bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deciphering the Role of Multiple Betaine-Carnitine-Choline Transporters in the Halophile Vibrio parahaemolyticus
Authors: Ongagna-Yhombi Serge Y. , McDonald Nathan D. , Boyd E. Fidelma 
Published: October 2014

ABSTRACT

Vibrio parahaemolyticus
is a halophile that is the predominant cause of bacterial seafood-related gastroenteritis worldwide. To survive in the marine environment,
V. parahaemolyticus
must have adaptive strategies to cope with salinity changes. Six putative compatible solute (CS) transport systems were previously predicted from the genome sequence of
V. parahaemolyticus
RIMD2210633. In this study, we determined the role of the four putative betaine-carnitine-choline transporter (BCCT) homologues VP1456, VP1723, VP1905, and VPA0356 in the NaCl stress response. Expression analysis of the four BCCTs subjected to NaCl upshock showed that VP1456, VP1905, and VPA0356, but not VP1723, were induced. We constructed in-frame single-deletion mutant strains for all four BCCTs, all of which behaved similarly to the wild-type strain, demonstrating a redundancy of the systems. Growth analysis of a quadruple mutant and four BCCT triple mutants demonstrated the requirement for at least one BCCT for efficient CS uptake. We complemented
Escherichia coli
MHK13, a CS synthesis- and transporter-negative strain, with each BCCT and examined CS uptake by growth analysis and
1
H nuclear magnetic resonance (NMR) spectroscopy analyses. These data demonstrated that VP1456 had the most diverse substrate transport ability, taking up glycine betaine (GB), proline, choline, and ectoine. VP1456 was the sole ectoine transporter. In addition, the data demonstrated that VP1723 can transport GB, proline, and choline, whereas VP1905 and VPA0356 transported only GB. Overall, the data showed that the BCCTs are functional and that there is redundancy among them.
Community Shift from Phototrophic to Chemotrophic Sulfide Oxidation following Anoxic Holomixis in a Stratified Seawater Lake
Authors: Pjevac Petra , Korlević Marino , Berg Jasmine S. , Bura-Nakić Elvira , Ciglenečki Irena , Amann Rudolf , Orlić Sandi 
Published: October 2014

ABSTRACT
Most stratified sulfidic holomictic lakes become oxygenated after annual turnover. In contrast, Lake Rogoznica, on the eastern Adriatic coast, has been observed to undergo a period of water column anoxia after water layer mixing and establishment of holomictic conditions. Although Lake Rogoznica's chemistry and hydrography have been studied extensively, it is unclear how the microbial communities typically inhabiting the oxic epilimnion and a sulfidic hypolimnion respond to such a drastic shift in redox conditions. We investigated the impact of anoxic holomixis on microbial diversity and microbially mediated sulfur cycling in Lake Rogoznica with an array of culture-independent microbiological methods. Our data suggest a tight coupling between the lake's chemistry and occurring microorganisms. During stratification, anoxygenic phototrophic sulfur bacteria were dominant at the chemocline and in the hypolimnion. After an anoxic mixing event, the anoxygenic phototrophic sulfur bacteria entirely disappeared, and the homogeneous, anoxic water column was dominated by a bloom of gammaproteobacterial sulfur oxidizers related to the GSO/SUP05 clade. This study is the first report of a community shift from phototrophic to chemotrophic sulfide oxidizers as a response to anoxic holomictic conditions in a seasonally stratified seawater lake.
Molecular and Metabolic Adaptations of Lactococcus lactis at Near-Zero Growth Rates
Authors: Ercan Onur , Wels Michiel , Smid Eddy J. , Kleerebezem Michiel 
Published: October 2014

ABSTRACT

This paper describes the molecular and metabolic adaptations of
Lactococcus lactis
during the transition from a growing to a near-zero growth state by using carbon-limited retentostat cultivation. Transcriptomic analyses revealed that metabolic patterns shifted between lactic- and mixed-acid fermentations during retentostat cultivation, which appeared to be controlled at the level of transcription of the corresponding pyruvate dissipation-encoding genes. During retentostat cultivation, cells continued to consume several amino acids but also produced specific amino acids, which may derive from the conversion of glycolytic intermediates. We identify a novel motif containing CTGTCAG in the upstream regions of several genes related to amino acid conversion, which we propose to be the target site for CodY in
L. lactis
KF147. Finally, under extremely low carbon availability, carbon catabolite repression was progressively relieved and alternative catabolic functions were found to be highly expressed, which was confirmed by enhanced initial acidification rates on various sugars in cells obtained from near-zero-growth cultures. The present integrated transcriptome and metabolite (amino acids and previously reported fermentation end products) study provides molecular understanding of the adaptation of
L. lactis
to conditions supporting low growth rates and expands our earlier analysis of the quantitative physiology of this bacterium at near-zero growth rates toward gene regulation patterns involved in zero-growth adaptation.
Inactivation of a
GAL4
-Like Transcription Factor Improves Cell Fitness and Product Yield in Glycoengineered Pichia pastoris Strains
Authors: Jiang Bo , Argyros Rebecca , Bukowski John , Nelson Stephanie , Sharkey Nathan , Kim Sehoon , Copeland Victoria , Davidson Robert C. , Chen Ronghua , Zhuang Jun , Sethuraman Natarajan , Stadheim Terrance A. 
Published: October 2014

ABSTRACT

With a completely reengineered and humanized glycosylation pathway, glycoengineered
Pichia pastoris
has emerged as a promising production host for the manufacture of therapeutic glycoproteins. However, the extensive genetic modifications have also negatively affected the overall fitness levels of the glycoengineered host cells. To make glycoengineered
Pichia
strains more compatible with a scalable industrial fermentation process, we sought to identify genetic solutions to broadly improve cell robustness during fermentation. In this study, we report that mutations within the
Pichia pastoris
ATT1
(
PpATT1
) gene (a homolog of the
Saccharomyces cerevisiae
GAL4
[
ScGAL4
] transcriptional activator) dramatically increased the cellular fitness levels of glycoengineered
Pichia
strains. We demonstrate that deletion of the
PpATT1
gene enabled glycoengineered
Pichia
strains to improve their thermal tolerance levels, reduce their cell lysis defects, and greatly improve fermentation robustness. The extension of the duration of fermentation enabled the
PpATT1
-modified glycoengineered
Pichia
strains to increase their product yields significantly without any sacrifice in product quality. Because the
ATT1
gene could be deleted from any
Pichia
strains, including empty hosts and protein-expressing production strains alike, we suggest that the findings described in this study are broadly applicable to any
Pichia
strains used for the production of therapeutic proteins, including monoclonal antibodies, Fc fusions, peptides, hormones, and growth factors.
Rotavirus Genotypes in Sewage Treatment Plants and in Children Hospitalized with Acute Diarrhea in Italy in 2010 and 2011
Authors: Ruggeri Franco M. , Bonomo Paolo , Ianiro Giovanni , Battistone Andrea , Delogu Roberto , Germinario Cinzia , Chironna Maria , Triassi Maria , Campagnuolo Rosalba , Cicala Antonella , Giammanco Giovanni M. , Castiglia Paolo , Serra Caterina , Gaggioli Andrea , Fiore Lucia 
Published: October 2014

ABSTRACT
Although the molecular surveillance network RotaNet-Italy provides useful nationwide data on rotaviruses causing severe acute gastroenteritis in children in Italy, scarce information is available on rotavirus circulation in the general Italian population, including adults with mild or asymptomatic infection. We investigated the genotypes of rotaviruses present in urban wastewaters and compared them with those of viral strains from clinical pediatric cases. During 2010 and 2011, 285 sewage samples from 4 Italian cities were tested by reverse transcription-PCRs (RT-PCRs) specific for rotavirus VP7 and VP4 genes. Rotavirus was detected in 172 (60.4%) samples, 26 of which contained multiple rotavirus G (VP7 gene) genotypes, for a total of 198 G types. Thirty-two samples also contained multiple P (VP4 gene) genotypes, yielding 204 P types in 172 samples. Genotype G1 accounted for 65.6% of rotaviruses typed, followed by genotypes G2 (20.2%), G9 (7.6%), G4 (4.6%), G6 (1.0%), G3 (0.5%), and G26 (0.5%). VP4 genotype P[8] accounted for 75.0% of strains, genotype P[4] accounted for 23.0% of strains, and the uncommon genotypes P[6], P[9], P[14], and P[19] accounted for 2.0% of strains altogether. These rotavirus genotypes were also found in pediatric patients hospitalized in the same areas and years but in different proportions. Specifically, genotypes G2, G9, and P[4] were more prevalent in sewage samples than among samples from patients, which suggests either a larger circulation of the latter strains through the general population not requiring medical care or their greater survival in wastewaters. A high level of nucleotide identity in the G1, G2, and G6 VP7 sequences was observed between strains from the environment and those from patients.
Uptake of Amino Acids and Their Metabolic Conversion into the Compatible Solute Proline Confers Osmoprotection to Bacillus subtilis
Authors: Zaprasis Adrienne , Bleisteiner Monika , Kerres Anne , Hoffmann Tamara , Bremer Erhard 
Published: October 2014

ABSTRACT

The data presented here reveal a new facet of the physiological adjustment processes through which
Bacillus subtilis
can derive osmostress protection. We found that the import of proteogenic (Glu, Gln, Asp, Asn, and Arg) and of nonproteogenic (Orn and Cit) amino acids and their metabolic conversion into proline enhances growth under otherwise osmotically unfavorable conditions. Osmoprotection by amino acids depends on the functioning of the ProJ-ProA-ProH enzymes, but different entry points into this biosynthetic route are used by different amino acids to finally yield the compatible solute proline. Glu, Gln, Asp, and Asn are used to replenish the cellular pool of glutamate, the precursor for proline production, whereas Arg, Orn, and Cit are converted into γ-glutamic semialdehyde/Δ
1
-pyrroline-5-carboxylate, an intermediate in proline biosynthesis. The import of Glu, Gln, Asp, Asn, Arg, Orn, and Cit did not lead to a further increase in the size of the proline pool that is already present in osmotically stressed cells. Hence, our data suggest that osmoprotection of
B. subtilis
by this group of amino acids rests on the savings in biosynthetic building blocks and energy that would otherwise have to be devoted either to the synthesis of the proline precursor glutamate or of proline itself. Since glutamate is the direct biosynthetic precursor for proline, we studied its uptake and found that GltT, an Na
+
-coupled symporter, is the main uptake system for both glutamate and aspartate in
B. subtilis
. Collectively, our data show how effectively
B. subtilis
can exploit environmental resources to derive osmotic-stress protection through physiological means.
A Novel DNA-Binding Protein, PhaR, Plays a Central Role in the Regulation of Polyhydroxyalkanoate Accumulation and Granule Formation in the Haloarchaeon Haloferax mediterranei
Authors: Cai Shuangfeng , Cai Lei , Zhao Dahe , Liu Guiming , Han Jing , Zhou Jian , Xiang Hua 
Published: October 2014

ABSTRACT

Polyhydroxyalkanoates (PHAs) are synthesized and assembled as PHA granules that undergo well-regulated formation in many microorganisms. However, this regulation remains unclear in haloarchaea. In this study, we identified a PHA granule-associated regulator (PhaR) that negatively regulates the expression of both its own gene and the granule structural gene
phaP
in the same operon (
phaRP
) in
Haloferax mediterranei
. Chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) assays demonstrated a significant interaction between PhaR and the
phaRP
promoter
in vivo
. Scanning mutagenesis of the
phaRP
promoter revealed a specific
cis
-element as the possible binding position of the PhaR. The haloarchaeal homologs of the PhaR contain a novel conserved domain that belongs to a swapped-hairpin barrel fold family found in AbrB-like proteins. Amino acid substitution indicated that this AbrB-like domain is critical for the repression activity of PhaR. In addition, the
phaRP
promoter had a weaker activity in the PHA-negative strains, implying a function of the PHA granules in titration of the PhaR. Moreover, the
H. mediterranei
strain lacking
phaR
was deficient in PHA accumulation and produced granules with irregular shapes. Interestingly, the PhaR itself can promote PHA synthesis and granule formation in a PhaP-independent manner. Collectively, our results demonstrated that the haloarchaeal PhaR is a novel bifunctional protein that plays the central role in the regulation of PHA accumulation and granule formation in
H. mediterranei
.
Effects of Actin-Like Proteins Encoded by Two Bacillus pumilus Phages on Unstable Lysogeny, Revealed by Genomic Analysis
Authors: Yuan Yihui , Peng Qin , Wu Dandan , Kou Zheng , Wu Yan , Liu Pengming , Gao Meiying 
Published: October 2014

ABSTRACT

We characterized two newly isolated myoviruses, Bp8p-C and Bp8p-T, infecting the ginger rhizome rot disease pathogen
Bacillus pumilus
GR8. The plaque of Bp8p-T exhibited a clear center with a turbid rim, suggesting that Bp8p-T could transform into latent phage. Lysogeny assays showed that both the two phages could form latent states, while Bp8p-T could form latent phage at a higher frequency and stability than Bp8p-C. The genomes of Bp8p-C and Bp8p-T were 151,417 and 151,419 bp, respectively; both encoded 212 putative proteins, and only differed by three nucleotides. Moreover, owing to this difference, Bp8p-C encoded a truncated, putative actin-like plasmid segregation protein Gp27-C. Functional analysis of protein Gp27 showed that Gp27-T encoded by Bp8p-T exhibited higher ATPase activity and assembly ability than Gp27-C. The results indicate that the difference in Gp27 affected the phage lysogenic ability. Structural proteome analysis of Bp8p-C virion resulted in the identification of 14 structural proteins, among which a pectin lyase-like protein, a putative poly-gamma-glutamate hydrolase, and three proteins with unknown function, were firstly identified as components of the phage virion. Both phages exhibited specific lytic ability to the host strain GR8. Bp8p-C showed better control effect on the pathogen in ginger rhizome slices than Bp8p-T, suggesting that Bp8p-C has a potential application in bio-control of ginger rhizome rot disease.
Mortalities of Eastern and Pacific Oyster Larvae Caused by the Pathogens Vibrio coralliilyticus and Vibrio tubiashii
Authors: Richards Gary P. , Watson Michael A. , Needleman David S. , Church Karlee M. , Häse Claudia C. 
Published: October 2014

ABSTRACT

Vibrio tubiashii
is reported to be a bacterial pathogen of larval Eastern oysters (
Crassostrea virginica
) and Pacific oysters (
Crassostrea gigas
) and has been associated with major hatchery crashes, causing shortages in seed oysters for commercial shellfish producers. Another bacterium,
Vibrio coralliilyticus
, a well-known coral pathogen, has recently been shown to elicit mortality in fish and shellfish. Several strains of
V. coralliilyticus
, such as ATCC 19105 and Pacific isolates RE22 and RE98, were misidentified as
V. tubiashii
until recently. We compared the mortalities caused by two
V. tubiashii
and four
V. coralliilyticus
strains in Eastern and Pacific oyster larvae. The 50% lethal dose (LD
50
) of
V. coralliilyticus
in Eastern oysters (defined here as the dose required to kill 50% of the population in 6 days) ranged from 1.1 × 10
4
to 3.0 × 10
4
CFU/ml seawater; strains RE98 and RE22 were the most virulent. This study shows that
V. coralliilyticus
causes mortality in Eastern oyster larvae. Results for Pacific oysters were similar, with LD
50
s between 1.2 × 10
4
and 4.0 × 10
4
CFU/ml.
Vibrio tubiashii
ATCC 19106 and ATCC 19109 were highly infectious toward Eastern oyster larvae but were essentially nonpathogenic toward healthy Pacific oyster larvae at dosages of ≥1.1 × 10
4
CFU/ml. These data, coupled with the fact that several isolates originally thought to be
V. tubiashii
are actually
V. coralliilyticus
, suggest that
V. coralliilyticus
has been a more significant pathogen for larval bivalve shellfish than
V. tubiashii
, particularly on the U.S. West Coast, contributing to substantial hatchery-associated morbidity and mortality in recent years.
High Incidence of Preharvest Colonization of Huanglongbing-Symptomatic Citrus sinensis Fruit by Lasiodiplodia theobromae (Diplodia natalensis) and Exacerbation of Postharvest Fruit Decay by That Fungus
Authors: Zhao Wei , Bai Jinhe , McCollum Greg , Baldwin Elizabeth 
Published: October 2014

ABSTRACTHuanglongbing (HLB), presumably caused by the bacterium “CandidatusLiberibacter asiaticus,” is a devastating citrus disease associated with excessive preharvest fruit drop.Lasiodiplodia theobromae(diplodia) is the causal organism of citrus stem end rot (SER). The pathogen infects citrus fruit under the calyx abscission zone (AZ-C) and is associated with cell wall hydrolytic enzymes similar to plant enzymes involved in abscission. By means of DNA sequencing, diplodia was found in “Ca. Liberibacter asiaticus”-positive juice from HLB-symptomatic fruit (S) but not in “Ca. Liberibacter asiaticus”-negative juice. Therefore, the incidence of diplodia in fruit tissues, the impact on HLB-related postharvest decay, and the implications for HLB-related preharvest fruit drop were investigated in Hamlin and Valencia oranges. Quantitative PCR results (qPCR) revealed a significantly (P< 0.001) greater incidence of diplodia in the AZ-C of HLB-symptomatic (S; “Ca. Liberibacter asiaticus” threshold cycle [CT] of <30) than in the AZ-C of in asymptomatic (AS; “Ca. Liberibacter asiaticus”CTof ≥30) fruit. In agreement with the qPCR results, 2 weeks after exposure to ethylene, the incidences of SER in S fruit were 66.7% (Hamlin) and 58.7% (Valencia), whereas for AS fruit the decay rates were 6.7% (Hamlin) and 5.3% (Valencia). Diplodia colonization of S fruit AZ-C was observed by scanning electron microscopy and confirmed by PCR test and morphology of conidia in isolates from the AZ-C after surface sterilization. DiplodiaCTvalues were negatively correlated with ethylene production (R= −0.838 for Hamlin;R= −0.858 for Valencia) in S fruit, and positively correlated with fruit detachment force (R= 0.855 for Hamlin;R= 0.850 for Valencia), suggesting that diplodia colonization in AZ-C may exacerbate HLB-associated preharvest fruit drop.
A Novel Function for Hog1 Stress-Activated Protein Kinase in Controlling White-Opaque Switching and Mating in Candida albicans
Authors: Liang Shen-Huan , Cheng Jen-Hua , Deng Fu-Sheng , Tsai Pei-An , Lin Ching-Hsuan 
Published: October 2014

ABSTRACT

Candida albicans
is a commensal in heathy people but has the potential to become an opportunistic pathogen and is responsible for half of all clinical infections in immunocompromised patients. Central to understanding
C. albicans
behavior is the white-opaque phenotypic switch, in which cells can undergo an epigenetic transition between the white state and the opaque state. The phenotypic switch regulates multiple properties, including biofilm formation, virulence, mating, and fungus-host interactions. Switching between the white and opaque states is associated with many external stimuli, such as oxidative stress, pH, and
N
-acetylglucosamine, and is directly regulated by the Wor1 transcriptional circuit. The Hog1 stress-activated protein kinase (SAPK) pathway is recognized as the main pathway for adapting to environmental stress in
C. albicans
. In this work, we first show that loss of the
HOG1
gene in
a
/
a
and α/α cells, but not
a
/α cells, results in 100% white-to-opaque switching when cells are grown on synthetic medium, indicating that switching is repressed by the
a1
/α2 heterodimer that represses
WOR1
gene expression. Indeed, switching in the
hog1
Δ strain was dependent on the presence of
WOR1
, as a
hog1
Δ
wor1
Δ strain did not show switching to the opaque state. Deletion of
PBS2
and
SSK2
also resulted in
C. albicans
cells switching from white to opaque with 100% efficiency, indicating that the entire Hog1 SAPK pathway is involved in regulating this unique phenotypic transition. Interestingly, all Hog1 pathway mutants also caused defects in shmoo formation and mating efficiencies. Overall, this work reveals a novel role for the Hog1 SAPK pathway in regulating white-opaque switching and sexual behavior in
C. albicans
.
Organisational participation and health among smallholder farmers: a longitudinal study in a Latin American context
Authors: Orozco Fadya , Mota Eduardo , Cole Donald C 
Published: October 2014

ObjectiveTo understand the impact of social organisation affiliation and farmers’ agricultural production practices on farmer health. Organisations facilitate the acquisition and exchange of forms of social capital which can influence the adoption of practices with potential health impacts. In countries such as Ecuador, smallholder agriculture is practised by socially vulnerable populations. Agricultural production often involves the use of extremely hazardous pesticides, while practices that reduce the use of chemicals through integrated pest management (IPM) remain uncommon.DesignLongitudinal study (2007–2010).Setting12 Ecuadorian communities, previously part of a participatory action research study.Participants208 small-scale farmers. Inclusion criteria were: age between 18 and 65 years, literate and resident in the community for the previous 3 years.Primary outcomesThe differential effects of the membership in social organisations (as aneffect modifier), on the relationship between the implementation of IPM practices (main independent variable) and farmers’ health, measured by neurocognitive performance scores (better higher value;dependent variable).ResultsAmong organisational participants, the coefficient of association between the implementation of IPM practices for the category good/very good (vs no use) and neurocognitive performance, when farmers were involved in organisations, was negative and moderate (β=−0.17, SE 0.21) though not significant (p>0.1); for the category little/moderate use, the coefficient was positive (β=0.34, SE 0.19) and significant. Among those who did not participate in organisations, both little/moderate use and good/very good use of IPM practices were associated with an increase in neurocognitive performance.ConclusionsThe effect of agricultural production practices on farmers’ health, transmitted through organisations, can be differentiated. Organisations as structures of social capital seem to be functional in the social reproduction process of the communities studied. Results highlight the need to redirect the analysis of social capital to a more integrated study of social determination of health.