bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a Dehydrogenase Required for Lactose Metabolism inCaulobacter crescentus
Authors: Arellano Benjamin H. , Ortiz Janett D. , Manzano Janet , Chen Joseph C. 
Published: February 2010

ABSTRACTCaulobacter crescentus, which thrives in freshwater environments with low nutrient levels, serves as a model system for studying bacterial cell cycle regulation and organelle development. We examined its ability to utilize lactose (i) to gain insight into the metabolic capacities of oligotrophic bacteria and (ii) to obtain an additional genetic tool for studying this model organism, aiming to eliminate the basal enzymatic activity that hydrolyzes the chromogenic substrate 5-bromo-4-chloro-3-indolyl-β-d-galactopyranoside (X-gal). Using a previously isolated transposon mutant, we identified a gene,lacA, that is required for growth on lactose as the sole carbon source and for turning colonies blue in the presence of X-gal. LacA, which contains a glucose-methanol-choline (GMC) oxidoreductase domain, has homology to the flavin subunit ofPectobacterium cypripedii's gluconate dehydrogenase. Sequence comparisons indicated that two genes nearlacA,lacBandlacC, encode the other subunits of the membrane-bound dehydrogenase. In addition to lactose, all threelacgenes are involved in the catabolism of three other β-galactosides (lactulose, lactitol, and methyl-β-d-galactoside) and two glucosides (salicin and trehalose). Dehydrogenase assays confirmed that thelacgene products oxidize lactose, salicin, and trehalose. This enzymatic activity is inducible, and increasedlacexpression in the presence of lactose and salicin likely contributes to the induction. Expression oflacAalso depends on the presence of thelacgenes, implying that the dehydrogenase participates in induction. The involvement of a dehydrogenase suggests that degradation of lactose and other sugars inC. crescentusmay resemble a proposed pathway inAgrobacterium tumefaciens.
Microbial and Physicochemical Characteristics of Compact Anaerobic Ammonium-Oxidizing Granules in an Upflow Anaerobic Sludge Blanket Reactor
Authors: Ni Bing-Jie , Hu Bao-Lan , Fang Fang , Xie Wen-Ming , Kartal Boran , Liu Xian-Wei , Sheng Guo-Ping , Jetten Mike , Zheng Ping , Yu Han-Qing 
Published: February 2010

ABSTRACT

Anaerobic ammonium oxidation (anammox) is a promising new process to treat high-strength nitrogenous wastewater. Due to the low growth rate of anaerobic ammonium-oxidizing bacteria, efficient biomass retention is essential for reactor operation. Therefore, we studied the settling ability and community composition of the anaerobic ammonium-oxidizing granules, which were cultivated in an upflow anaerobic sludge blanket (UASB) reactor seeded with aerobic granules. With this seed, the start-up period was less than 160 days at a NH
4
+
-N removal efficiency of 94% and a loading rate of 0.064 kg N per kg volatile suspended solids per day. The formed granules were bright red and had a high settling velocity (41 to 79 m h
−1
). Cells and extracellular polymeric substances were evenly distributed over the anaerobic ammonium-oxidizing granules. The high percentage of anaerobic ammonium-oxidizing bacteria in the granules could be visualized by fluorescent
in situ
hybridization and electron microscopy. The copy numbers of 16S rRNA genes of anaerobic ammonium-oxidizing bacteria in the granules were determined to be 4.6 × 10
8
copies ml
−1
. The results of this study could be used for a better design, shorter start-up time, and more stable operation of anammox systems for the treatment of nitrogen-rich wastewaters.
Identification of
Bacillus cereus
Genes Specifically Expressed during Growth at Low Temperatures
Authors: Brillard Julien , Jéhanno Isabelle , Dargaignaratz Claire , Barbosa Isabelle , Ginies Christian , Carlin Frédéric , Fedhila Sinda , Nguyen-the Christophe , Broussolle Véronique , Sanchis Vincent 
Published: February 2010

ABSTRACT

The mechanisms involved in the ability of
Bacillus cereus
to multiply at low temperatures were investigated. It was assumed that many genes involved in cold acclimation would be upregulated at low temperatures. Recombinase-based
in vivo
expression technology (IVET) was adapted to the detection of the transient activation of
B. cereus
promoters during growth at 10°C. Four independent screenings of a promoter library from type strain ATCC 14579 were performed, and 17 clones were isolated. They corresponded to 17 promoter regions that displayed reproducibly elevated expression at 10°C relative to expression at 30°C. This analysis revealed several genes that may be important for
B. cereus
to grow successfully under the restrictive conditions of cold habitats. Among them, a locus corresponding to open reading frames BC5402 to BC5398, harboring a lipase-encoding gene and a putative transcriptional regulator, was identified three times. While a mutation in the putative regulator-encoding gene did not cause any particular phenotype, a mutant deficient in the lipase-encoding gene showed reduced growth abilities at low temperatures compared with the parental strain. The mutant did not change its fatty acid profiles in the same way as the wild type when grown at 12°C instead of 37°C. This study demonstrates the feasibility of a promoter trap strategy for identifying cold-induced genes. It outlines a first picture of the different processes involved in
B. cereus
cold acclimation.
Putative TetR Family Transcriptional Regulator SCO1712 Encodes an Antibiotic Downregulator in
Streptomyces coelicolor
Authors: Lee Han-Na , Huang Jianqiang , Im Jong-Hyuk , Kim Seon-Hye , Noh Jun-Hee , Cohen Stanley N. , Kim Eung-Soo 
Published: February 2010

ABSTRACT

A
tetR
family transcriptional regulatory gene (SCO1712) was identified as a global antibiotic regulatory gene from a
Streptomyces
interspecies DNA microarray analysis. SCO1712 disruption in
S
treptomyces coelicolor
not only upregulated antibiotic biosynthesis through pathway-specific regulators when a previously identified pleiotropic downregulatory
wblA
was expressed but also further stimulated antibiotic production in a
wblA
deletion mutant, implying that SCO1712 might encode a novel antibiotic downregulator.
Responses of Ammonia-Oxidizing Bacterial and Archaeal Populations to Organic Nitrogen Amendments in Low-Nutrient Groundwater
Authors: Reed David W. , Smith Jason M. , Francis Christopher A. , Fujita Yoshiko 
Published: February 2010

ABSTRACT

To evaluate the potential for organic nitrogen addition to stimulate the
in situ
growth of ammonia oxidizers during a field scale bioremediation trial, samples collected from the Eastern Snake River Plain Aquifer in Idaho before, during, and after the addition of molasses and urea were subjected to PCR analysis of ammonia monooxygenase subunit A (
amoA
) genes. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) were present in all of the samples tested, with AOA
amoA
genes outnumbering AOB
amoA
genes in all of the samples. Following urea addition, nitrate levels rose and bacterial
amoA
copy numbers increased dramatically, suggesting that urea hydrolysis stimulated nitrification. Bacterial
amoA
diversity was limited to two
Nitrosomonas
phylotypes, whereas archaeal
amoA
analyses revealed 20 distinct operational taxonomic units, including several that were markedly different from all previously reported sequences. Results from this study demonstrate the likelihood of stimulating ammonia-oxidizing communities during field scale manipulation of groundwater conditions to promote urea hydrolysis.
Bacterial and Viral Pathogens in Live Oysters: 2007 United States Market Survey
Authors: DePaola Angelo , Jones Jessica L. , Woods Jacquelina , Burkhardt William , Calci Kevin R. , Krantz Jeffrey A. , Bowers John C. , Kasturi Kuppuswamy , Byars Robin H. , Jacobs Emily , Williams-Hill Donna , Nabe Khamphet 
Published: February 2010

ABSTRACT

Two samples of market oysters, primarily from retail establishments, were collected twice each month in each of nine states during 2007. Samples were shipped refrigerated overnight to five U.S. Food and Drug Administration laboratories on a rotating basis and analyzed by most probable number (MPN) for total and pathogenic
Vibrio parahaemolyticus
and
V. vulnificus
numbers and for the presence of toxigenic
V. cholerae
,
Salmonella
spp., norovirus (NoV), and hepatitis A virus (HAV). Levels of indicator organisms, including fecal coliforms (MPN),
Escherichia coli
(MPN), male-specific bacteriophage, and aerobic plate counts, were also determined.
V. parahaemolyticus
and
V. vulnificus
levels were distributed seasonally and geographically by harvest region and were similar to levels observed in a previous study conducted in 1998-1999. Levels of pathogenic
V. parahaemolyticus
were typically several logs lower than total
V. parahaemolyticus
levels regardless of season or region. Pathogenic
V. parahaemolyticus
levels in the Gulf and Mid-Atlantic regions were about two logs greater than the levels observed in the Pacific and North Atlantic regions. Pathogens generally associated with fecal pollution were detected sporadically or not at all (toxigenic
V. cholerae
, 0%;
Salmonella
, 1.5%; NoV, 3.9%; HAV, 4.4%). While seasonal prevalences of NoV and HAV were generally greater in oysters harvested from December to March, the low detection frequency obscured any apparent seasonal effects. Overall, there was no relationship between the levels of indicator microorganisms and the presence of enteric viruses. These data provide a baseline that can be used to further validate risk assessment predictions, determine the effectiveness of new control measures, and compare the level of protection provided by the U.S. shellfish sanitation system to those in other countries.
Differential Effects of Rare Specific Flavonoids on Compatible and Incompatible Strains in the
Myrica gale
-
Frankia
Actinorhizal Symbiosis
Authors: Popovici Jean , Comte Gilles , Bagnarol Émilie , Alloisio Nicole , Fournier Pascale , Bellvert Floriant , Bertrand Cédric , Fernandez Maria P. 
Published: February 2010

ABSTRACT

Plant secondary metabolites, and specifically phenolics, play important roles when plants interact with their environment and can act as weapons or positive signals during biotic interactions. One such interaction, the establishment of mutualistic nitrogen-fixing symbioses, typically involves phenolic-based recognition mechanisms between host plants and bacterial symbionts during the early stages of interaction. While these mechanisms are well studied in the rhizobia-legume symbiosis, little is known about the role of plant phenolics in the symbiosis between actinorhizal plants and
Frankia
genus strains. In this study, the responsiveness of
Frankia
strains to plant phenolics was correlated with their symbiotic compatibility. We used
Myrica gale
, a host species with narrow symbiont specificity, and a set of compatible and noncompatible
Frankia
strains.
M. gale
fruit exudate phenolics were extracted, and 8 dominant molecules were purified and identified as flavonoids by high-resolution spectroscopic techniques. Total fruit exudates, along with two purified dihydrochalcone molecules, induced modifications of bacterial growth and nitrogen fixation according to the symbiotic specificity of strains, enhancing compatible strains and inhibiting incompatible ones. Candidate genes involved in these effects were identified by a global transcriptomic approach using ACN14a strain whole-genome microarrays. Fruit exudates induced differential expression of 22 genes involved mostly in oxidative stress response and drug resistance, along with the overexpression of a
whiB
transcriptional regulator. This work provides evidence for the involvement of plant secondary metabolites in determining symbiotic specificity and expands our understanding of the mechanisms, leading to the establishment of actinorhizal symbioses.
Intervention of Bro1 in pH-Responsive Rim20 Localization in Saccharomyces cerevisiae
Authors: Boysen Jacob H. , Subramanian Shoba , Mitchell Aaron P. 
Published: February 2010

ABSTRACT

Yeast cells contain two Bro1 domain proteins: Bro1, which is required for endosomal trafficking, and Rim20, which is required for the response to the external pH via the Rim101 pathway. Rim20 associates with endosomal structures under alkaline growth conditions, when it promotes activation of Rim101 through proteolytic cleavage. We report here that the pH-dependent localization of Rim20 is contingent on the amount of Bro1 in the cell. Cells that lack Bro1 have increased endosomal Rim20-green fluorescent protein (GFP) under acidic conditions; cells that overexpress Bro1 have reduced endosomal Rim20-GFP under acidic or alkaline conditions. The novel endosomal association of Rim20-GFP in the absence of Bro1 requires ESCRT components including Vps27 but not specific Rim101 pathway components such as Dfg16. Vps27 influences the localization of Bro1 but is not required for RIM101 pathway activation in wild-type cells, thus suggesting that Rim20 enters the Bro1 localization pathway when a vacancy exists. Despite altered localization of Rim20, the lack of Bro1 does not bypass the need for signaling protein Dfg16 to activate Rim101, as evidenced by the expression levels of the Rim101 target genes
RIM8
and
SMP1
. Therefore, endosomal association of Rim20 is not sufficient to promote Rim101 activation.
Major Role for Cysteine Proteases during the Early Phase of Acanthamoeba castellanii Encystment
Authors: Leitsch David , Köhsler Martina , Marchetti-Deschmann Martina , Deutsch Andrea , Allmaier Günter , Duchêne Michael , Walochnik Julia 
Published: February 2010

ABSTRACT

Acanthamoeba castellanii
is a facultative pathogen that has a two-stage life cycle comprising the vegetatively growing trophozoite stage and the dormant cyst stage. Cysts are formed when the cell encounters unfavorable conditions, such as environmental stress or food deprivation. Due to their rigid double-layered wall,
Acanthamoeba
cysts are highly resistant to antiamoebic drugs. This is problematic as cysts can survive initially successful chemotherapeutic treatment and cause relapse of the disease. We studied the
Acanthamoeba
encystment process by using two-dimensional gel electrophoresis (2DE) and found that most changes in the protein content occur early in the process. Truncated actin isoforms were found to abound in the encysting cell, and the levels of translation elongation factor 2 (EF2) were sharply decreased, indicating that the rate of protein synthesis must be low at this stage. In the advanced stage of encystment, however, EF2 levels and the trophozoite proteome were partly restored. The protease inhibitors PMSF (phenylmethylsulfonyl fluoride) and E64d [(2S,3S)-
trans
-epoxysuccinyl-
l
-leucylamido-3-methylbutane ethyl ester] inhibited the onset of encystment, whereas the protein synthesis inhibitor cycloheximide was ineffective. Changes in the protein profile, similar to those of encysting cells, could be observed with trophozoite homogenates incubated at room temperature for several hours. Interestingly, these changes could be inhibited significantly by cysteine protease inhibitors but not by inhibitors against other proteases. Taken together, we conclude that the encystment process in
A. castellanii
is of a bipartite nature consisting of an initial phase of autolysis and protein degradation and an advanced stage of restoration accompanied by the expression of encystment-specific genes.
A Trk/HKT-Type K
+
Transporter from Trypanosoma brucei
Authors: Mosimann Marc , Goshima Shinobu , Wenzler Tanja , Lüscher Alexandra , Uozumi Nobuyuki , Mäser Pascal 
Published: February 2010

ABSTRACT

The molecular mechanisms of K
+
homeostasis are only poorly understood for protozoan parasites.
Trypanosoma brucei
subsp. parasites, the causative agents of human sleeping sickness and nagana, are strictly extracellular and need to actively concentrate K
+
from their hosts’ body fluids. The
T. brucei
genome contains two putative K
+
channel genes, yet the trypanosomes are insensitive to K
+
antagonists and K
+
channel-blocking agents, and they do not spontaneously depolarize in response to high extracellular K
+
concentrations. However, the trypanosomes are extremely sensitive to K
+
ionophores such as valinomycin. Surprisingly,
T. brucei
possesses a member of the Trk/HKT superfamily of monovalent cation permeases which so far had only been known from bacteria, archaea, fungi, and plants. The protein was named TbHKT1 and functions as a Na
+
-independent K
+
transporter when expressed in
Escherichia coli
,
Saccharomyces cerevisiae
, or
Xenopus laevis
oocytes. In trypanosomes,
TbHKT1
is expressed in both the mammalian bloodstream stage and the Tsetse fly midgut stage; however, RNA interference (RNAi)-mediated silencing of
TbHKT1
expression did not produce a growth phenotype in either stage. The presence of
HKT
genes in trypanosomatids adds a further piece to the enigmatic phylogeny of the Trk/HKT superfamily of K
+
transporters. Parsimonial analysis suggests that the transporters were present in the first eukaryotes but subsequently lost in several of the major eukaryotic lineages, in at least four independent events.
Use of the Plant Defense Protein Osmotin To Identify Fusarium oxysporum Genes That Control Cell Wall Properties
Authors: Lee Hyeseung , Damsz Barbara , Woloshuk Charles P. , Bressan Ray A. , Narasimhan Meena L. 
Published: February 2010

ABSTRACT

Fusarium oxysporum
is the causative agent of fungal wilt disease in a variety of crops. The capacity of a fungal pathogen such as
F. oxysporum
f. sp.
nicotianae
to establish infection on its tobacco (
Nicotiana tabacum
) host depends in part on its capacity to evade the toxicity of tobacco defense proteins, such as osmotin.
Fusarium
genes that control resistance to osmotin would therefore reflect coevolutionary pressures and include genes that control mutual recognition, avoidance, and detoxification. We identified
FOR
(

F
usarium

O

smotin

R

esistance) genes on the basis of their ability to confer osmotin resistance to an osmotin-sensitive strain of
Saccharomyces cerevisiae
.
FOR1
encodes a putative cell wall glycoprotein.
FOR2
encodes the structural gene for glutamine:fructose-6-phosphate amidotransferase, the first and rate-limiting step in the biosynthesis of hexosamine and cell wall chitin.
FOR3
encodes
a
homolog of
SSD1
, which controls cell wall composition, longevity, and virulence in
S. cerevisiae
. A
for3
null mutation increased osmotin sensitivity of conidia and hyphae of
F. oxysporum
f. sp.
nicotianae
and also reduced cell wall β-1,3-glucan content. Together our findings show that conserved fungal genes that determine cell wall properties play a crucial role in regulating fungal susceptibility to the plant defense protein osmotin.
Basidiomycete Mating Type Genes and Pheromone Signaling
Authors: Raudaskoski Marjatta , Kothe Erika 
Published: February 2010

ABSTRACTThe genome sequences of the basidiomyceteAgaricomycetesspeciesCoprinopsis cinerea,Laccaria bicolor,Schizophyllum commune,Phanerochaete chrysosporium, andPostia placenta, as well as ofCryptococcus neoformansandUstilago maydis, are now publicly available. Out of these fungi,C. cinerea,S. commune, andU. maydis, together with the budding yeastSaccharomyces cerevisiae, have been investigated for years genetically and molecularly for signaling in sexual reproduction. The comparison of the structure and organization of mating type genes in fungal genomes reveals an amazing conservation of genes regulating the sexual reproduction throughout the fungal kingdom. In agaricomycetes, two mating type loci,A, coding for homeodomain type transcription factors, andB, encoding a pheromone/receptor system, regulate the four typical mating interactions of tetrapolar species. Evidence for bothAandBmating type genes can also be identified in basidiomycetes with bipolar systems, where only two mating interactions are seen. In some of these fungi, theBlocus has lost its self/nonself discrimination ability and thus its specificity while retaining the other regulatory functions in development.In silicoanalyses now also permit the identification of putative components of the pheromone-dependent signaling pathways. Induction of these signaling cascades leads to development of dikaryotic mycelia, fruiting body formation, and meiotic spore production. In pheromone-dependent signaling, the role of heterotrimeric G proteins, components of a mitogen-activated protein kinase (MAPK) cascade, and cyclic AMP-dependent pathways can now be defined. Additionally, the pheromone-dependent signaling through monomeric, small GTPases potentially involved in creating the polarized cytoskeleton for reciprocal nuclear exchange and migration during mating is predicted.
SprB Is the Molecular Link between
Salmonella
Pathogenicity Island 1 (SPI1) and SPI4
Authors: Saini Supreet , Rao Christopher V. 
Published: February 2010

ABSTRACT

Salmonella
pathogenicity island 1 (SPI1) and SPI4 have previously been shown to be jointly regulated. We report that SPI1 and SPI4 gene expression is linked through a transcriptional activator, SprB, encoded within SPI1 and regulated by HilA. SprB directly activates SPI4 gene expression and weakly represses SPI1 gene expression through HilD.
A Novel Sialic Acid Utilization and Uptake System in the Periodontal Pathogen
Tannerella forsythia
Authors: Roy Sumita , Douglas C. W. Ian , Stafford Graham P. 
Published: February 2010

ABSTRACT

Tannerella forsythia
is a key contributor to periodontitis, but little is known of its virulence mechanisms. In this study we have investigated the role of sialic acid in biofilm growth of this periodontal pathogen. Our data show that biofilm growth of
T. forsythia
is stimulated by sialic acid, glycolyl sialic acid, and sialyllactose, all three of which are common sugar moieties on a range of important host glycoproteins. We have also established that growth on sialyllactose is dependent on the sialidase of
T. forsythia
since the sialidase inhibitor oseltamivir suppresses growth on sialyllactose. The genome of
T. forsythia
contains a sialic acid utilization locus, which also encodes a putative inner membrane sialic acid permease (NanT), and we have shown this is functional when it is expressed in
Escherichia coli
. This genomic locus also contains a putatively novel TonB-dependent outer membrane sialic acid transport system (TF0033-TF0034). In complementation studies using an
Escherichia coli
strain devoid of its outer membrane sialic acid transporters, the cloning and expression of the
TF0033-TF0034
genes enabled an
E. coli nanR nanC ompR
strain to utilize sialic acid as the sole carbon and energy source. We have thus identified a novel sialic acid uptake system that couples an inner membrane permease with a TonB-dependent outer membrane transporter, and we propose to rename these novel sialic acid uptake genes
nanO
and
nanU
, respectively. Taken together, these data indicate that sialic acid is a key growth factor for this little-characterized oral pathogen and may be key to its physiology
in vivo
.
Complete Genome Sequence of
Bifidobacterium animalis
subsp.
lactis
BB-12, a Widely Consumed Probiotic Strain
Authors: Garrigues Christel , Johansen Eric , Pedersen Martin B. 
Published: February 2010

ABSTRACT

Bifidobacterium animalis
subsp.
lactis
BB-12 is a commercially available probiotic strain used throughout the world in a variety of functional foods and dietary supplements. The benefits of BB-12 have been documented in a number of independent clinical trials. Determination of the complete genome sequence reveals a single circular chromosome of 1,942,198 bp with 1,642 predicted protein-encoding genes, 4 rRNA operons, and 52 tRNA genes. Knowledge of this sequence will lead to insight into the specific features which give this strain its probiotic properties.