bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic and Physiological Characterization of the Verrucomicrobia Isolate Diplosphaera colitermitum gen. nov., sp. nov., Reveals Microaerophily and Nitrogen Fixation Genes
Authors: Wertz John T. , Kim Eunji , Breznak John A. , Schmidt Thomas M. , Rodrigues Jorge L. M. 
Published: December 2011

ABSTRACT

Previously we reported the cultivation of novel verrucomicrobia, including strain TAV2 (93% 16S rRNA gene identity to its nearest cultivated representative,
Opitutus terreae
PB90-1) from the gut of the termite
Reticulitermes flavipes
. To gain better insight into the
Verrucomicrobia
as a whole and understand the role of verrucomicrobia within the termite gut ecosystem, we analyzed a draft genome and undertook a physiological characterization of TAV2. Strain TAV2 is an autochthonous member of the
R. flavipes
gut microbiota and groups phylogenetically among diverse
Verrucomicrobia
from
R. flavipes
and other termites that are represented by 16S rRNA gene sequences alone. TAV2 is a microaerophile, possessing a high-affinity
cbb
3
-type terminal oxidase-encoding gene and exhibiting an optimum growth rate between 2 and 8% (vol/vol) oxygen. It has the genetic potential to degrade cellulose, an important function within termite guts, but its
in vitro
substrate utilization spectrum was limited to starch and a few mono- and disaccharides. Growth occurred on nitrogen-free medium, and genomic screening revealed genes for dinitrogenases, heretofore detected in only a few members of the
Verrucomicrobia
. This represents the first (i) characterization of a verrucomicrobial species from the termite gut, (ii) report of
nif
and
anf
genes in a nonacidophilic verrucomicrobial species, and (iii) description of a microaerophilic genotype and phenotype in this phylum of bacteria. The genetic and physiological distinctiveness of TAV2 supports its recognition as the type strain of a new genus and species, for which the name
Diplosphaera colitermitum
gen. nov., sp. nov., is proposed.
Calcium Increases Xylella fastidiosa Surface Attachment, Biofilm Formation, and Twitching Motility
Authors: Cruz Luisa F. , Cobine Paul A. , De La Fuente Leonardo 
Published: December 2011

ABSTRACTXylella fastidiosais a plant-pathogenic bacterium that forms biofilms inside xylem vessels, a process thought to be influenced by the chemical composition of xylem sap. In this work, the effect of calcium on the production ofX. fastidiosabiofilm and movement was analyzed underin vitroconditions. After a dose-response study with 96-well plates using eight metals, the strongest increase of biofilm formation was observed when medium was supplemented with at least 1.0 mM CaCl2. The removal of Ca by extracellular (EGTA, 1.5 mM) and intracellular [1,2-bis(o-aminophenoxy)ethane-N,N,N′,N′-tetraacetic acid acetoxymethyl ester (BAPTA/AM), 75 μM] chelators reduced biofilm formation without compromising planktonic growth. The concentration of Ca influenced the force of adhesion to the substrate, biofilm thickness, cell-to-cell aggregation, and twitching motility, as shown by assays with microfluidic chambers and other assays. The effect of Ca on attachment was lost when cells were treated with tetracycline, suggesting that Ca has a metabolic or regulatory role in cell adhesion. A double mutant (fimA pilO) lacking type I and type IV pili did not improve biofilm formation or attachment when Ca was added to the medium, while single mutants of type I (fimA) or type IV (pilB) pili formed more biofilm under conditions of higher Ca concentrations. The concentration of Ca in the medium did not significantly influence the levels of exopolysaccharide produced. Our findings indicate that the role of Ca in biofilm formation may be related to the initial surface and cell-to-cell attachment and colonization stages of biofilm establishment, which rely on critical functions by fimbrial structures.
Isolation of a Novel Cutinase Homolog with Polyethylene Terephthalate-Degrading Activity from Leaf-Branch Compost by Using a Metagenomic Approach
Authors: Sulaiman Sintawee , Yamato Saya , Kanaya Eiko , Kim Joong-Jae , Koga Yuichi , Takano Kazufumi , Kanaya Shigenori 
Published: December 2011

ABSTRACT

The gene encoding a cutinase homolog, LC-cutinase, was cloned from a fosmid library of a leaf-branch compost metagenome by functional screening using tributyrin agar plates. LC-cutinase shows the highest amino acid sequence identity of 59.7% to
Thermomonospora curvata
lipase. It also shows the 57.4% identity to
Thermobifida fusca
cutinase. When LC-cutinase without a putative signal peptide was secreted to the periplasm of
Escherichia coli
cells with the assistance of the pelB leader sequence, more than 50% of the recombinant protein, termed LC-cutinase*, was excreted into the extracellular medium. It was purified and characterized. LC-cutinase* hydrolyzed various fatty acid monoesters with acyl chain lengths of 2 to 18, with a preference for short-chain substrates (C
4
substrate at most) most optimally at pH 8.5 and 50°C, but could not hydrolyze olive oil. It lost activity with half-lives of 40 min at 70°C and 7 min at 80°C. LC-cutinase* had an ability to degrade poly(ε-caprolactone) and polyethylene terephthalate (PET). The specific PET-degrading activity of LC-cutinase* was determined to be 12 mg/h/mg of enzyme (2.7 mg/h/μkat of
p
NP-butyrate-degrading activity) at pH 8.0 and 50°C. This activity is higher than those of the bacterial and fungal cutinases reported thus far, suggesting that LC-cutinase* not only serves as a good model for understanding the molecular mechanism of PET-degrading enzyme but also is potentially applicable for surface modification and degradation of PET.
Accurate, Rapid Taxonomic Classification of Fungal Large-Subunit rRNA Genes
Authors: Liu Kuan-Liang , Porras-Alfaro Andrea , Kuske Cheryl R. , Eichorst Stephanie A. , Xie Gary 
Published: December 2011

ABSTRACT

Taxonomic and phylogenetic fingerprinting based on sequence analysis of gene fragments from the large-subunit rRNA (LSU) gene or the internal transcribed spacer (ITS) region is becoming an integral part of fungal classification. The lack of an accurate and robust classification tool trained by a validated sequence database for taxonomic placement of fungal LSU genes is a severe limitation in taxonomic analysis of fungal isolates or large data sets obtained from environmental surveys. Using a hand-curated set of 8,506 fungal LSU gene fragments, we determined the performance characteristics of a naïve Bayesian classifier across multiple taxonomic levels and compared the classifier performance to that of a sequence similarity-based (BLASTN) approach. The naïve Bayesian classifier was computationally more rapid (>460-fold with our system) than the BLASTN approach, and it provided equal or superior classification accuracy. Classifier accuracies were compared using sequence fragments of 100 bp and 400 bp and two different PCR primer anchor points to mimic sequence read lengths commonly obtained using current high-throughput sequencing technologies. Accuracy was higher with 400-bp sequence reads than with 100-bp reads. It was also significantly affected by sequence location across the 1,400-bp test region. The highest accuracy was obtained across either the D1 or D2 variable region. The naïve Bayesian classifier provides an effective and rapid means to classify fungal LSU sequences from large environmental surveys. The training set and tool are publicly available through the Ribosomal Database Project (
http://rdp.cme.msu.edu/classifier/classifier.jsp
).
Desiccation as a Long-Term Survival Mechanism for the Archaeon Methanosarcina barkeri
Authors: Anderson Kimberly L. , Apolinario Ethel E. , Sowers Kevin R. 
Published: December 2011

ABSTRACT

Viable methanogens have been detected in dry, aerobic environments such as dry reservoir sediment, dry rice paddies and aerobic desert soils, which suggests that methanogens have mechanisms for long-term survival in a desiccated state. In this study, we quantified the survival rates of the methanogenic archaeon
Methanosarcina barkeri
after desiccation under conditions equivalent to the driest environments on Earth and subsequent exposure to different stress factors. There was no significant loss of viability after desiccation for 28 days for cells grown with either hydrogen or the methylotrophic substrates, but recovery was affected by growth phase, with cells desiccated during the stationary phase of growth having a higher rate of recovery after desiccation. Synthesis of methanosarcinal extracellular polysaccharide (EPS) significantly increased the viability of desiccated cells under both anaerobic and aerobic conditions compared with that of non-EPS-synthesizing cells. Desiccated
M. barkeri
exposed to air at room temperature did not lose significant viability after 28 days, and exposure of
M. barkeri
to air after desiccation appeared to improve the recovery of viable cells compared with that of desiccated cells that were never exposed to air. Desiccated
M. barkeri
was more resistant to higher temperatures, and although resistance to oxidative conditions such as ozone and ionizing radiation was not as robust as in other desiccation-resistant microorganisms, the protection mechanisms are likely adequate to maintain cell viability during periodic exposure events. The results of this study demonstrate that after desiccation
M. barkeri
has the innate capability to survive extended periods of exposure to air and lethal temperatures.
Small-Molecule Modulators of Listeria monocytogenes Biofilm Development
Authors: Nguyen Uyen T. , Wenderska Iwona B. , Chong Matthew A. , Koteva Kalinka , Wright Gerard D. , Burrows Lori L. 
Published: December 2011

ABSTRACT

Listeria monocytogenes
is an important food-borne pathogen whose ability to form disinfectant-tolerant biofilms on a variety of surfaces presents a food safety challenge for manufacturers of ready-to-eat products. We developed here a high-throughput biofilm assay for
L. monocytogenes
and, as a proof of principle, used it to screen an 80-compound protein kinase inhibitor library to identify molecules that perturb biofilm development. The screen yielded molecules toxic to multiple strains of
Listeria
at micromolar concentrations, as well as molecules that decreased (≤50% of vehicle control) or increased (≥200%) biofilm formation in a dose-dependent manner without affecting planktonic cell density. Toxic molecules—including the protein kinase C antagonist sphingosine—had antibiofilm activity at sub-MIC concentrations. Structure-activity studies of the biofilm inhibitory compound palmitoyl-
d,l
-carnitine showed that while
Listeria
biofilm formation was inhibited with a 50% inhibitory concentration of 5.85 ± 0.24 μM,
d,l
-carnitine had no effect, whereas palmitic acid had stimulatory effects. Saturated fatty acids between C
9:0
and C
14:0
were
Listeria
biofilm inhibitors, whereas fatty acids of C
16:0
or longer were stimulators, showing chain length specificity.
De novo
-synthesized short-chain acyl carnitines were less effective biofilm inhibitors than the palmitoyl forms. These molecules, whose activities against bacteria have not been previously established, are both useful probes of
L. monocytogenes
biology and promising leads for the further development of antibiofilm strategies.
HAVCR1 Gene Haplotypes and Infection by Different Viral Hepatitis C Virus Genotypes
Authors: Abad-Molina Cristina , Garcia-Lozano José-Raúl , Montes-Cano Marco-Antonio , Torres-Cornejo Almudena , Torrecillas Fuensanta , Aguilar-Reina José , Romero-Gómez Manuel , López-Cortés Luis-Fernando , Núñez-Roldan Antonio , González-Escribano María-Francisca 
Published: December 2011

ABSTRACTThe hepatitis A virus cellular receptor 1 (HAVCR1) gene is highly polymorphic, and several variants have been associated with susceptibility to allergic and autoimmune diseases. The HAVCR1 gene region was identified as a candidate for hepatitis C virus (HCV) natural clearance in a genotyping study of selected immune response genes in both European-American and African-American populations. The aim of the present study was to explore the influence of HAVCR1 in the outcome of HCV infection in the Spanish population. Three cohorts, consisting of 354 subjects with persistent HCV infection (285 with persistent HCV monoinfection and 69 with natural clearance), 182 coinfected HIV/HCV patients, and 320 controls, were included. Samples were genotyped in several polymorphic positions, insertion/deletion variants in exon 4 and tag single nucleotide polymorphisms (SNPs), in order to define previously described HAVCR1 haplotypes (haplotypes A to D). No statistically significant differences were observed with spontaneous resolution of infection or with viral clearance after treatment. Nevertheless, different rates of infection by viral genotypes (G's) were observed among the HAVCR1 haplotypes. Individuals bearing haplotype C had the highest viral G1 infection rate when compared to individuals bearing other haplotypes (75.82% versus 57.72%, respectively; correctedPvalue [Pc], 3.2 × 10−4; odds ratio [OR], 2.30; 95% confidence interval [CI], 1.51 to 3.47). Thus, HAVCR1 could be involved in susceptibility or resistance to infection by a particular HCV genotype.
Helicobacter pylori Relies Primarily on the Purine Salvage Pathway for Purine Nucleotide Biosynthesis
Authors: Liechti George , Goldberg Joanna B. 
Published: December 2011

ABSTRACT

Helicobacter pylori
is a chronic colonizer of the gastric epithelium and plays a major role in the development of gastritis, peptic ulcer disease, and gastric cancer. In its coevolution with humans, the streamlining of the
H. pylori
genome has resulted in a significant reduction in metabolic pathways, one being purine nucleotide biosynthesis. Bioinformatic analysis has revealed that
H. pylori
lacks the enzymatic machinery for
de novo
production of IMP, the first purine nucleotide formed during GTP and ATP biosynthesis. This suggests that
H. pylori
must rely heavily on salvage of purines from the environment. In this study, we deleted several genes putatively involved in purine salvage and processing. The growth and survival of these mutants were analyzed in both nutrient-rich and minimal media, and the results confirmed the presence of a robust purine salvage pathway in
H. pylori
. Of the two phosphoribosyltransferase genes found in the
H. pylori
genome, only
gpt
appears to be essential, and an Δ
apt
mutant strain was still capable of growth on adenine, suggesting that adenine processing via Apt is not essential. Deletion of the putative nucleoside phosphorylase gene
deoD
resulted in an inability of
H. pylori
to grow on purine nucleosides or the purine base adenine. Our results suggest a purine requirement for growth of
H. pylori
in standard media, indicating that
H. pylori
possesses the ability to utilize purines and nucleosides from the environment in the absence of a
de novo
purine nucleotide biosynthesis pathway.
Generation of Transmitted/Founder HIV-1 Infectious Molecular Clones and Characterization of Their Replication Capacity in CD4 T Lymphocytes and Monocyte-Derived Macrophages
Authors: Ochsenbauer Christina , Edmonds Tara G. , Ding Haitao , Keele Brandon F. , Decker Julie , Salazar Maria G. , Salazar-Gonzalez Jesus F. , Shattock Robin , Haynes Barton F. , Shaw George M. , Hahn Beatrice H. , Kappes John C. 
Published: December 2011

ABSTRACT

Genome sequences of transmitted/founder (T/F) HIV-1 have been inferred by analyzing single genome amplicons of acute infection plasma viral RNA in the context of a mathematical model of random virus evolution; however, few of these T/F sequences have been molecularly cloned and biologically characterized. Here, we describe the derivation and biological analysis of ten infectious molecular clones, each representing a T/F genome responsible for productive HIV-1 clade B clinical infection. Each of the T/F viruses primarily utilized the CCR5 coreceptor for entry and replicated efficiently in primary human CD4
+
T lymphocytes. This result supports the conclusion that single genome amplification-derived sequences from acute infection allow for the inference of T/F viral genomes that are consistently replication competent. Studies with monocyte-derived macrophages (MDM) demonstrated various levels of replication among the T/F viruses. Although all T/F viruses replicated in MDM, the overall replication efficiency was significantly lower compared to prototypic “highly macrophage-tropic” virus strains. This phenotype was transferable by expressing the
env
genes in an isogenic proviral DNA backbone, indicating that T/F virus macrophage tropism mapped to Env. Furthermore, significantly higher concentrations of soluble CD4 were required to inhibit T/F virus infection compared to prototypic macrophage-tropic virus strains. Our findings suggest that the acquisition of clinical HIV-1 subtype B infection occurs by mucosal exposure to virus that is not highly macrophage tropic and that the generation and initial biological characterization of 10 clade B T/F infectious molecular clones provides new opportunities to probe virus-host interactions involved in HIV-1 transmission.
Accelerated Atherosclerosis in

Apoe
−/−

Mice Heterozygous for the Insulin Receptor and the Insulin Receptor Substrate-1
Authors: Galkina Elena V. , Butcher Matthew , Keller Susanna R. , Goff Matthew , Bruce Anthony , Pei Hong , Sarembock Ian J. , Sanders John M. , Nagelin Melissa H. , Srinivasan Suseela , Kulkarni Rohit N. , Hedrick Catherine C. , Lattanzio Frank A. , Dobrian Anca D. , Nadler Jerry L. , Ley Klaus 
Published: December 2011

Objective—
Prediabetic states are associated with accelerated atherosclerosis, but the availability of mouse models to study connections between these diseases has been limited. The aim of this study was to test the selective role of impaired insulin receptor/insulin receptor substrate-1 signaling on atherogenesis.

Methods and Results—

To address the effects of impaired insulin signaling associated with hyperinsulinemia on atherosclerosis in the absence of obesity and hyperglycemia, we generated insulin receptor (
Insr
)/insulin receptor substrate-1 (
Insr1
) double heterozygous apolipoprotein (
Apoe
)-knockout mice (

Insr
+/−
Irs1
+/−
Apoe
−/−

) mice.

Insr
+/−
Irs1
+/−
Apoe
−/−

mice fed a Western diet for 15 weeks showed elevated levels of fasting insulin compared to

Insr
+/+
Irs1
+/+
Apoe
−/−

mice. There were no significant differences in glucose, triglyceride, HDL, VLDL, cholesterol levels or free fatty acid in the plasma of

Insr
+/−
Irs1
+/−
Apoe
−/−

and

Insr
+/+
Irs1
+/+
Apoe
−/−

mice. Atherosclerotic lesions were increased in male (brachiocephalic artery) and female (aortic tree)

Insr
+/−
Irs1
+/−
Apoe
−/−

compared to

Insr
+/+
Irs1
+/+
Apoe
−/−

mice. Bone marrow transfer experiments demonstrated that nonhematopoietic cells have to be

Insr
+/−
Irs1
+/−

to accelerate atherosclerosis. Impaired insulin signaling resulted in decreased levels of vascular phospho-eNOS, attenuated endothelium-dependent vasorelaxation and elevated VCAM-1 expression in aortas of

Insr
+/−
Irs1
+/−
Apoe
−/−

mice. In addition, phospho-ERK and vascular smooth muscle cell proliferation were significantly elevated in aortas of

Insr
+/−
Irs1
+/−
Apoe
−/−

mice.

Conclusion—

These results demonstrate that defective insulin signaling is involved in accelerated atherosclerosis in

Insr
+/−
Irs1
+/−
Apoe
−/−

mice by promoting vascular dysfunction and inflammation.
Non-specific alterations of craniocervical venous drainage in multiple sclerosis revealed by cardiac-gated phase-contrast MRI
Authors: Ertl-Wagner Birgit , Koerte Inga , Kümpfel Tania , Blaschek Astrid , Laubender Ruediger P , Schick Max , Steffinger Denise , Kaufmann David , Heinen Florian , Reiser Maximilian , Alperin Noam , Hohlfeld Reinhard 
Published: December 2011

Objective: There is an on-going controversy about venous drainage abnormalities in multiple sclerosis (MS). We applied cardiac-gated phase-contrast and venographic magnetic resonance (MR) techniques to compare venous drainage patterns in patients with MS, healthy controls, and subjects with migraine. Methods: A total of 27 patients with MS (21 female, age 12–59 years, mean disease duration 8.4 ± 8.5 years) and 27 age- and gender-matched healthy controls (21 female, age 12–60 years) were investigated with velocity-encoded cine-phase contrast MR sequences and a 2D time-of-flight MR venography of the cervicocranial region on a 3-T MRI. The data were compared with 26 patients with chronic migraine headaches (19 female, age 17–62 years), previously investigated with the same protocol. The degree of primary and secondary venous outflow in relation to the total cerebral blood flow (tCBF) was compared both quantitatively and qualitatively. Statistical analyses were performed using linear regression models. Results: Secondary venous outflow was significantly increased in patients with MS compared with healthy controls, both qualitatively ( p < 0.001) and quantitatively ( p < 0.013). The observed changes were independent of age and disease duration. Very similar alterations of venous drainage were detectable with the same approach in patients with migraine, without significant differences between MS and migraine patients ( p = 0.65). Conclusion: Our MRI-based study suggests that patients with MS have alterations of cerebral venous drainage similar to subjects with chronic migraine. These non-disease-specific changes seem to a secondary phenomenon rather than being of primary pathogenic importance.
Comprehensive analysis of tandem amino acid repeats from ten angiosperm genomes
Authors: Zhou Yuan , Liu Jing , Han Lei , Li Zhi-Gang , Zhang Ziding 
Published: December 2011

Abstract

Background
The presence of tandem amino acid repeats (AARs) is one of the signatures of eukaryotic proteins. AARs were thought to be frequently involved in bio-molecular interactions. Comprehensive studies that primarily focused on metazoan AARs have suggested that AARs are evolving rapidly and are highly variable among species. However, there is still controversy over causal factors of this inter-species variation. In this work, we attempted to investigate this topic mainly by comparing AARs in orthologous proteins from ten angiosperm genomes.

Results
Angiosperm AAR content is positively correlated with the GC content of the protein coding sequence. However, based on observations from fungal AARs and insect AARs, we argue that the applicability of this kind of correlation is limited by AAR residue composition and species' life history traits. Angiosperm AARs also tend to be fast evolving and structurally disordered, supporting the results of comprehensive analyses of metazoans. The functions of conserved long AARs are summarized. Finally, we propose that the rapid mRNA decay rate, alternative splicing and tissue specificity are regulatory processes that are associated with angiosperm proteins harboring AARs.

Conclusions
Our investigation suggests that GC content is a predictor of AAR content in the protein coding sequence under certain conditions. Although angiosperm AARs lack conservation and 3D structure, a fraction of the proteins that contain AARs may be functionally important and are under extensive regulation in plant cells.