bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of Mycobacterium infections in patients with Mendelian susceptibility to mycobacterial disease with venous thromboembolism
Authors: Alinejad Dizaj Maryam , Mahdaviani Seyed Alireza , Tabarsi Payam , Ahari Hamed , Ebrahimi Ahmad , Nadji Seyed Alireza , Emami Habib , Mortaz Esmaeil 
Published: October 2016

ABSTRACTAn association between a hypercoagulable state and Mendelian susceptibility to mycobacterial disease (MSMD) has been established in a few studies; resultant thrombosis is considered rare. In a case‐control study, the prevalence of factor V Leiden, prothrombin G20210A and methylenetetrahydrofolate reductase (MTHFR) C677T, A1298C mutations were investigated in mycobacterium‐infected patients. The study comprised 30 patients with mycobacterial infections (invasive, disseminated and/or recurrent infections with Bacille Calmette–Guerin or non‐tuberculosis mycobacteria and Mycobacterium Tuberculosis with positive results for acid‐fast bacilli and tuberculin skin tests) and 30 normal healthy controls. Forty female (66.7%) and 20 male subjects (33.3%) aged from 3 to 70 years were recruited into this study. Genotyping of targeted genes was performed by RT‐PCR and cytokine TNF‐α concentrations were quantified using a commercially available ELISA kit. Significant associations between mycobacterial infection and TNF‐α production after stimulating peripheral blood mononuclear cells with LPS alone and with IFN‐γ plus LPS were identified. Moreover, genotyping analysis in the studied population revealed a significant association between MTHFR c.677C>T (OR, 3.28; 95% CI, 1.35–7.92; P < 0.05), MTHFR c.1298A>C (OR, 2.33; 95% CI, 1.10–4.93; P < 0.05) and mycobacterial infection in affected patients, indicating susceptibility to venous thromboembolism according to previous studies. Additionally, mycobacterium‐infected patients had a significantly greater prevalence of MTHFR C677T and A1298C mutations than controls.
Communicating Conservation Status: How Different Statistical Assessment Criteria Affect Perceptions of Extinction Risk
Authors: Song Hwanseok , Schuldt Jonathon P. 
Published: October 2016

AbstractAlthough alternative forms of statistical and verbal information are routinely used to convey species’ extinction risk to policymakers and the public, little is known about their effects on audience information processing and risk perceptions. To address this gap in literature, we report on an experiment that was designed to explore how perceptions of extinction risk differ as a function of five different assessment benchmarks (Criteria A–E) used by scientists to classify species within IUCN Red List risk levels (e.g., Critically Endangered, Vulnerable), as well as the role of key individual differences in these effects (e.g., rational and experiential thinking styles, environmental concern). Despite their normative equivalence within the IUCN classification system, results revealed divergent effects of specific assessment criteria: on average, describing extinction risk in terms of proportional population decline over time (Criterion A) and number of remaining individuals (Criterion D) evoked the highest level of perceived risk, whereas the single‐event probability of a species becoming extinct (Criterion E) engendered the least perceived risk. Furthermore, participants scoring high in rationality (analytic thinking) were less prone to exhibit these biases compared to those low in rationality. Our findings suggest that despite their equivalence in the eyes of scientific experts, IUCN criteria are indeed capable of engendering different levels of risk perception among lay audiences, effects that carry direct and important implications for those tasked with communicating about conservation status to diverse publics.
Novel Capsular Polysaccharide Loci and New Diagnostic Tools for High-Throughput Capsular Gene Typing in Streptococcus suis
Authors: Qiu Xiaotong , Bai Xuemei , Lan Ruiting , Zheng Han , Xu Jianguo 
Published: October 2016

ABSTRACT

Streptococcus suis
is an important pathogen of pigs and may cause serious disease in humans. Serotyping is an important tool for detection and epidemiological studies of
S. suis
. Thirty-three reference serotypes and nine novel
cps
loci (NCLs) are recognized in
S. suis
. To gain a better understanding of the prevalence and genetic characteristics of NCLs, we investigated the serotype identity of 486 isolates isolated between 2013 and 2015 in China by capsular gene typing methods. Two hundred seventy-six isolates carried NCLs belonging to 16 groups, 8 of which appear to have not been reported previously. These isolates showed autoagglutination, polyagglutination, or nonagglutination with reference antisera and thus were nonserotypeable. Almost all isolates carrying the unknown NCLs were encapsulated, with various capsular thicknesses, indicating that they are most likely novel serotypes. To simultaneously identify the currently recognized 17 NCLs, an 18-plex detection system using the Luminex xTAG universal array technology was developed. Our data also provide valuable genetic information for monitoring the variations within NCLs by investigating the genetic characteristics of different subtypes within NCLs.

IMPORTANCE
Nonserotypeable
Streptococcus suis
isolates have been reported in many studies, and 9 novel
cps
loci (NCLs) have already been identified in nonserotypeable isolates. Moreover, novel
cps
loci are continually being found. The main purpose of this study was to investigate the prevalence and characteristics of NCLs in
S. suis
isolates recovered between 2013 and 2015 in China. This study provides valuable genetic information for monitoring the variations within NCLs. Meanwhile, a fast and cost-effective 18-plex detection system that can simultaneously identify the currently recognized 17 NCLs was developed in this study. This system will serve as a valuable tool for detecting known and identifying additional novel
cps
loci among nonserotypeable
S. suis
isolates.
Phylogenetic Evidence for Ancient and Persistent Environmental Symbiont Reacquisition in Largidae (Hemiptera: Heteroptera)
Authors: Gordon Eric Robert Lucien , McFrederick Quinn , Weirauch Christiane 
Published: October 2016

ABSTRACT

The insect order Hemiptera, one of the best-studied insect lineages with respect to bacterial symbioses, still contains major branches that lack comprehensive characterization of associated bacterial symbionts. The Pyrrhocoroidea (Largidae [220 species] and Pyrrhocoridae [∼300 species]) is a clade of the hemipteran infraorder Pentatomomorpha. Studies on bacterial symbionts of this group have focused on members of Pyrrhocoridae, but recent examination of species of two genera of Largidae demonstrated divergent symbiotic complexes in these putative sister families. We surveyed the associated bacterial diversity of this group using paired-end Illumina sequencing and targeted Sanger sequencing of bacterial 16S rRNA amplicons of 30 pyrrhocoroid taxa, including 17 species of Largidae, in order to determine bacterial associates and the similarity of associated microbial communities among species. We also used molecular data (4,800 bp in 5 loci, for 57 ingroup and 12 outgroup taxa) to infer a phylogeny of the host superfamily, in order to trace the evolution of symbiotic complexes among Pentatomomorpha species. We undertook multiple lines of investigation (i.e., experimental rearing, fluorescence
in situ
hybridization microscopy, and phylogenetic and coevolutionary analyses) to elucidate potential transmission routes for largid symbionts. We found a prevalent and specific association of Largidae with
Burkholderia
strains of the plant-associated beneficial and environmental clade, housed in midgut tubules. As in other distantly related Heteroptera, symbiotic bacteria seem to be acquired from the environment every generation. We review the current understanding of symbiotic complexes within Pentatomomorpha and discuss means to further investigate the evolution and function of these symbioses.

IMPORTANCE
Obligate symbioses with bacteria are common in insects, particularly Hemiptera, in which various forms of symbiosis occur. However, knowledge regarding symbionts remains incomplete for major hemipteran lineages. Thus, an accurate understanding of how these partnerships evolved and changed over millions of years is not yet achievable. We contribute to our understanding of the evolution of symbiotic complexes in Hemiptera by characterizing bacterial associates of Pyrrhocoroidea, focusing on the family Largidae. Members of Largidae are associated with specific symbiotic
Burkholderia
strains from a different clade than
Burkholderia
symbionts in other
Burkholderia
-associated Hemiptera. Evidence suggests that species of Largidae reacquire specific symbiotic bacteria from the environment every generation, which is a rare strategy for insects, with potentially volatile evolutionary ramifications, but one that must have persisted in Largidae and related lineages since their origin in the Cretaceous Period.
Ferredoxin:NAD
+
Oxidoreductase of Thermoanaerobacterium saccharolyticum and Its Role in Ethanol Formation
Authors: Tian Liang , Lo Jonathan , Shao Xiongjun , Zheng Tianyong , Olson Daniel G. , Lynd Lee R. 
Published: October 2016

ABSTRACT

Ferredoxin:NAD
+
oxidoreductase (NADH-FNOR) catalyzes the transfer of electrons from reduced ferredoxin to NAD
+
. This enzyme has been hypothesized to be the main enzyme responsible for ferredoxin oxidization in the NADH-based ethanol pathway in
Thermoanaerobacterium saccharolyticum
; however, the corresponding gene has not yet been identified. Here, we identified the Tsac_1705 protein as a candidate FNOR based on the homology of its functional domains. We then confirmed its activity
in vitro
with a ferredoxin-based FNOR assay. To determine its role in metabolism, the
tsac_1705
gene was deleted in different strains of
T. saccharolyticum
. In wild-type
T. saccharolyticum
, deletion of
tsac_1705
resulted in a 75% loss of NADH-FNOR activity, which indicated that Tsac_1705 is the main NADH-FNOR in
T.
saccharolyticum
. When both NADH- and NADPH-linked FNOR genes were deleted, the ethanol titer decreased and the ratio of ethanol to acetate approached unity, indicative of the absence of FNOR activity. Finally, we tested the effect of heterologous expression of Tsac_1705 in
Clostridium thermocellum
and found improvements in both the titer and the yield of ethanol.

IMPORTANCE
Redox balance plays a crucial role in many metabolic engineering strategies. Ferredoxins are widely used as electron carriers for anaerobic microorganism and plants. This study identified the gene responsible for electron transfer from ferredoxin to NAD
+
, a key reaction in the ethanol production pathway of this organism and many other metabolic pathways. Identification of this gene is an important step in transferring the ethanol production ability of this organism to other organisms.
Internalization of Heterologous Sugar Transporters by Endogenous α-Arrestins in the Yeast Saccharomyces cerevisiae
Authors: Sen Arpita , Acosta-Sampson Ligia , Alvaro Christopher G. , Ahn Jonathan S. , Cate Jamie H. D. , Thorner Jeremy 
Published: October 2016

ABSTRACT

When expressed in
Saccharomyces cerevisiae
using either of two constitutive yeast promoters (

PGK1
prom

and

CCW12
prom

), the transporters CDT-1 and CDT-2 from the filamentous fungus
Neurospora crassa
are able to catalyze, respectively, active transport and facilitated diffusion of cellobiose (and, for CDT-2, also xylan and its derivatives). In
S. cerevisiae
, endogenous permeases are removed from the plasma membrane by clathrin-mediated endocytosis and are marked for internalization through ubiquitinylation catalyzed by Rsp5, a HECT class ubiquitin:protein ligase (E3). Recruitment of Rsp5 to specific targets is mediated by a 14-member family of endocytic adaptor proteins, termed α-arrestins. Here we demonstrate that CDT-1 and CDT-2 are subject to α-arrestin-mediated endocytosis, that four α-arrestins (Rod1, Rog3, Aly1, and Aly2) are primarily responsible for this internalization, that the presence of the transport substrate promotes transporter endocytosis, and that, at least for CDT-2, residues located in its C-terminal cytosolic domain are necessary for its efficient endocytosis. Both α-arrestin-deficient cells expressing CDT-2 and otherwise wild-type cells expressing CDT-2 mutants unresponsive to α-arrestin-driven internalization exhibit an increased level of plasma membrane-localized transporter compared to that of wild-type cells, and they grow, utilize the transport substrate, and generate ethanol anaerobically better than control cells.

IMPORTANCE
Ethanolic fermentation of the breakdown products of plant biomass by budding yeast
Saccharomyces cerevisiae
remains an attractive biofuel source. To achieve this end, genes for heterologous sugar transporters and the requisite enzyme(s) for subsequent metabolism have been successfully expressed in this yeast. For one of the heterologous transporters examined in this study, we found that the amount of this protein residing in the plasma membrane was the rate-limiting factor for utilization of the cognate carbon source (cellobiose) and its conversion to ethanol.
Genomic Comparisons of Lactobacillus crispatus and Lactobacillus iners Reveal Potential Ecological Drivers of Community Composition in the Vagina
Authors: France Michael T. , Mendes-Soares Helena , Forney Larry J. 
Published: October 2016

ABSTRACT

Lactobacillus crispatus
and
Lactobacillus iners
are common inhabitants of the healthy human vagina. These two species are closely related and are thought to perform similar ecological functions in the vaginal environment. Temporal data on the vaginal microbiome have shown that nontransient instances of cooccurrence are uncommon, while transitions from an
L. iners
-dominated community to one dominated by
L. crispatus
, and vice versa, occur often. This suggests that there is substantial overlap in the fundamental niches of these species. Given this apparent niche overlap, it is unclear how they have been maintained as common inhabitants of the human vagina. In this study, we characterized and compared the genomes of
L. iners
and
L. crispatus
to gain insight into possible mechanisms driving the maintenance of this species diversity. Our results highlight differences in the genomes of these two species that may facilitate the partitioning of their shared niche space. Many of the identified differences may impact the protective benefits provided to the host by these two species.

IMPORTANCE
The microbial communities that inhabit the human vagina play a critical role in the maintenance of vaginal health through the production of lactic acid and lowering the environmental pH. This precludes the growth of nonindigenous organisms and protects against infectious disease. The two most common types of vaginal communities are dominated by either
Lactobacillus iners
or
Lactobacillus crispatus
, while some communities alternate between the two over time. We combined ecological theory with state-of-the-art genome analyses to characterize how these two species might partition their shared niche space in the vagina. We show that the genomes of
L. iners
and
L. crispatus
differ in many respects, several of which may drive differences in their competitive abilities in the vagina. Our results provide insight into factors that drive the complicated temporal dynamics of the vaginal microbiome and demonstrate how closely related microbial species partition shared fundamental niche space.
Microbial Glucuronoyl Esterases: 10 Years after Discovery
Authors: Biely Peter 
Published: October 2016

ABSTRACT

A carbohydrate esterase called glucuronoyl esterase (GE) was discovered 10 years ago in a cellulolytic system of the wood-rotting fungus
Schizophyllum commune
. Genes coding for GEs were subsequently found in a number of microbial genomes, and a new family of carbohydrate esterases (CE15) has been established. The multidomain structures of GEs, together with their catalytic properties on artificial substrates and positive effect on enzymatic saccharification of plant biomass, led to the view that the esterases evolved for hydrolysis of the ester linkages between 4-
O
-methyl-
d
-glucuronic acid of plant glucuronoxylans and lignin alcohols, one of the crosslinks in the plant cell walls. This idea of the function of GEs is further supported by the effects of cloning of fungal GEs in plants and by very recently reported evidence for changes in the size of isolated lignin-carbohydrate complexes due to uronic acid de-esterification. These facts make GEs interesting candidates for biotechnological applications in plant biomass processing and genetic modification of plants. This article is a brief summary of current knowledge of these relatively recent and unexplored esterases.
Freshwater Bacteria Release Methane as a By-Product of Phosphorus Acquisition
Authors: Yao Mengyin , Henny Cynthia , Maresca Julia A. 
Published: October 2016

ABSTRACT

Freshwater lakes emit large amounts of methane, some of which is produced in oxic surface waters. Two potential pathways for aerobic methane production exist: methanogenesis in oxygenated water, which has been observed in some lakes, and demethylation of small organic molecules. Although methane is produced via demethylation in oxic marine environments, this mechanism of methane release has not yet been demonstrated in freshwater systems. Genes related to the C-P lyase pathway, which cleaves C-P bonds in phosphonate compounds, were found in a metagenomic survey of the surface water of Lake Matano, which is chronically P starved and methane rich. We demonstrate that four bacterial isolates from Lake Matano obtain P from methylphosphonate and release methane and that this activity is repressed by phosphate. We further demonstrate that expression of
phnJ
, which encodes the enzyme that releases methane, is higher in the presence of methylphosphonate and lower when both methylphosphonate and phosphate are added. This gene is also found in most of the metagenomic data sets from freshwater environments. These experiments link methylphosphonate degradation and methane production with gene expression and phosphate availability in freshwater organisms and suggest that some of the excess methane in the Lake Matano surface water, and in other methane-rich lakes, may be produced by P-starved bacteria.

IMPORTANCE
Methane is an important greenhouse gas and contributes substantially to global warming. Although freshwater environments are known to release methane into the atmosphere, estimates of the amount of methane emitted by freshwater lakes vary from 8 to 73 Tg per year. Methane emissions are difficult to predict in part because the source of the methane can vary: it is the end product of the energy-conserving pathway in methanogenic archaea, which live predominantly in anoxic sediments or waters but have also been identified in some oxic freshwater environments. More recently, methane release from small organic molecules has been observed in oxic marine environments. Here we show that demethylation of methylphosphonate may also contribute to methane release from lakes and that phosphate can repress this activity. Since lakes are typically phosphorus limited, some methane release in these environments may be a by-product of phosphorus metabolism rather than carbon or energy metabolism. Methane emissions from lakes are currently predicted using primary production, eutrophication status, extent of anoxia, and the shape and size of the lake; to improve prediction of methane emissions, phosphorus availability and sources may also need to be included in these models.
Phosphinothricin Acetyltransferases Identified Using
In Vivo
,
In Vitro
, and Bioinformatic Analyses
Authors: VanDrisse Chelsey M. , Hentchel Kristy L. , Escalante-Semerena Jorge C. 
Published: October 2016

ABSTRACT

Acetylation of small molecules is widespread in nature, and in some cases, cells use this process to detoxify harmful chemicals.
Streptomyces
species utilize a
G
cn5

N

-
a
cetyl
t
ransferase (GNAT), known as Bar, to acetylate and detoxify a self-produced toxin,
p
hos
p
hino
t
hricin (PPT), a glutamate analogue. Bar homologues, such as MddA from
Salmonella enterica
, acetylate methionine analogues such as methionine sulfoximine (MSX) and methionine sulfone (MSO), but not PPT, even though Bar homologues are annotated as PPT acetyltransferases.
S. enterica
was used as a heterologous host to determine whether or not putative PPT acetyltransferases from various sources could acetylate PPT, MSX, and MSO.
In vitro
and
in vivo
analyses identified substrates acetylated by putative PPT acetyltransferases from
Deinococcus radiodurans
(DR_1057 and DR_1182) and
Geobacillus kaustophilus
(GK0593 and GK2920).
In vivo
, synthesis of DR_1182, GK0593, and GK2920 blocked the inhibitory effects of PPT, MSX, and MSO. In contrast, DR_1057 did not detoxify any of the above substrates. Results of
in vitro
studies were consistent with the
in vivo
results. In addition, phylogenetic analyses were used to predict the functionality of annotated PPT acetyltransferases in
Burkholderia xenovorans
,
Bacillus subtilis
,
Staphylococcus aureus
,
Acinetobacter baylyi
, and
Escherichia coli
.

IMPORTANCE
The work reported here provides an example of the use of a heterologous system for the identification of enzyme function. Many members of this superfamily of proteins do not have a known function, or it has been annotated solely on the basis of sequence homology to previously characterized enzymes. The critical role of
G
cn5

N

-
a
cetyl
t
ransferases (GNATs) in the modulation of central metabolic processes, and in controlling metabolic stress, necessitates approaches that can reveal their physiological role. The combination of
in vivo
,
in vitro
, and bioinformatics approaches reported here identified GNATs that can acetylate and detoxify phosphinothricin.
Correlation of global risk assessment with cardiovascular complications in patients with diabetes mellitus living in Puerto Rico
Authors: Rodríguez-Vigil Efraín , Rodríguez-Chacón Migdalia , Ruiz Valcarcel José J 
Published: October 2016

ObjectiveThe objective of this study was to assess the current relationship between certain demographics and chemical factors, and the risk of cardiovascular complications, within a Puerto Rican population with diabetes mellitus.Research design and methodsA total of 2075 patients with diabetes mellitus were retrospectively evaluated to determine the influence of certain demographics and chemical variables on the appearance of cardiovascular complications. A group of demographic and laboratory variables were analyzed. Our sample was obtained, based on convenience, from an endocrinologist's office in an area of about 250 000 people. All the patients met the American Diabetes Association (ADA) definitions for diabetes mellitus. The study covered a time period of 8 years. The patients signed an informed consent document at their first office visit. Data were obtained by the endocrinologist in charge.ResultsWe considered the demographic variables of sex, age, time with diabetes, lipid profile, metabolic control (measured with glycated hemoglobin levels), and microalbumin renal excretion. Cardiovascular complications were more prevalent in patients with poor metabolic control, those with prolonged disease duration, men, and patients who were more than 50 years of age. We found no relationship between cardiovascular disease, systolic blood pressure over 130 mm Hg, body mass index and low-density lipoprotein cholesterol levels over 100 mg/dL.ConclusionsIn Puerto Rican patients with diabetes mellitus, there is a statistically significant relationship between patient's gender, age, disease duration, glycemic control and increased kidney microalbumin excretion with cardiovascular complications.