bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome Dynamics of Pseudomonas putida KT2440 under Water Stress
Authors: Gülez Gamze , Dechesne Arnaud , Workman Christopher T. , Smets Barth F. 
Published: December 2011

ABSTRACTWater deprivation can be a major stressor to microbial life in surface and subsurface soil. In unsaturated soils, the matric potential (Ψm) is often the main component of the water potential, which measures the thermodynamic availability of water. A low matric potential usually translates into water forming thin liquid films in the soil pores. Little is known of how bacteria respond to such conditions, where, in addition to facing water deprivation that might impair their metabolism, they have to adapt their dispersal strategy as swimming motility may be compromised. Using the pressurized porous surface model (PPSM), which allows creation of thin liquid films by controlling Ψm, we examined the transcriptome dynamics ofPseudomonas putidaKT2440. We identified the differentially expressed genes in cells exposed to a mild matric stress (−0.4 MPa) for 4, 24, or 72 h. The major response was detected at 4 h before gradually disappearing. Upregulation of alginate genes was notable in this early response. Flagellar genes were not downregulated, and the microarray data even suggested increasing expression as the stress prolonged. Moreover, we tested the effect of polyethylene glycol 8000 (PEG 8000), a nonpermeating solute often used to simulate Ψm, on the gene expression profile and detected a different profile than that observed by directly imposing Ψm. This study is the first transcriptome profiling of KT2440 under directly controlled Ψmand also the first to show the difference in gene expression profiles between a PEG 8000-simulated and a directly controlled Ψm.
Surveillance Study of Hepatitis A Virus RNA on Fig and Date Samples
Authors: Boxman Ingeborg L. A. , te Loeke Nathalie A. J. M. , Klunder Kyara , Hägele Geke , Jansen Claudia C. C. 
Published: December 2011

ABSTRACT
A total of 91 fig and 185 date samples were analyzed by reverse transcription (RT) real-time PCR for the presence of hepatitis A virus (HAV) RNA. Two batches of dates tested positive, and the HAV RNA detected was genotyped as IA. These findings warrant further development of methods applicable to food which is consumed untreated and is exported from countries in which HAV is endemic.
Bifidobacterium longum subsp. infantis ATCC 15697 α-Fucosidases Are Active on Fucosylated Human Milk Oligosaccharides
Authors: Sela David A. , Garrido Daniel , Lerno Larry , Wu Shuai , Tan Kemin , Eom Hyun-Ju , Joachimiak Andrzej , Lebrilla Carlito B. , Mills David A. 
Published: December 2011

ABSTRACT

Bifidobacterium longum
subsp.
infantis
ATCC 15697 utilizes several small-mass neutral human milk oligosaccharides (HMOs), several of which are fucosylated. Whereas previous studies focused on endpoint consumption, a temporal glycan consumption profile revealed a time-dependent effect. Specifically, among preferred HMOs, tetraose was favored early in fermentation, with other oligosaccharides consumed slightly later. In order to utilize fucosylated oligosaccharides, ATCC 15697 possesses several fucosidases, implicating GH29 and GH95 α-
l
-fucosidases in a gene cluster dedicated to HMO metabolism. Evaluation of the biochemical kinetics demonstrated that ATCC 15697 expresses three fucosidases with a high turnover rate. Moreover, several ATCC 15697 fucosidases are active on the linkages inherent to the HMO molecule. Finally, the HMO cluster GH29 α-
l
-fucosidase possesses a crystal structure that is similar to previously characterized fucosidases.
Improvement of the Redox Balance Increasesl-Valine Production by Corynebacterium glutamicum under Oxygen Deprivation Conditions
Authors: Hasegawa Satoshi , Uematsu Kimio , Natsuma Yumi , Suda Masako , Hiraga Kazumi , Jojima Toru , Inui Masayuki , Yukawa Hideaki 
Published: December 2011

ABSTRACTProduction ofl-valine under oxygen deprivation conditions byCorynebacterium glutamicumlacking the lactate dehydrogenase geneldhAand overexpressing thel-valine biosynthesis genesilvBNCDEwas repressed. This was attributed to imbalanced cofactor production and consumption in the overalll-valine synthesis pathway: two moles of NADH was generated and two moles of NADPH was consumed per mole ofl-valine produced from one mole of glucose. In order to solve this cofactor imbalance, the coenzyme requirement forl-valine synthesis was converted from NADPH to NADH via modification of acetohydroxy acid isomeroreductase encoded byilvCand introduction ofLysinibacillus sphaericusleucine dehydrogenase in place of endogenous transaminase B, encoded byilvE. The intracellular NADH/NAD+ratio significantly decreased, and glucose consumption andl-valine production drastically improved. Moreover,l-valine yield increased and succinate formation decreased concomitantly with the decreased intracellular redox state. These observations suggest that the intracellular NADH/NAD+ratio, i.e., reoxidation of NADH, is the primary rate-limiting factor forl-valine production under oxygen deprivation conditions. Thel-valine productivity and yield were even better and by-products derived from pyruvate further decreased as a result of a feedback resistance-inducing mutation in the acetohydroxy acid synthase encoded byilvBN. The resultant strain produced 1,470 mMl-valine after 24 h with a yield of 0.63 mol mol of glucose−1, and thel-valine productivity reached 1,940 mM after 48 h.
Hydrazine Synthase, a Unique Phylomarker with Which To Study the Presence and Biodiversity of Anammox Bacteria
Authors: Harhangi Harry R. , Le Roy Mathilde , van Alen Theo , Hu Bao-lan , Groen Joost , Kartal Boran , Tringe Susannah G. , Quan Zhe-Xue , Jetten Mike S. M. , Op den Camp Huub J. M. 
Published: December 2011

ABSTRACT

Anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the biogeochemical cycling of nitrogen. They derive their energy for growth from the conversion of ammonium and nitrite into dinitrogen gas in the complete absence of oxygen. Several methods have been used to detect the presence and activity of anammox bacteria in the environment, including 16S rRNA gene-based approaches. The use of the 16S rRNA gene to study biodiversity has the disadvantage that it is not directly related to the physiology of the target organism and that current primers do not completely capture the anammox diversity. Here we report the development of PCR primer sets targeting a subunit of the hydrazine synthase (
hzsA
), which represents a unique phylogenetic marker for anammox bacteria. The tested primers were able to retrieve
hzsA
gene sequences from anammox enrichment cultures, full-scale anammox wastewater treatment systems, and a variety of freshwater and marine environmental samples, covering all known anammox genera.
False-Negative Rate and Recovery Efficiency Performance of a Validated Sponge Wipe Sampling Method
Authors: Krauter Paula A. , Piepel Greg F. , Boucher Raymond , Tezak Matt , Amidan Brett G. , Einfeld Wayne 
Published: December 2011

ABSTRACT

Recovery of spores from environmental surfaces varies due to sampling and analysis methods, spore size and characteristics, surface materials, and environmental conditions. Tests were performed to evaluate a new, validated sponge wipe method using
Bacillus atrophaeus
spores. Testing evaluated the effects of spore concentration and surface material on recovery efficiency (RE), false-negative rate (FNR), limit of detection (LOD), and their uncertainties. Ceramic tile and stainless steel had the highest mean RE values (48.9 and 48.1%, respectively). Faux leather, vinyl tile, and painted wood had mean RE values of 30.3, 25.6, and 25.5, respectively, while plastic had the lowest mean RE (9.8%). Results show roughly linear dependences of RE and FNR on surface roughness, with smoother surfaces resulting in higher mean REs and lower FNRs. REs were not influenced by the low spore concentrations tested (3.10 × 10
−3
to 1.86 CFU/cm
2
). Stainless steel had the lowest mean FNR (0.123), and plastic had the highest mean FNR (0.479). The LOD
90
(≥1 CFU detected 90% of the time) varied with surface material, from 0.015 CFU/cm
2
on stainless steel up to 0.039 on plastic. It may be possible to improve sampling results by considering surface roughness in selecting sampling locations and interpreting spore recovery data. Further, FNR values (calculated as a function of concentration and surface material) can be used presampling to calculate the numbers of samples for statistical sampling plans with desired performance and postsampling to calculate the confidence in characterization and clearance decisions.
Distribution of Microbial Biomass and Potential for Anaerobic Respiration in Hanford Site 300 Area Subsurface Sediment
Authors: Lin Xueju , Kennedy David , Peacock Aaron , McKinley James , Resch Charles T. , Fredrickson James , Konopka Allan 
Published: December 2011

ABSTRACT

Subsurface sediments were recovered from a 52-m-deep borehole cored in the 300 Area of the Hanford Site in southeastern Washington State to assess the potential for biogeochemical transformation of radionuclide contaminants. Microbial analyses were made on 17 sediment samples traversing multiple geological units: the oxic coarse-grained Hanford formation (9 to 17.4 m), the oxic fine-grained upper Ringold formation (17.7 to 18.1 m), and the reduced Ringold formation (18.3 to 52 m). Microbial biomass (measured as phospholipid fatty acids) ranged from 7 to 974 pmols per g in discrete samples, with the highest numbers found in the Hanford formation. On average, strata below 17.4 m had 13-fold less biomass than those from shallower strata. The
nosZ
gene that encodes nitrous oxide reductase (measured by quantitative real-time PCR) had an abundance of 5 to 17 relative to that of total 16S rRNA genes below 18.3 m and <5 above 18.1 m. Most
nosZ
sequences were affiliated with
Ochrobactrum anthropi
(97 sequence similarity) or had a nearest neighbor of
Achromobacter xylosoxidans
(90 similarity). Passive multilevel sampling of groundwater geochemistry demonstrated a redox gradient in the 1.5-m region between the Hanford-Ringold formation contact and the Ringold oxic-anoxic interface. Within this zone, copies of the
dsrA
gene and
Geobacteraceae
had the highest relative abundance. The majority of
dsrA
genes detected near the interface were related to
Desulfotomaculum
spp. These analyses indicate that the region just below the contact between the Hanford and Ringold formations is a zone of active biogeochemical redox cycling.
Protein Kinase A Contributes to the Negative Control of Snf1 Protein Kinase in Saccharomyces cerevisiae
Authors: Barrett LaKisha , Orlova Marianna , Maziarz Marcin , Kuchin Sergei 
Published: December 2011

ABSTRACT

Snf1 protein kinase regulates responses to glucose limitation and other stresses. Snf1 activation requires phosphorylation of its T-loop threonine by partially redundant upstream kinases (Sak1, Tos3, and Elm1). Under favorable conditions, Snf1 is turned off by Reg1-Glc7 protein phosphatase. The
reg1
mutation causes increased Snf1 activation and slow growth. To identify new components of the Snf1 pathway, we searched for mutations that, like
snf1
, suppress
reg1
for the slow-growth phenotype. In addition to mutations in genes encoding known pathway components (
SNF1
,
SNF4
, and
SAK1
), we recovered “fast” mutations, designated
fst1
and
fst2
. Unusual morphology of the mutants in the Σ1278b strains employed here helped us identify
fst1
and
fst2
as mutations in the RasGAP genes
IRA1
and
IRA2
. Cells lacking Ira1, Ira2, or Bcy1, the negative regulatory subunit of cyclic AMP (cAMP)-dependent protein kinase A (PKA), exhibited reduced Snf1 pathway activation. Conversely, Snf1 activation was elevated in cells lacking the Gpr1 sugar receptor, which contributes to PKA signaling. We show that the Snf1-activating kinase Sak1 is phosphorylated
in vivo
on a conserved serine (Ser1074) within an ideal PKA motif. However, this phosphorylation alone appears to play only a modest role in regulation, and Sak1 is not the only relevant target of the PKA pathway. Collectively, our results suggest that PKA, which integrates multiple regulatory inputs, could contribute to Snf1 regulation under various conditions via a complex mechanism. Our results also support the view that, like its mammalian counterpart, AMP-activated protein kinase (AMPK), yeast Snf1 participates in metabolic checkpoint control that coordinates growth with nutrient availability.
SWP5, a Spore Wall Protein, Interacts with Polar Tube Proteins in the Parasitic Microsporidian Nosema bombycis
Authors: Li Zhi , Pan Guoqing , Li Tian , Huang Wei , Chen Jie , Geng Lina , Yang Donglin , Wang Linling , Zhou Zeyang 
Published: December 2011

ABSTRACT

Microsporidia are a group of eukaryotic intracellular parasites that infect almost all vertebrates and invertebrates. The microsporidian invasion process involves the extrusion of a unique polar tube into host cells. Both the spore wall and the polar tube play an important role in microsporidian pathogenesis. So far, five spore wall proteins (SWP1, SWP2, Enp1, Enp2, and EcCDA) from
Encephalitozoon intestinalis
and
Encephalitozoon cuniculi
and five spore wall proteins (SWP32, SWP30, SWP26, SWP25, and NbSWP5) from the silkworm pathogen
Nosema bombycis
have been identified. Here we report the identification and characterization of a spore wall protein (SWP5) with a molecular mass of 20.3 kDa in
N. bombycis
. This protein has low sequence similarity to other eukaryotic proteins. Immunolocalization analysis showed SWP5 localized to the exospore and the region of the polar tube in mature spores. Immunoprecipitation, mass spectrometry, and immunofluorescence analyses revealed that SWP5 interacts with the polar tube proteins PTP2 and PTP3. Anti-SWP5 serum pretreatment of mature spores significantly decreased their polar tube extrusion rate. Taken together, our results show that SWP5 is a spore wall protein localized to the spore wall and that it interacts with the polar tube, may play an important role in supporting the structural integrity of the spore wall, and potentially modulates the course of infection of
N. bombycis
.
The Polo-Like Kinase PLKA in Aspergillus nidulans Is Not Essential but Plays Important Roles during Vegetative Growth and Development
Authors: Mogilevsky Klarita , Glory Amandeep , Bachewich Catherine 
Published: December 2011

ABSTRACT

The Polo-like kinases (Plks) are conserved, multifunctional cell cycle regulators that are induced in many forms of cancer and play additional roles in metazoan development. We previously identified
plkA
in
Aspergillus nidulans
, the only Plk investigated in filamentous fungi to date, and partially characterized its function through overexpression. Here, we report the
plkA
null phenotype. Surprisingly,
plkA
was not essential, unlike Plks in other organisms that contain a single homologue. A subset of cells lacking PLKA contained defects in spindle formation and chromosome organization, supporting some conservation in cell cycle function. However, septa were present, suggesting that PLKA, unlike other Plks, is not a central regulator of septation. Colonies lacking PLKA were compact with multibranched hyphae, implying a role for this factor in aspects of hyphal morphogenesis. These defects were suppressed by high temperature or low concentrations of benomyl, suggesting that PLKA may function during vegetative growth by influencing microtubule dynamics. However, the colonies also showed reduced conidiation and precocious formation of sexual Hülle cells in a benomyl- and temperature-insensitive manner. This result suggests that PLKA may influence reproduction through distinct mechanisms and represents the first example of a link between Plk function and development in fungi. Finally, filamentous fungal Plks have distinct features, and phylogenetic analyses reveal that they may group more closely with metazoan PLK4. In contrast, yeast Plks are more similar to metazoan proteins PLK1 to PLK3. Thus,
A. nidulans
PLKA shows some conservation in cell cycle function but may also play novel roles during hyphal morphogenesis and development.
A Machine Learning Approach To Identify Hydrogenosomal Proteins in Trichomonas vaginalis
Authors: Burstein David , Gould Sven B. , Zimorski Verena , Kloesges Thorsten , Kiosse Fuat , Major Peter , Martin William F. , Pupko Tal , Dagan Tal 
Published: December 2011

ABSTRACT

The protozoan parasite
Trichomonas vaginalis
is the causative agent of trichomoniasis, the most widespread nonviral sexually transmitted disease in humans. It possesses hydrogenosomes—anaerobic mitochondria that generate H
2
, CO
2
, and acetate from pyruvate while converting ADP to ATP via substrate-level phosphorylation.
T. vaginalis
hydrogenosomes lack a genome and translation machinery; hence, they import all their proteins from the cytosol. To date, however, only 30 imported proteins have been shown to localize to the organelle. A total of 226 nuclear-encoded proteins inferred from the genome sequence harbor a characteristic short N-terminal presequence, reminiscent of mitochondrial targeting peptides, which is thought to mediate hydrogenosomal targeting. Recent studies suggest, however, that the presequences might be less important than previously thought. We sought to identify new hydrogenosomal proteins within the 59,672 annotated open reading frames (ORFs) of
T. vaginalis
, independent of the N-terminal targeting signal, using a machine learning approach. Our training set included 57 gene and protein features determined for all 30 known hydrogenosomal proteins and 576 nonhydrogenosomal proteins. Several classifiers were trained on this set to yield an import score for all proteins encoded by
T. vaginalis
ORFs, predicting the likelihood of hydrogenosomal localization. The machine learning results were tested through immunofluorescence assay and immunodetection in isolated cell fractions of 14 protein predictions using hemagglutinin constructs expressed under the homologous SCSα promoter in transiently transformed
T. vaginalis
cells. Localization of 6 of the 10 top predicted hydrogenosome-localized proteins was confirmed, and two of these were found to lack an obvious N-terminal targeting signal.
Adaptation of Cryptococcus neoformans to Mammalian Hosts: Integrated Regulation of Metabolism and Virulence
Authors: Kronstad Jim , Saikia Sanjay , Nielson Erik David , Kretschmer Matthias , Jung Wonhee , Hu Guanggan , Geddes Jennifer M. H. , Griffiths Emma J. , Choi Jaehyuk , Cadieux Brigitte , Caza Mélissa , Attarian Rodgoun 
Published: December 2011

ABSTRACT

The basidiomycete fungus
Cryptococcus neoformans
infects humans via inhalation of desiccated yeast cells or spores from the environment. In the absence of effective immune containment, the initial pulmonary infection often spreads to the central nervous system to result in meningoencephalitis. The fungus must therefore make the transition from the environment to different mammalian niches that include the intracellular locale of phagocytic cells and extracellular sites in the lung, bloodstream, and central nervous system. Recent studies provide insights into mechanisms of adaptation during this transition that include the expression of antiphagocytic functions, the remodeling of central carbon metabolism, the expression of specific nutrient acquisition systems, and the response to hypoxia. Specific transcription factors regulate these functions as well as the expression of one or more of the major known virulence factors of
C. neoformans
. Therefore, virulence factor expression is to a large extent embedded in the regulation of a variety of functions needed for growth in mammalian hosts. In this regard, the complex integration of these processes is reminiscent of the master regulators of virulence in bacterial pathogens.
Lag Phase Is a Distinct Growth Phase That Prepares Bacteria for Exponential Growth and Involves Transient Metal Accumulation
Authors: Rolfe Matthew D. , Rice Christopher J. , Lucchini Sacha , Pin Carmen , Thompson Arthur , Cameron Andrew D. S. , Alston Mark , Stringer Michael F. , Betts Roy P. , Baranyi József , Peck Michael W. , Hinton Jay C. D. 
Published: December 2011

ABSTRACT

Lag phase represents the earliest and most poorly understood stage of the bacterial growth cycle. We developed a reproducible experimental system and conducted functional genomic and physiological analyses of a 2-h lag phase in
Salmonella enterica
serovar Typhimurium. Adaptation began within 4 min of inoculation into fresh LB medium with the transient expression of genes involved in phosphate uptake. The main lag-phase transcriptional program initiated at 20 min with the upregulation of 945 genes encoding processes such as transcription, translation, iron-sulfur protein assembly, nucleotide metabolism, LPS biosynthesis, and aerobic respiration. ChIP-chip revealed that RNA polymerase was not “poised” upstream of the bacterial genes that are rapidly induced at the beginning of lag phase, suggesting a mechanism that involves
de novo
partitioning of RNA polymerase to transcribe 522 bacterial genes within 4 min of leaving stationary phase. We used inductively coupled plasma mass spectrometry (ICP-MS) to discover that iron, calcium, and manganese are accumulated by
S
. Typhimurium during lag phase, while levels of cobalt, nickel, and sodium showed distinct growth-phase-specific patterns. The high concentration of iron during lag phase was associated with transient sensitivity to oxidative stress. The study of lag phase promises to identify the physiological and regulatory processes responsible for adaptation to new environments.
The Sulfur Oxygenase Reductase from the Mesophilic Bacterium Halothiobacillus neapolitanus Is a Highly Active Thermozyme
Authors: Veith Andreas , Botelho Hugo M. , Kindinger Florian , Gomes Cláudio M. , Kletzin Arnulf 
Published: December 2011

ABSTRACT

A biochemical, biophysical, and phylogenetic study of the sulfur oxygenase reductase (SOR) from the mesophilic gammaproteobacterium
Halothiobacillus neapolitanus
(
Hn
SOR) was performed in order to determine the structural and biochemical properties of the enzyme. SOR proteins from 14 predominantly chemolithoautotrophic bacterial and archaeal species are currently available in public databases. Sequence alignment and phylogenetic analysis showed that they form a coherent protein family. The
Hn
SOR purified from
Escherichia coli
after heterologous gene expression had a temperature range of activity of 10 to 99°C with an optimum at 80°C (42 U/mg protein). Sulfite, thiosulfate, and hydrogen sulfide were formed at various stoichiometries in a range between pH 5.4 and 11 (optimum pH 8.4). Circular dichroism (CD) spectroscopy and dynamic light scattering showed that the
Hn
SOR adopts secondary and quaternary structures similar to those of the 24-subunit enzyme from the hyperthermophile
Acidianus ambivalens
(
Aa
SOR). The melting point of the
Hn
SOR was ≈20°C lower than that of the
Aa
SOR, when analyzed with CD-monitored thermal unfolding. Homology modeling showed that the secondary structure elements of single subunits are conserved. Subtle changes in the pores of the outer shell and increased flexibility might contribute to activity at low temperature. We concluded that the thermostability was the result of a rigid protein core together with the stabilizing effect of the 24-subunit hollow sphere.