations in water, oysters, and sediment in three coastal areas of the United States. Because ecologically unique sites were included in the study, it was possible to analyze individual parameters over wide ranges. Molecular methods were used to detect genes for thermolabile hemolysin (
tlh
), thermostable direct hemolysin (
tdh
), and
tdh
-related hemolysin (
trh
) as indicators of
V. parahaemolyticus
and the hemolysin gene
vvhA
for
V. vulnificus
. SST and suspended particulate matter were found to be strong predictors of total and potentially pathogenic
V. parahaemolyticus
and
V. vulnificus
. Other predictors included chlorophyll
a
, salinity, and dissolved organic carbon. For the ecologically unique sites included in the study, SST was confirmed as an effective predictor of annual variation in vibrio abundance, with other parameters explaining a portion of the variation not attributable to SST.
Effects of UV-B Radiation and Periodic Desiccation on the Morphogenesis of the Edible Terrestrial Cyanobacterium Nostoc flagelliforme
Authors: Feng Yan-Na , Zhang Zhong-Chun , Feng Jun-Li , Qiu Bao-Sheng 
Published: August 2012

ABSTRACT

The terrestrial cyanobacterium
Nostoc flagelliforme
Berk. et M. A. Curtis has been a popular food and herbal ingredient for hundreds of years. To meet great market demand and protect the local ecosystem, for decades researchers have tried to cultivate
N. flagelliforme
but have failed to get macroscopic filamentous thalli. In this study, single trichomes with 50 to 200 vegetative cells were induced from free-living cells by low light and used to investigate the morphogenesis of
N. flagelliforme
under low UV-B radiation and periodic desiccation. Low-fluence-rate UV-B (0.1 W m
−2
) did not inhibit trichome growth; however, it significantly increased the synthesis of extracellular polysaccharides and mycosporine-like amino acids and promoted sheath formation outside the trichomes. Under low UV-B radiation, single trichomes developed into filamentous thalli more than 1 cm long after 28 days of cultivation, most of which grew separately in liquid BG11 medium. With periodic desiccation treatment, the single trichomes formed flat or banded thalli that grew up to 2 cm long after 3 months on solid BG11 medium. When trichomes were cultivated on solid BG11 medium with alternate treatments of low UV-B and periodic desiccation, dark and scraggly filamentous thalli that grew up to about 3 cm in length after 40 days were obtained. In addition, the cultivation of trichomes on nitrogen-deficient solid BG11 medium (BG11
0
) suggested that nitrogen availability could affect the color and lubricity of newly developed thalli. This study provides promising techniques for artificial cultivation of
N. flagelliforme
in the future.
Influence of Seasonal and Geochemical Changes on the Geomicrobiology of an Iron Carbonate Mineral Water Spring
Authors: Hegler Florian , Lösekann-Behrens Tina , Hanselmann Kurt , Behrens Sebastian , Kappler Andreas 
Published: August 2012

ABSTRACT

Fuschna Spring in the Swiss Alps (Engadin region) is a bicarbonate iron(II)-rich, pH-neutral mineral water spring that is dominated visually by dark green microbial mats at the side of the flow channel and orange iron(III) (oxyhydr)oxides in the flow channel. Gradients of O
2
, dissolved iron(II), and bicarbonate establish in the water. Our goals were to identify the dominating biogeochemical processes and to determine to which extent changing geochemical conditions along the flow path and seasonal changes influence mineral identity, crystallinity, and microbial diversity. Geochemical analysis showed microoxic water at the spring outlet which became fully oxygenated within 2.3 m downstream. X-ray diffraction and Mössbauer spectroscopy revealed calcite (CaCO
3
) and ferrihydrite [Fe(OH)
3
] to be the dominant minerals which increased in crystallinity with increasing distance from the spring outlet. Denaturing gradient gel electrophoresis banding pattern cluster analysis revealed that the microbial community composition shifted mainly with seasons and to a lesser extent along the flow path. 16S rRNA gene sequence analysis showed that microbial communities differ between the flow channel and the flanking microbial mat. Microbial community analysis in combination with most-probable-number analyses and quantitative PCR (qPCR) showed that the mat was dominated by cyanobacteria and the channel was dominated by microaerophilic Fe(II) oxidizers (1.97 × 10
7
± 4.36 × 10
6
16S rRNA gene copies g
−1
using
Gallionella
-specific qPCR primers), while high numbers of Fe(III) reducers (10
9
cells/g) were identified in both the mat and the flow channel. Phototrophic and nitrate-reducing Fe(II) oxidizers were present as well, although in lower numbers (10
3
to 10
4
cells/g). In summary, our data suggest that mainly seasonal changes caused microbial community shifts, while geochemical gradients along the flow path influenced mineral crystallinity.
A Wide Variety of Clostridium perfringens Type A Food-Borne Isolates That Carry a ChromosomalcpeGene Belong to One Multilocus Sequence Typing Cluster
Authors: Xiao Yinghua , Wagendorp Arjen , Moezelaar Roy , Abee Tjakko , Wells-Bennik Marjon H. J. 
Published: August 2012

ABSTRACTOf 98 suspected food-borneClostridium perfringensisolates obtained from a nationwide survey by the Food and Consumer Product Safety Authority in The Netherlands, 59 strains were identified asC. perfringenstype A. Using PCR-based techniques, thecpegene encoding enterotoxin was detected in eight isolates, showing a chromosomal location for seven isolates and a plasmid location for one isolate. Further characterization of these strains by using (GTG)5fingerprint repetitive sequence-based PCR analysis distinguishedC. perfringensfrom other sulfite-reducing clostridia but did not allow for differentiation between various types ofC. perfringensstrains. To characterize theC. perfringensstrains further, multilocus sequence typing (MLST) analysis was performed on eight housekeeping genes of both enterotoxic and non-cpeisolates, and the data were combined with a previous global survey covering strains associated with food poisoning, gas gangrene, and isolates from food or healthy individuals. This revealed that the chromosomalcpestrains (food strains and isolates from food poisoning cases) belong to a distinct cluster that is significantly distant from all the othercpeplasmid-carrying andcpe-negative strains. These results suggest that different groups ofC. perfringenshave undergone niche specialization and that a distinct group of food isolates has specific core genome sequences. Such findings have epidemiological and evolutionary significance. Better understanding of the origin and reservoir of enterotoxicC. perfringensmay allow for improved control of this organism in foods.
Comparison of the Multiple-Sample Means with Composite Sample Results for Fecal Indicator Bacteria by Quantitative PCR and Culture
Authors: Converse Reagan R. , Wymer Larry J. , Dufour Alfred P. , Wade Timothy J. 
Published: August 2012

ABSTRACT
Few studies have addressed the efficacy of composite sampling for measuring indicator bacteria by quantitative PCR (qPCR). We compared results from composited samples with multiple-sample means for culture- and qPCR-based water quality monitoring. Results from composited samples for both methods were similarly correlated to multiple-sample means and predicted criteria exceedances equally.
The Type 3 Protein Secretion System of Cupriavidus taiwanensis Strain LMG19424 Compromises Symbiosis with Leucaena leucocephala
Authors: Saad Maged M. , Crèvecoeur Michèle , Masson-Boivin Catherine , Perret Xavier 
Published: August 2012

ABSTRACT

Cupriavidus taiwanensis
forms proficient symbioses with a few
Mimosa
species. Inactivation of a type III protein secretion system (T3SS) had no effect on
Mimosa pudica
but allowed
C. taiwanensis
to establish chronic infections and fix nitrogen in
Leucaena leucocephala
. Unlike what was observed for other rhizobia, glutamate rather than plant flavonoids mediated transcriptional activation of this atypical T3SS.
Characterization of a Novel Subgroup of Extracellular Medium-Chain-Length Polyhydroxyalkanoate Depolymerases from Actinobacteria
Authors: Gangoiti Joana , Santos Marta , Prieto María Auxiliadora , de la Mata Isabel , Serra Juan L. , Llama María J. 
Published: August 2012

ABSTRACT

Nineteen medium-chain-length (mcl) poly(3-hydroxyalkanoate) (PHA)-degrading microorganisms were isolated from natural sources. From them, seven Gram-positive and three Gram-negative bacteria were identified. The ability of these microorganisms to hydrolyze other biodegradable plastics, such as short-chain-length (scl) PHA, poly(ε-caprolactone) (PCL), poly(ethylene succinate) (PES), and poly(
l
-lactide) (PLA), has been studied. On the basis of the great ability to degrade different polyesters,
Streptomyces roseolus
SL3 was selected, and its extracellular depolymerase was biochemically characterized. The enzyme consisted of one polypeptide chain of 28 kDa with a pI value of 5.2. Its maximum activity was observed at pH 9.5 with chromogenic substrates. The purified enzyme hydrolyzed mcl PHA and PCL but not scl PHA, PES, and PLA. Moreover, the mcl PHA depolymerase can hydrolyze various substrates for esterases, such as tributyrin and
p
-nitrophenyl (
p
NP)-alkanoates, with its maximum activity being measured with
p
NP-octanoate. Interestingly, when poly(3-hydroxyoctanoate-co-3-hydroxyhexanoate [11%]) was used as the substrate, the main hydrolysis product was the monomer (
R
)-3-hydroxyoctanoate. In addition, the genes of several
Actinobacteria
strains, including
S. roseolus
SL3, were identified on the basis of the peptide
de novo
sequencing of the
Streptomyces venezuelae
SO1 mcl PHA depolymerase by tandem mass spectrometry. These enzymes did not show significant similarity to mcl PHA depolymerases characterized previously. Our results suggest that these distinct enzymes might represent a new subgroup of mcl PHA depolymerases.
Synergistic Activation of the Pathogenicity-Related Proline Iminopeptidase Gene in Xanthomonas campestris pv. campestris by HrpX and a LuxR Homolog
Authors: Zhang Jingxi , Kan Jinhong , Zhang Jieqiong , Guo Ping , Chen Xiaoying , Fang Rongxiang , Jia Yantao 
Published: August 2012

ABSTRACT

Xanthomonas campestris
pv. campestris strain 8004 contains an orphan quorum-sensing (QS) locus,
xccR
-
pip

Xcc

, in which the proline iminopeptidase (
pip

Xcc

) gene (where “
Xcc
” indicates that the
pip
gene is from
X. campestris
pv. campestris) is positively regulated by the LuxR homologue XccR by binding to the
luxXc
box of the
pip

Xcc

promoter. The disruption of
pip

Xcc

significantly attenuated the virulence of
X. campestris
pv. campestris. An imperfect plant-inducible promoter (PIP) box is located in the upstream region of the
pip

Xcc

promoter, which is the putative binding site of the transcriptional activator HrpX. To explore whether the expression of the
pip

Xcc

gene is regulated by HrpX, the expression level of a
pip

Xcc

promoter-
gusA
fusion gene was assayed in an
hrpX
disruption mutant. The results showed that the lack of HrpX dramatically decreased the β-glucuronidase (GUS) activity. Further analyses using an electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP)-PCR indicated that the imperfect PIP box in
X. campestris
pv. campestris is specifically bound to HrpX. These data demonstrated that the
pip

Xcc

gene belongs to the hrp regulon and that the imperfect PIP box of the
pip

Xcc

promoter could be a
cis
element for the HrpX protein. We further showed in a pulldown assay that XccR can bind HrpX, suggesting that these two regulatory proteins coactivate the virulence factor by binding to the different
cis
elements of the
pip

Xcc

gene and adapt to the host environment during
X. campestris
pv. campestris infection.
Hal Is a Bacillus anthracis Heme Acquisition Protein
Authors: Balderas Miriam A. , Nobles Christopher L. , Honsa Erin S. , Alicki Embriette R. , Maresso Anthony W. 
Published: August 2012

ABSTRACTThe metal iron is a limiting nutrient for bacteria during infection.Bacillus anthracis, the causative agent of anthrax and a potential weapon of bioterrorism, grows rapidly in mammalian hosts, which suggests that it efficiently attains iron during infection. Recent studies have uncovered both heme (isd) and siderophore-mediated (asb) iron transport pathways in this pathogen. Whereas deletion of theasbgenes results in reduced virulence, the loss of three surface components fromisdhad no effect, thereby leaving open the question of what additional factors inB. anthracisare responsible for iron uptake from the most abundant iron source for mammals, heme. Here, we describe the first functional characterization ofbas0520, a gene recently implicated in anthrax disease progression.bas0520encodes a single near-iron transporter (NEAT) domain and several leucine-rich repeats. The NEAT domain binds heme, despite lacking a stabilizing tyrosine common to the NEAT superfamily of hemoproteins. The NEAT domain also binds hemoglobin and can acquire heme from hemoglobin in solution. Finally, deletion ofbas0520resulted in bacilli unable to grow efficiently on heme or hemoglobin as an iron source and yielded the most significant phenotype relative to that for other putative heme uptake systems, a result that suggests that this protein plays a prominent role in the replication ofB. anthracisin hematogenous environments. Thus, we have assigned the name of Hal (heme-acquisitionleucine-rich repeat protein) to BAS0520. These studies advance our understanding of heme acquisition by this dangerous pathogen and justify efforts to determine the mechanistic function of this novel protein for vaccine or inhibitor development.
Phosphoketolase Pathway for Xylose Catabolism in Clostridium acetobutylicum Revealed by
13
C Metabolic Flux Analysis
Authors: Liu Lixia , Zhang Lei , Tang Wei , Gu Yang , Hua Qiang , Yang Sheng , Jiang Weihong , Yang Chen 
Published: August 2012

ABSTRACT

Solvent-producing clostridia are capable of utilizing pentose sugars, including xylose and arabinose; however, little is known about how pentose sugars are catabolized through the metabolic pathways in clostridia. In this study, we identified the xylose catabolic pathways and quantified their fluxes in
Clostridium acetobutylicum
based on [1-
13
C]xylose labeling experiments. The phosphoketolase pathway was found to be active, which contributed up to 40% of the xylose catabolic flux in
C. acetobutylicum
. The split ratio of the phosphoketolase pathway to the pentose phosphate pathway was markedly increased when the xylose concentration in the culture medium was increased from 10 to 20 g liter
−1
. To our knowledge, this is the first time that the
in vivo
activity of the phosphoketolase pathway in clostridia has been revealed. A phosphoketolase from
C. acetobutylicum
was purified and characterized, and its activity with xylulose-5-P was verified. The phosphoketolase was overexpressed in
C. acetobutylicum
, which resulted in slightly increased xylose consumption rates during the exponential growth phase and a high level of acetate accumulation.
Genome-Wide Responses of the Model Archaeon Halobacterium sp. Strain NRC-1 to Oxygen Limitation
Authors: DasSarma Priya , Zamora Regie C. , Müller Jochen A. , DasSarma Shiladitya 
Published: August 2012

ABSTRACT

As part of a comprehensive postgenomic investigation of the model archaeon
Halobacterium
sp. strain NRC-1, we used whole-genome DNA microarrays to compare transcriptional profiles of cells grown under anaerobic or aerobic conditions. When anaerobic growth supported by arginine fermentation was compared to aerobic growth, genes for arginine fermentation (
arc
) and anaerobic respiration (
dms
), using trimethylamine
N
-oxide (TMAO) as the terminal electron acceptor, were highly upregulated, as was the
bop
gene, required for phototrophic growth. When arginine fermentation was compared to anaerobic respiration with TMAO, the
arc
and
dms
genes were both induced with arginine, while TMAO induced the
bop
gene and major gas vesicle protein (
gvpAC
) genes specifying buoyant gas vesicles. Anaerobic conditions with either TMAO or arginine also upregulated the
cba
genes, encoding one of three cytochrome oxidases. In-frame deletion of two COG3413 family regulatory genes,
bat
and
dmsR
, showed downregulation of the
bop
gene cluster and loss of purple membrane synthesis and downregulation of the
dms
operon and loss of anaerobic respiration capability, respectively. Bioinformatic analysis identified additional regulatory and sensor genes that are likely involved in the full range of cellular responses to oxygen limitation. Our results show that the
Halobacterium
sp. has evolved a carefully orchestrated set of responses to oxygen limitation. As conditions become more reducing, cells progressively increase buoyancy, as well as capabilities for phototrophy, scavenging of molecular oxygen, anaerobic respiration, and fermentation.
Role of the Helicobacter pylori Sensor Kinase ArsS in Protein Trafficking and Acid Acclimation
Authors: Marcus Elizabeth A. , Sachs George , Wen Yi , Feng Jing , Scott David R. 
Published: August 2012

ABSTRACT

Helicobacter pylori
survives and grows at low pHs via acid acclimation mechanisms that enable periplasmic pH homeostasis. Important components include a cytoplasmic urease; a pH-gated urea channel, UreI; and periplasmic α-carbonic anhydrase. To allow the rapid adjustment of periplasmic pH, acid acclimation components are recruited to the inner membrane in acid. The ArsRS two-component system, in an acid-responsive manner, controls the transcription of the urease gene cluster and α-carbonic anhydrase. The aim of this study is to determine the role of ArsS in protein trafficking as a component of acid acclimation.
H. pylori
wild-type and Δ
arsS
bacteria were incubated at acidic and neutral pHs. Intact bacteria, purified membranes, and total protein were analyzed by Western blotting and urease activity measurements. The total urease activity level was decreased in the Δ
arsS
strain, but the acid activation of UreI was unaffected. A 30-min acid exposure increased the level and activity of urease proteins at the membrane in the wild type but not in the Δ
arsS
strain. The urease levels and activity of the Δ
arsS
strain after a 90-min acid exposure were similar to those of the wild type. ArsS, in addition to its role in urease gene transcription, is also involved in the recruitment of urease proteins to the inner membrane to augment acid acclimation during acute acid exposure. Urease membrane recruitment following prolonged acid exposure in the absence of ArsS was similar to that of the wild type, suggesting a compensatory mechanism, possibly regulated by FlgS, underscoring the importance of urease membrane recruitment and activation in periplasmic pH homeostasis.
Nearly Constant Shedding of Diverse Enteric Viruses by Two Healthy Infants
Authors: Kapusinszky Beatrix , Minor Philip , Delwart Eric 
Published: August 2012

ABSTRACT

Stool samples from two healthy infant siblings collected at about weekly intervals during their first year of life were analyzed by PCR for 15 different enteric viral genera.
Adenovirus
,
Aichi virus
,
Anellovirus
,
Astrovirus
,
Bocavirus
,
Enterovirus
,
Parechovirus
,
Picobirnavirus
, and
Rotavirus
were detected. Not detected were
Coronavirus
,
Cardiovirus
,
Cosavirus
,
Salivirus
,
Sapovirus
, and
Norovirus
. Long-term virus shedding, lasting from one to 12 months, was observed for adenoviruses, anelloviruses, bocaviruses, enteroviruses, parechoviruses, and picobirnaviruses. Repeated administration of oral poliovirus vaccine resulted in progressively shorter periods of poliovirus detection. Four nonpolio enterovirus genotypes were also detected. An average of 1.8 distinct human viruses were found per time point. Ninety-two percent (66/72) of the fecal samples tested contained one to five different human viruses. Two British siblings in the mid-1980s showed nearly constant fecal viral shedding. Our results demonstrate that frequent enteric infections with diverse viruses occur during early childhood in the absence of severe clinical symptoms.