bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Diversity of Bacteroidales in Fecal and Environmental Samples and Swine-Associated Subpopulations
Authors: Lamendella Regina , Li Kent C. , Oerther Daniel , Santo Domingo Jorge W. 
Published: November 2012

ABSTRACT

Several swine-specific microbial source tracking methods are based on PCR assays targeting
Bacteroidales
16S rRNA gene sequences. The limited application of these assays can be explained by the poor understanding of their molecular diversity in fecal sources and environmental waters. In order to address this, we studied the diversity of 9,340 partial (>600 bp in length)
Bacteroidales
16S rRNA gene sequences from 13 fecal sources and nine feces-contaminated watersheds. The compositions of major
Bacteroidales
populations were analyzed to determine which host and environmental sequences were contributing to each group. This information allowed us to identify populations which were both exclusive to swine fecal sources and detected in swine-contaminated waters. Phylogenetic and diversity analyses revealed that some markers previously believed to be highly specific to swine populations are shared by multiple hosts, potentially explaining the cross-amplification signals obtained with nontargeted hosts. These data suggest that while many
Bacteroidales
populations are cosmopolitan, others exhibit a preferential host distribution and may be able to survive different environmental conditions. This study further demonstrates the importance of elucidating the diversity patterns of targeted bacterial groups to develop more inclusive fecal source tracking applications.
Improved Production of
l
-Threonine in Escherichia coli by Use of a DNA Scaffold System
Authors: Lee Jun Hyoung , Jung Suk-Chae , Bui Le Minh , Kang Kui Hyeon , Song Ji-Joon , Kim Sun Chang 
Published: November 2012

ABSTRACT

Despite numerous approaches for the development of
l
-threonine-producing strains, strain development is still hampered by the intrinsic inefficiency of metabolic reactions caused by simple diffusion and random collisions of enzymes and metabolites. A scaffold system, which can promote the proximity of metabolic enzymes and increase the local concentration of intermediates, was reported to be one of the most promising solutions. Here, we report an improvement in
l
-threonine production in
Escherichia coli
using a DNA scaffold system, in which a zinc finger protein serves as an adapter for the site-specific binding of each enzyme involved in
l
-threonine production to a precisely ordered location on a DNA double helix to increase the proximity of enzymes and the local concentration of metabolites to maximize production. The optimized DNA scaffold system for
l
-threonine production significantly increased the efficiency of the threonine biosynthetic pathway in
E. coli
, substantially reducing the production time for
l
-threonine (by over 50%). In addition, this DNA scaffold system enhanced the growth rate of the host strain by reducing the intracellular concentration of toxic intermediates, such as homoserine. Our DNA scaffold system can be used as a platform technology for the construction and optimization of artificial metabolic pathways as well as for the production of many useful biomaterials.
Contribution of Bacillomycin D in Bacillus amyloliquefaciens SQR9 to Antifungal Activity and Biofilm Formation
Authors: Xu Zhihui , Shao Jiahui , Li Bing , Yan Xin , Shen Qirong , Zhang Ruifu 
Published: November 2012

ABSTRACT

Bacillus amyloliquefaciens
strains are capable of suppressing soilborne pathogens through the secretion of an array of lipopeptides and root colonization, and biofilm formation ability is considered a prerequisite for efficient root colonization. In this study, we report that one of the lipopeptide compounds (bacillomycin D) produced by the rhizosphere strain
Bacillus amyloliquefaciens
SQR9 not only plays a vital role in the antagonistic activity against
Fusarium oxysporum
but also affects the expression of the genes involved in biofilm formation. When the bacillomycin D and fengycin synthesis pathways were individually disrupted, mutant SQR9M1, which was deficient in the production of bacillomycin D, only showed minor antagonistic activity against
F. oxysporum
, but another mutant, SQR9M2, which was deficient in production of fengycin, showed antagonistic activity equivalent to that of the wild-type strain of
B. amyloliquefaciens
SQR9. The results from
in vitro
, root
in situ
, and quantitative reverse transcription-PCR studies demonstrated that bacillomycin D contributes to the establishment of biofilms. Interestingly, the addition of bacillomycin D could significantly increase the expression levels of
kinC
gene, but KinC activation is not triggered by leaking of potassium. These findings suggest that bacillomycin D contributes not only to biocontrol activity but also to biofilm formation in strain
B. amyloliquefaciens
SQR9.
Profiling
In Situ
Microbial Community Structure with an Amplification Microarray
Authors: Chandler Darrell P. , Knickerbocker Christopher , Bryant Lexi , Golova Julia , Wiles Cory , Williams Kenneth H. , Peacock Aaron D. , Long Philip E. 
Published: November 2012

ABSTRACT

The objectives of this study were to unify amplification, labeling, and microarray hybridization chemistries within a single, closed microfluidic chamber (an amplification microarray) and verify technology performance on a series of groundwater samples from an
in situ
field experiment designed to compare U(VI) mobility under conditions of various alkalinities (as HCO
3
−
) during stimulated microbial activity accompanying acetate amendment. Analytical limits of detection were between 2 and 200 cell equivalents of purified DNA. Amplification microarray signatures were well correlated with 16S rRNA-targeted quantitative PCR results and hybridization microarray signatures. The succession of the microbial community was evident with and consistent between the two microarray platforms. Amplification microarray analysis of acetate-treated groundwater showed elevated levels of iron-reducing bacteria (
Flexibacter
,
Geobacter
,
Rhodoferax
, and
Shewanella
) relative to the average background profile, as expected. Identical molecular signatures were evident in the transect treated with acetate plus NaHCO
3
, but at much lower signal intensities and with a much more rapid decline (to nondetection).
Azoarcus
,
Thaurea
, and
Methylobacterium
were responsive in the acetate-only transect but not in the presence of bicarbonate. Observed differences in microbial community composition or response to bicarbonate amendment likely had an effect on measured rates of U reduction, with higher rates probable in the part of the field experiment that was amended with bicarbonate. The simplification in microarray-based work flow is a significant technological advance toward entirely closed-amplicon microarray-based tests and is generally extensible to any number of environmental monitoring applications.
Reconstruction of Novel Cyanobacterial Siphovirus Genomes from Mediterranean Metagenomic Fosmids
Authors: Mizuno Carolina Megumi , Rodriguez-Valera Francisco , Garcia-Heredia Inmaculada , Martin-Cuadrado Ana-Belen , Ghai Rohit 
Published: November 2012

ABSTRACT

Cellular metagenomes are primarily used for investigating microbial community structure and function. However, cloned fosmids from such metagenomes capture phage genome fragments that can be used as a source of phage genomes. We show that fosmid cloning from cellular metagenomes and sequencing at a high coverage is a credible alternative to constructing metaviriomes and allows capturing and assembling novel, complete phage genomes. It is likely that phages recovered from cellular metagenomes are those replicating within cells during sample collection and represent “active” phages, naturally amplifying their genomic DNA and increasing chances for cloning. We describe five sets of siphoviral contigs (MEDS1, MEDS2, MEDS3, MEDS4, and MEDS5), obtained by sequencing fosmids from the cellular metagenome of the deep chlorophyll maximum in the Mediterranean. Three of these represent complete siphoviral genomes and two represent partial ones. This is the first set of phage genomes assembled directly from cellular metagenomic fosmid libraries. They exhibit low sequence similarities to one another and to known siphoviruses but are remarkably similar in overall genome architecture. We present evidence suggesting they infect picocyanobacteria, likely
Synechococcus
. Four of these sets also define a novel branch in the phylogenetic tree of phage large subunit terminases. Moreover, some of these siphoviral groups are globally distributed and abundant in the oceans, comparable to some known myoviruses and podoviruses. This suggests that, as more siphoviral genomes become available, we will be better able to assess the abundance and influence of this diverse and polyphyletic group in the marine habitat.
Biological and Physicochemical Wastewater Treatment Processes Reduce the Prevalence of Virulent Escherichia coli
Authors: Frigon Dominic , Biswal Basanta Kumar , Mazza Alberto , Masson Luke , Gehr Ronald 
Published: November 2012

ABSTRACT

Effluents discharged from wastewater treatment plants are possible sources of pathogenic bacteria, including
Escherichia coli
, in the freshwater environment, and determining the possible selection of pathogens is important. This study evaluated the impact of activated sludge and physicochemical wastewater treatment processes on the prevalence of potentially virulent
E. coli
. A total of 719
E. coli
isolates collected from four municipal plants in Québec before and after treatment were characterized by using a customized DNA microarray to determine the impact of treatment processes on the frequency of specific pathotypes and virulence genes. The percentages of potentially pathogenic
E. coli
isolates in the plant influents varied between 26 and 51%, and in the effluents, the percentages were 14 to 31%, for a reduction observed at all plants ranging between 14 and 45%. Pathotypes associated with extraintestinal pathogenic
E. coli
(ExPEC) were the most abundant at three of the four plants and represented 24% of all isolates, while intestinal pathogenic
E. coli
pathotypes (IPEC) represented 10% of the isolates. At the plant where ExPEC isolates were not the most abundant, a large number of isolates were classified as both ExPEC and IPEC; overall, 6% of the isolates were classified in both groups, with the majority being from the same plant. The reduction of the proportion of pathogenic
E. coli
could not be explained by the preferential loss of one virulence gene or one type of virulence factor; however, the quinolone resistance gene (
qnrS
) appears to enhance the loss of virulence genes, suggesting a mechanism involving the loss of pathogenicity islands.
Diverse Microhabitats Experienced by Halomonas variabilis on Salt-Secreting Leaves
Authors: Burch Adrien Y. , Finkel Omri M. , Cho Juliana K. , Belkin Shimshon , Lindow Steven E. 
Published: November 2012

ABSTRACTThe leaf surfaces of the salt-excreting treeTamarix aphyllaharbor a wide diversity of halophilic microorganisms, includingHalomonassp., but little is known of the factors that shape community composition in this extreme habitat. We isolated a strain ofHalomonas variabilisfrom the leaf surface ofT. aphyllaand used it to determine the heterogeneity of salt concentrations experienced by bacteria in this environment. This halophilic strain was transformed with aproU::gfpreporter gene fusion, the fluorescence of which was responsive to NaCl concentrations up to 200 g liter−1. These bioreporting cells were applied toT. aphyllaleaves and were subsequently recovered from dew droplets adhering to the leaf surface. Although cells from within a given dew droplet exhibited similar green fluorescent protein fluorescence, the fluorescence intensity varied between droplets and was correlated with the salt concentration measured in each drop. Growth ofH. variabiliswas observed in all droplets, regardless of the salt concentration. However, cells found in desiccated microniches between dew drops were low in abundance and generally dead. Other bacteria recovered fromT. aphylladisplayed higher desiccation tolerance thanH. variabilis, both in culture and on inoculated plants, despite having lower osmotic tolerance. Thus, theTamarixleaf surface can be described as a salty desert with occasional oases where water droplets form under humid conditions. While halotolerant bacteria such asHalomonasgrow in high concentrations of salt in such wet microniches, other organisms are better suited to survive desiccation in sites that are not wetted.
Clinical Specificity of the Enzyme Immunoassay Test for Coccidioidomycosis Varies According to the Reason for Its Performance
Authors: Blair Janis E. , Mendoza Neil , Force Shannon , Chang Yu-Hui H. , Grys Thomas E. 
Published: November 2012

ABSTRACT
The diagnosis of coccidioidomycosis relies heavily on serologic test results in addition to clinical history, physical examination, and radiographic findings. Use of the enzyme immunoassay (EIA) has increased because it is rapidly performed and does not require referral to a reference laboratory, as do complement fixation and immunodiffusion tests. However, interpretation of immunoglobulin M (IgM) reactivity by EIA in the absence of immunoglobulin G (IgG) reactivity has been problematic. We conducted a retrospective medical record review of all patients with such IgM reactivity at our institution to identify situations where the finding was more likely to be clinically specific for coccidioidal infection. From 1 January 2004 through 31 December 2008, a total of 1,117 patients had positive EIA coccidioidal serology or EIA IgM-only reactivity; of these, 102 patients (9%) had EIA IgM-only reactivity. Among the 102 patients with EIA IgM-only reactivity, 60 were tested to evaluate symptomatic illness, 13 for follow-up of previously abnormal serology, and 29 for screening purposes. Of the 102 patients, 80 (78%) had positive serologic findings by other methods or had positive culture or histology. Fifty-four (90%) of the 60 patients whose serology was performed to evaluate symptomatic illness had coccidioidal infection, whereas 13 (45%) of 29 patients whose serology was performed for screening purposes had coccidioidal infection. Of the 102 patients with isolated IgM reactivity by EIA, 12 later seroconverted to IgG and IgM reactivity. The use of EIA for screening in 29 asymptomatic persons was associated with unconfirmable results in 13 (45%). Although the majority of patients in our study with isolated IgM reactivity by EIA had probable or confirmed coccidioidomycosis, this result must be interpreted with caution for asymptomatic patients.
Intracellular Trafficking and Glycobiology of TbPDI2, a Stage-Specific Protein Disulfide Isomerase in Trypanosoma brucei
Authors: Schwartz Kevin J. , Peck Ronald F. , Bangs James D. 
Published: November 2012

ABSTRACT

Trypanosoma brucei
protein disulfide isomerase 2 (TbPDI2) is a bloodstream stage-specific lumenal endoplasmic reticulum (ER) glycoprotein. ER localization is dependent on the TbPDI2 C-terminal tetrapeptide (KQDL) and is mediated by TbERD2, an orthologue of the yeast ER retrieval receptor. Consistent with this function, TbERD2 localizes prominently to ER exit sites, and RNA interference (RNAi) knockdown results in specific secretion of a surrogate ER retention reporter, BiPN:KQDL. TbPDI2 is highly N-glycosylated and is reactive with tomato lectin, suggesting the presence of poly-
N
-acetyllactosamine modifications, which are common on lyso/endosomal proteins in trypanosomes but are inconsistent with ER localization. However, TbPDI2 is reactive with tomato lectin immediately following biosynthesis—far too rapidly for transport to the Golgi compartment, the site of poly-
N
-acetyllactosamine addition. TbPDI2 also fails to react with
Erythrina cristagalli
lectin, confirming the absence of terminal
N
-acetyllactosamine units. We propose that tomato lectin binds the Manβ1-4GlcNAcβ1-4GlcNAc trisaccharide core of paucimannose glycans on both newly synthesized and mature TbPDI2. Consistent with this proposal, α-mannosidase treatment renders oligomannose
N
-glycans on the
T. brucei
cathepsin L orthologue TbCatL reactive with tomato lectin. These findings resolve contradictory evidence on the location and glycobiology of TbPDI2 and provide a cautionary note on the use of tomato lectin as a poly-
N
-acetyllactosamine-specific reagent.
Promoting physical activity in sedentary elderly Malays with type 2 diabetes: a protocol for randomised controlled trial
Authors: Sazlina Shariff-Ghazali , Browning Colette Joy , Yasin Shajahan 
Published: November 2012

IntroductionLike many countries Malaysia is facing an increase in the number of people with type 2 diabetes mellitus diabetes (T2DM) and modifiable lifestyle factors such as sedentary behaviour are important drivers of this increase. The level of physical activity is low among elderly Malay people. In Malaysia, strategies to promote physical activity in elderly Malay people with T2DM are not well documented in the research literature. This paper discusses an intervention to increase physical activity in elderly Malay people with T2DM. The aim of our study was to evaluate the effectiveness of personalised feedback alone and in combination with peer support in promoting and maintaining physical activity in comparison with usual care.Methods and analysisA three-arm randomised controlled trial will be conducted among sedentary Malay adults aged 60 years and above with T2DM attending an urban primary healthcare clinic in Malaysia. The participants will be randomised into three groups for a 12-week intervention with a follow-up at 24 and 36 weeks to assess adherence. The primary outcome of this study is pedometer-determined physical activity. Glycaemic and blood pressure control, body composition, cardiorespiratory fitness, balance, lipid profile, health-related quality of life, psychological well-being, social support and self-efficacy for exercise are the secondary measures. Linear mixed models will be used to determine the effect of the intervention over time and between groups.Ethical and disseminationThe Monash University Human Research Ethics Committee and the Malaysian Ministry of Health's Medical Research Ethics Committee approved this protocol. The findings of this study will be presented at international conferences and published in peer-reviewed journals.Trial registrationThis study protocol has been registered with the Malaysian National Medical Research Registry and with the Current Controlled Trial Ltd (http://www.controlled-trials.com/ISRCTN71447000/).
Participation of natural killer cells in the pathogenesis of bile duct lesions in biliary atresia
Authors: Okamura Atsushi , Harada Kenichi , Nio Masaki , Nakanuma Yasuni 
Published: November 2012

AimsImmunological disturbances including innate immunity after a suspected viral infection are considered important to the pathogenesis of bile duct lesions in cases of biliary atresia (BA). In this study, we tried to evaluate whether natural killer (NK) cells and CX3CL1 (Fractalkine) and its receptor (CX3CR1) are involved in the bile duct injury.MethodsUsing the section of BA (22 cases) and controls, immunohistochemistry for CD56, CD16, CD68, CX3CL1 and CX3CR1 was performed. Moreover, using cultured biliary epithelial cells (BECs) and NK cells, the production of CX3CL1 in BECs and the migration of NK cells were evaluated.ResultsIt was found that CD56(−)CD16(+)CD68(−) NK cells were increased around the damaged small and large bile ducts in BA and hepatitis C virus-related chronic hepatitis in comparison with other controls. CX3CL1 was strongly expressed on the damaged bile ducts in BA, while this expression was relatively weak or absent in the bile ducts of normal liver. The results suggest the CD56(−)CD16(+) NK cells to be involved in the development of bile duct injuries in BA. These CD16(+) NK cells were positive for CX3CR1, and attracted by CX3CL1 expressed on bile ducts. Further study revealed that stimulation with poly(I:C) (a synthetic analogue of viral dsRNA) increased the expression of CX3CL1 on cultured BECs followed by increased migrational activity of cultured NK cells.ConclusionsCD56(−)CD16(+) NK cells with reduced NK activity may be involved in the bile duct damage in BA, and CD16(+) NK cells expressing CX3CR1 may be attracted by and interact with bile ducts expressing CX3CL1.
Augmenting Antitumor T-Cell Responses to Mimotope Vaccination by Boosting with Native Tumor Antigens
Authors: Buhrman Jonathan D. , Jordan Kimberly R. , U'Ren Lance , Sprague Jonathan , Kemmler Charles B. , Slansky Jill E. 
Published: November 2012

AbstractVaccination with antigens expressed by tumors is one strategy for stimulating enhanced T-cell responses against tumors. However, these peptide vaccines rarely result in efficient expansion of tumor-specific T cells or responses that protect against tumor growth. Mimotopes, or peptide mimics of tumor antigens, elicit increased numbers of T cells that crossreact with the native tumor antigen, resulting in potent antitumor responses. Unfortunately, mimotopes may also elicit cells that do not crossreact or have low affinity for tumor antigen. We previously showed that one such mimotope of the dominant MHC class I tumor antigen of a mouse colon carcinoma cell line stimulates a tumor-specific T-cell clone and elicits antigen-specific cells in vivo, yet protects poorly against tumor growth. We hypothesized that boosting the mimotope vaccine with the native tumor antigen would focus the T-cell response elicited by the mimotope toward high affinity, tumor-specific T cells. We show that priming T cells with the mimotope, followed by a native tumor-antigen boost, improves tumor immunity compared with T cells elicited by the same prime with a mimotope boost. Our data suggest that the improved tumor immunity results from the expansion of mimotope-elicited tumor-specific T cells that have increased avidity for the tumor antigen. The enhanced T cells are phenotypically distinct and enriched for T-cell receptors previously correlated with improved antitumor immunity. These results suggest that incorporation of native antigen into clinical mimotope vaccine regimens may improve the efficacy of antitumor T-cell responses. Cancer Res; 73(1); 74–85. ©2012 AACR.