bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Vasectomy on Seminal Plasma Alkaline Phosphatase in Male Alpacas (Vicugña pacos)
Authors: Pearson LK , Campbell AJ , Sandoval S , Tibary A 
Published: June 2013

ContentsAzoospermia is a common finding in male alpacas which present for infertility. The challenge is to differentiate azoospermia of testicular origin from non‐testicular origin. In several species, alkaline phosphatase (AP) concentrations in seminal plasma have been used as a diagnostic marker of contributions of the testis and epididymis to the ejaculate. The purpose of this study was to determine whetherAPassay could differentiate testicular from non‐testicular azoospermia in male alpacas. An experimental model of bilateral outflow obstruction (pre‐scrotal vasectomy) was used in 22 male alpacas, aged 2–9 years. No reproductive history was available. Animals were submitted for electroejaculation (EE) under general anaesthesia and vasectomy performed. Five weeks later, animals were submitted forEE. Vasectomy was not successful in one animal, which was removed from analysis.APlevels were compared in seminal plasma in the pre‐ and post‐vasectomy samples. The mean ± SEMconcentration ofAPin pre‐vasectomy seminal plasma was 504.29 ± 166.45 U/l (range 10–2910); the post‐vasectomy levels were 252.48 ± 81.77 U/l (range 0–1640; p = 0.06). In 71.4% of animals,APlevels decreased, varying from 18% to 100% reduction. Results of this study suggest thatAPis not produced exclusively by the testis and epididymis in alpacas and thatAPassay is not a valid diagnostic test for determination of origin of azoospermia; the gold standard for diagnosis of origin of azoospermia remains testicular biopsy.
Organic Geochemistry of the Cenomanian–Turonian Bahloul Formation Petroleum Source Rock, Central and Northern Tunisia
Authors: Affouri Hassene , Montacer Mabrouk , Disnar Jean‐Robert 
Published: June 2013

AbstractTotal organic carbon (TOC) determination, Rock‐Eval pyrolysis, extractable organic matter content (EOM) fractionation, gas chromatography (GC) and gas chromatography–mass spectrometry (GC–MS) analyses, were carried out on 79 samples from eleven outcrop cross sections of the Bahloul Formation in central and northern Tunisia. The TOC content varied between 0.23 to 35.6%, the highest average values (18.73%, 8.46% and 4.02%) being at the east of the study area (at Ain Zakkar, Oued Bahloul and Dyr Ouled Yahia localities, respectively). The Rock‐Eval maximum pyrolysis temperature (Tmax) values in the 424–453°C range delineated a general east‐west trend increase in the organic matter (OM) maturity. The disparity in hydrogen index (HI) values, in the range 114–824 mg hydrocarbons (HC) g−1 TOC, is relevant for the discrepancy in the level of OM preservation and maturity among localities and samples. The n‐alkane distributions, maximizing in the C17 to C20 range, are typical for a marine planktonic origin, whereas pristine/phytane (Pr/Ph) average values in the 1–2 range indicate an oxic to suboxic depositional environment. Pr/n‐C17 and Ph/n‐C18 ratios in the 0.38–6.2 and 0.68–3.25 range, respectively, are consistent with other maturity indicators and the contribution of specific bacteria to phytol as a precursor of isoprenoids. The thermal maturity varies between late diagenesis to main‐stage of petroleum generation based on the optic and the cis‐trans isomerisation of the C29 sterane [20S/(20S+20R) and 14β(H),17β(H)/(14β(H),17β(H)+14α(H),17α(H)), respectively] and the terpane [18α(H)22,29,30‐Trisnorneohopane/(18α(H)22,29,30‐Trisnorneohopane+17α(H)22,29,30‐Trisnorhopane): Ts/(Ts+Tm)] ratios. The Bahloul OM is represented by an open marine to estuarine algal facies with a specific bacterial contribution as revealed by the relative abundance of the ααα‐20R C27 (33–44%), C28 (22–28%) and C29 (34–41%) steranes and by the total terpanes/total steranes ratio (1.2–5.33). These results attested that the Bahloul OM richness was controlled both by an oxygen minimum zone induced by high productivity and restricted circulation in narrow half graben structures and around diapirs of the Triassic salt.
Phylogenetic relationships of Microdontinae (Diptera: Syrphidae) based on molecular and morphological characters
Authors: REEMER MENNO , STÅHLS GUNILLA 
Published: June 2013

AbstractThe intrasubfamilial classification of Microdontinae Rondani (Diptera: Syrphidae) has been a challenge: until recently more than 300 out of more than 400 valid species names were classified in Microdon Meigen. We present phylogenetic analyses of molecular and morphological characters (both separate and combined) of Microdontinae. The morphological dataset contains 174 characters, scored for 189 taxa (9 outgroup), representing all 43 presently recognized genera and several subgenera and species groups. The molecular dataset, representing 90 ingroup species of 28 genera, comprises sequences of five partitions in total from the mitochondrial gene COI and the nuclear ribosomal genes 18S and 28S. We test the sister‐group relationship of Spheginobaccha with the other Microdontinae, attempt to elucidate phylogenetic relationships within the Microdontinae and discuss uncertainties in the classification of Microdontinae. Trees based on molecular characters alone are poorly resolved, but combined data are better resolved. Support for many deeper nodes is low, and placement of such nodes differs between parsimony and Bayesian analyses. However, Spheginobaccha is recovered as highly supported sister group in both. Both analyses agree on the early branching of Mixogaster, Schizoceratomyia, Afromicrodon and Paramicrodon. The taxonomical rank in relation to the other Syrphidae is discussed briefly. An additional analysis based on morphological characters only, including all 189 taxa, used implied weighting. A range of weighting strengths (k‐values) is applied, chosen such that values of character fit of the resulting trees are divided into regular intervals. Results of this analysis are used for discussing the phylogenetic relationships of genera unrepresented in the molecular dataset.
Association of IL‐10 and CCL5 single nucleotide polymorphisms with tuberculosis in the Sudanese population
Authors: Mhmoud Najwa , Fahal Ahmed , Wendy van de Sande W. J. 
Published: June 2013

AbstractObjectiveTo investigate the genetic determinants for developing tuberculosis in Sudan.MethodsCase study of 232 patients with tuberculosis and 206 healthy matched controls from Sudan. In the study population, three single nucleotide polymorphisms (SNPs) in the promoter regions of CCL5 and two in the promoter region of IL‐10 were genotyped using polymerase chain reaction and restriction fragment length polymorphism (PCR‐RFLP). These five SNPs influence the expression of these genes.ResultsThere were significant differences in allele distribution for CCL5 ‐28 C/G (rs 2280788) and IL‐10 ‐592 A/C (rs1800872) in patients with tuberculosis compared with healthy controls.ConclusionThis indicates that the genotypes obtained for CCL5 and IL‐10 are associated with an increased risk of developing active TB.
Preload‐adjusted left ventricular dP/dtmax: a sensitive, continuous, load‐independent contractility index
Authors: Blaudszun Grégoire , Licker Marc J. , Morel Denis R. 
Published: June 2013

New findings
What is the central question of this study?The preload‐adjusted maximal change in pressure over time (PAdP/dtmax) accurately reflects systolic performance in varying conditions of inotropy and afterload. The objective of this study was to address whether PAdP/dtmax is a valid indicator of left ventricular function in the setting of large variations in preload.
What is the main finding and its importance?In a model of acute preload reduction, PAdP/dtmax properly reflected left ventricular systolic function. Given its simplicity, this real‐time index derived from single beat analysis should be tested further in clinical settings.
The classical indicators of left ventricular (LV) performances have been derived from pressure–volume (PV) and stroke work–volume plots obtained during various loading or pharmacological interventions. More recently, the preload‐adjusted maximal change in pressure over time (PAdP/dtmax), derived from single beat PV analysis, has been shown to reflect the LV systolic performance accurately in varying conditions of inotropy and afterload. The objective of this study was to address whether PAdP/dtmax is a valid indicator of LV function in the setting of large preload variations, compared with the classical dP/dtmax–end‐diastolic volume (EDV) and stroke work–EDV (preload recruitable stroke work) relationships. Nine anaesthetized and mechanically ventilated rats were instrumented with a ventricular conductance catheter. Stepwise preload reduction was achieved by repeated blood withdrawals (up to a total of 5 ml). Steady‐state and dynamic PV loops were recorded during brief occlusion of the inferior vena cava, and LV function parameters were derived from these recordings. Our results demonstrate that PAdP/dtmax behaved in a similar manner to preload recruitable stroke work, reflecting well‐maintained LV contractility during controlled haemorrhage until mean arterial pressure decreased below 40 mmHg. In contrast, dP/dtmax–EDV increased significantly and exhibited a curvilinear response that was associated with a large inter‐ and intra‐animal variability. In a model of acute preload reduction, PAdP/dtmax was found to be the best indicator of systolic LV function. Given its simplicity, this real‐time index derived from single beat analysis should be tested further in clinical settings.
Direct Assessment of Viral Diversity in Soils by Random PCR Amplification of Polymorphic DNA
Authors: Srinivasiah Sharath , Lovett Jacqueline , Polson Shawn , Bhavsar Jaysheel , Ghosh Dhritiman , Roy Krishnakali , Fuhrmann Jeffry J. , Radosevich Mark , Wommack K. Eric 
Published: June 2013

ABSTRACT
Viruses are the most abundant and diverse biological entities within soils, yet their ecological impact is largely unknown. Defining how soil viral communities change with perturbation or across environments will contribute to understanding the larger ecological significance of soil viruses. A new approach to examining the composition of soil viral communities based on random PCR amplification of polymorphic DNA (RAPD-PCR) was developed. A key methodological improvement was the use of viral metagenomic sequence data for the design of RAPD-PCR primers. This metagenomically informed approach to primer design enabled the optimization of RAPD-PCR sensitivity for examining changes in soil viral communities. Initial application of RAPD-PCR viral fingerprinting to soil viral communities demonstrated that the composition of autochthonous soil viral assemblages noticeably changed over a distance of meters along a transect of Antarctic soils and across soils subjected to different land uses. For Antarctic soils, viral assemblages segregated upslope from the edge of dry valley lakes. In the case of temperate soils at the Kellogg Biological Station, viral communities clustered according to land use treatment. In both environments, soil viral communities changed along with environmental factors known to shape the composition of bacterial host communities. Overall, this work demonstrates that RAPD-PCR fingerprinting is an inexpensive, high-throughput means for addressing first-order questions of viral community dynamics within environmental samples and thus fills a methodological gap between narrow single-gene approaches and comprehensive shotgun metagenomic sequencing for the analysis of viral community diversity.
Bacterially Induced Weathering of Ultramafic Rock and Its Implications for Phytoextraction
Authors: Becerra-Castro Cristina , Kidd Petra , Kuffner Melanie , Prieto-Fernández Ángeles , Hann Stephan , Monterroso Carmela , Sessitsch Angela , Wenzel Walter , Puschenreiter Markus 
Published: June 2013

ABSTRACT

The bioavailability of metals in soil is often cited as a limiting factor of phytoextraction (or phytomining). Bacterial metabolites, such as organic acids, siderophores, or biosurfactants, have been shown to mobilize metals, and their use to improve metal extraction has been proposed. In this study, the weathering capacities of, and Ni mobilization by, bacterial strains were evaluated. Minimal medium containing ground ultramafic rock was inoculated with either of two
Arthrobacter
strains: LA44 (indole acetic acid [IAA] producer) or SBA82 (siderophore producer, PO
4
solubilizer, and IAA producer). Trace elements and organic compounds were determined in aliquots taken at different time intervals after inoculation. Trace metal fractionation was carried out on the remaining rock at the end of the experiment. The results suggest that the strains act upon different mineral phases. LA44 is a more efficient Ni mobilizer, apparently solubilizing Ni associated with Mn oxides, and this appeared to be related to oxalate production. SBA82 also leads to release of Ni and Mn, albeit to a much lower extent. In this case, the concurrent mobilization of Fe and Si indicates preferential weathering of Fe oxides and serpentine minerals, possibly related to the siderophore production capacity of the strain. The same bacterial strains were tested in a soil-plant system: the Ni hyperaccumulator
Alyssum serpyllifolium
subsp.
malacitanum
was grown in ultramafic soil in a rhizobox system and inoculated with each bacterial strain. At harvest, biomass production and shoot Ni concentrations were higher in plants from inoculated pots than from noninoculated pots. Ni yield was significantly enhanced in plants inoculated with LA44. These results suggest that Ni-mobilizing inoculants could be useful for improving Ni uptake by hyperaccumulator plants.
Roles of the Yap1 Transcription Factor and Antioxidants in Saccharomyces cerevisiae's Tolerance to Furfural and 5-Hydroxymethylfurfural, Which Function as Thiol-Reactive Electrophiles Generating Oxidative Stress
Authors: Kim Daehee , Hahn Ji-Sook 
Published: June 2013

ABSTRACT

Development of the tolerance of
Saccharomyces cerevisiae
strains to furfural and 5-hydroxymethylfurfural (HMF) is an important issue for cellulosic ethanol production. Although furfural and HMF are known to induce oxidative stress, the underlying mechanisms are largely unknown. In this study, we show that both furfural and HMF act as thiol-reactive electrophiles, thus directly activating the Yap1 transcription factor via the H
2
O
2
-independent pathway, depleting cellular glutathione (GSH) levels, and accumulating reactive oxygen species in
Saccharomyces cerevisiae
. However, furfural showed higher reactivity than did HMF toward GSH
in vitro
and
in vivo
. In line with such toxic mechanisms, overexpression of
YAP1

C620F

, a constitutively active mutant of
YAP1
, and Yap1 target genes encoding catalases (
CTA1
and
CTT1
) increased tolerance to furfural and HMF. However, increasing GSH levels by overexpression of genes for GSH biosynthesis (
GSH1
and
GLR1
) or by the exogenous addition of GSH to the culture medium enhanced tolerance to furfural but not to HMF.
Facility-Specific “House” Microbiome Drives Microbial Landscapes of Artisan Cheesemaking Plants
Authors: Bokulich Nicholas A. , Mills David A. 
Published: June 2013

ABSTRACT

Cheese fermentations involve the growth of complex microbial consortia, which often originate in the processing environment and drive the development of regional product qualities. However, the microbial milieus of cheesemaking facilities are largely unexplored and the true nature of the fermentation-facility relationship remains nebulous. Thus, a high-throughput sequencing approach was employed to investigate the microbial ecosystems of two artisanal cheesemaking plants, with the goal of elucidating how the processing environment influences microbial community assemblages. Results demonstrate that fermentation-associated microbes dominated most surfaces, primarily
Debaryomyces
and
Lactococcus
, indicating that establishment of these organisms on processing surfaces may play an important role in microbial transfer, beneficially directing the course of sequential fermentations. Environmental organisms detected in processing environments dominated the surface microbiota of washed-rind cheeses maturing in both facilities, demonstrating the importance of the processing environment for populating cheese microbial communities, even in inoculated cheeses. Spatial diversification within both facilities reflects the functional adaptations of microbial communities inhabiting different surfaces and the existence of facility-specific “house” microbiota, which may play a role in shaping site-specific product characteristics.
Adjustment of Trehalose Metabolism in Wine Saccharomyces cerevisiae Strains To Modify Ethanol Yields
Authors: Rossouw D. , Heyns E. H. , Setati M. E. , Bosch S. , Bauer F. F. 
Published: June 2013

ABSTRACTThe ability ofSaccharomyces cerevisiaeto efficiently produce high levels of ethanol through glycolysis has been the focus of much scientific and industrial activity. Despite the accumulated knowledge regarding glycolysis, the modification of flux through this pathway to modify ethanol yields has proved difficult. Here, we report on the systematic screening of 66 strains with deletion mutations of genes encoding enzymes involved in central carbohydrate metabolism for altered ethanol yields. Five of these strains showing the most prominent changes in carbon flux were selected for further investigation. The genes were representative of trehalose biosynthesis (TPS1, encoding trehalose-6-phosphate synthase), central glycolysis (TDH3, encoding glyceraldehyde-3-phosphate dehydrogenase), the oxidative pentose phosphate pathway (ZWF1, encoding glucose-6-phosphate dehydrogenase), and the tricarboxylic acid (TCA) cycle (ACO1andACO2, encoding aconitase isoforms 1 and 2). Two strains exhibited lower ethanol yields than the wild type (tps1Δ andtdh3Δ), while the remaining three showed higher ethanol yields. To validate these findings in an industrial yeast strain, theTPS1gene was selected as a good candidate for genetic modification to alter flux to ethanol during alcoholic fermentation in wine. Using low-strength promoters active at different stages of fermentation, the expression of theTPS1gene was slightly upregulated, resulting in a decrease in ethanol production and an increase in trehalose biosynthesis during fermentation. Thus, the mutant screening approach was successful in terms of identifying target genes for genetic modification in commercial yeast strains with the aim of producing lower-ethanol wines.
Application of Denaturing High-Performance Liquid Chromatography for Monitoring Sulfate-Reducing Bacteria in Oil Fields
Authors: Priha Outi , Nyyssönen Mari , Bomberg Malin , Laitila Arja , Simell Jaakko , Kapanen Anu , Juvonen Riikka 
Published: June 2013

ABSTRACT

Sulfate-reducing bacteria (SRB) participate in microbially induced corrosion (MIC) of equipment and H
2
S-driven reservoir souring in oil field sites. Successful management of industrial processes requires methods that allow robust monitoring of microbial communities. This study investigated the applicability of denaturing high-performance liquid chromatography (DHPLC) targeting the dissimilatory sulfite reductase ß-subunit (
dsrB
) gene for monitoring SRB communities in oil field samples from the North Sea, the United States, and Brazil. Fifteen of the 28 screened samples gave a positive result in real-time PCR assays, containing 9 × 10
1
to 6 × 10
5
dsrB
gene copies ml
−1
. DHPLC and denaturing gradient gel electrophoresis (DGGE) community profiles of the PCR-positive samples shared an overall similarity; both methods revealed the same samples to have the lowest and highest diversity. The SRB communities were diverse, and different
dsrB
compositions were detected at different geographical locations. The identified
dsrB
gene sequences belonged to several phylogenetic groups, such as
Desulfovibrio
,
Desulfococcus
,
Desulfomicrobium
,
Desulfobulbus
,
Desulfotignum
,
Desulfonatronovibrio
, and
Desulfonauticus
. DHPLC showed an advantage over DGGE in that the community profiles were very reproducible from run to run, and the resolved gene fragments could be collected using an automated fraction collector and sequenced without a further purification step. DGGE, on the other hand, included casting of gradient gels, and several rounds of rerunning, excising, and reamplification of bands were needed for successful sequencing. In summary, DHPLC proved to be a suitable tool for routine monitoring of the diversity of SRB communities in oil field samples.
Substantial within-Animal Diversity of Salmonella Isolates from Lymph Nodes, Feces, and Hides of Cattle at Slaughter
Authors: Gragg Sara E. , Loneragan Guy H. , Nightingale Kendra K. , Brichta-Harhay Dayna M. , Ruiz Henry , Elder Jacob R. , Garcia Lyda G. , Miller Markus F. , Echeverry Alejandro , Ramírez Porras Rosa G. , Brashears Mindy M. 
Published: June 2013

ABSTRACT

Lymph nodes (mandibular, mesenteric, mediastinal, and subiliac;
n
= 68) and fecal (
n
= 68) and hide (
n
= 35) samples were collected from beef carcasses harvested in an abattoir in Mexico. Samples were analyzed for
Salmonella
, and presumptive colonies were subjected to latex agglutination. Of the isolates recovered, a subset of 91 was characterized by serotyping, pulsed-field gel electrophoresis (PFGE), and antimicrobial susceptibility phenotyping.
Salmonella
was isolated from 100% (hide), 94.1% (feces), 91.2% (mesenteric), 76.5% (subiliac), 55.9% (mandibular), and 7.4% (mediastinal) of samples. From the 87 typeable isolates, eight
Salmonella enterica
serotypes, including Kentucky (32.2%), Anatum (29.9%), Reading (17.2%), Meleagridis (12.6%), Cerro (4.6%), Muenster (1.1%), Give (1.1%), and Mbandaka (1.1%), were identified.
S
. Meleagridis was more likely (
P
= 0.03) to be recovered from lymph nodes than from feces or hides, whereas
S
. Kentucky was more likely (
P
= 0.02) to be recovered from feces and hides than from lymph nodes. The majority (59.3%) of the
Salmonella
isolates were pansusceptible; however, multidrug resistance was observed in 13.2% of isolates. Typing by PFGE revealed that
Salmonella
strains generally clustered by serotype, but some serotypes (Anatum, Kentucky, Meleagridis, and Reading) were comprised of multiple PFGE subtypes. Indistinguishable PFGE subtypes and, therefore, serotypes were isolated from multiple sample types, and multiple PFGE subtypes were commonly observed within an animal. Given the overrepresentation of some serotypes within lymph nodes, we hypothesize that certain
Salmonella
strains may be better at entering the bovine host than other
Salmonella
strains or that some may be better adapted for survival within lymph nodes. Our data provide insight into the ecology of
Salmonella
within cohorts of cattle and offer direction for intervention opportunities.