bluuebunny/crossref_metadata_2025 huggingface dataset:
Left Atrial Function in Cats with Left‐Sided Cardiac Disease and Pleural Effusion or Pulmonary Edema
Authors: Johns S.M. , Nelson O.L. , Gay J.M.
Published: July 2012

Background

Congestive heart failure (CHF) in cats with left‐sided heart disease is sometimes manifest as pleural effusion, in other cases as pulmonary edema.

Hypothesis

Those cats with pleural effusion have more severe left atrial (LA) dysfunction than cats with pulmonary edema.

Animals

30 healthy cats, 22 cats with pleural effusion, and 12 cats with pulmonary edema. All cats were client owned.

Methods

Retrospective study. Measurements ofLAsize and function were made using commercial software on archived echocardiograms. Cases were identified through searches of medical records and of archived echocardiograms for cats with these conditions.

Results

There was no difference (P = .3) inLAsize between cats with pleural effusion and cats with pulmonary edema. Cats with pleural effusion had poorer (P = .04)LAactive emptying and increased (P = .006) right ventricular (RV) diameter when compared with cats with pulmonary edema and healthy cats. Cats that exhibitedLAactive emptying of <7.9%, total emptying of <13.6% (diameter) or <19.4% (area), orRVdiameter of >3.6 mm were significantly (P < .001) more likely to manifest pleural effusion.

Conclusions and Clinical Importance

PoorerLAfunction and increasedRVdimensions are associated with pleural effusion in cats with left‐sided heart disease.
The role of exchange reactions in oxygen isotope fractionation during CAI and chondrule formation
Authors: NAGAHARA Hiroko , OZAWA Kazuhito
Published: July 2012

Abstract— The role of oxygen isotope exchange during evaporation and condensation of silicate melt is quantitatively evaluated. Silicate dusts instantaneously heated above liquidus temperature are assumed to cool in gas and experience partial evaporation and subsequent recondensation. The results show that isotopic exchange effectively suppresses mass‐dependent O‐isotope fractionation even if the degree of evaporation is large, which is the fundamental difference from the case without isotopic exchange. The final composition of silicate melt strongly depends on the initial abundance of oxygen in the ambient gas relative to that in silicate dust, but not on the cooling rate of the system. The model was applied to O‐isotope evolution of silicate melts in isotopically distinct gas of the protoplanetary disk. It was found that deviation from a straight mixing line toward the δ18O‐rich side on the three‐oxygen isotope diagram is inevitable when mass‐dependent fractionation and isotopic exchange take place simultaneously; the degree of deviation depends on the abundance of oxygen in an ambient gas and isotopic exchange efficiency. The model is applied to explain O‐isotopic compositions of igneous CAIs and chondrules.
Optimization of amorphous TiOx-based thin film transistors fabricated by dc magnetron sputtering
Authors: Choi Kwang-Hyuk , Kim Han-Ki
Published: July 2012

Amorphous TiOx semiconductor-based thin-film transistors (TFTs) have been optimized with respect to key parameters, such as rapid thermal annealing (RTA) temperature, ambient gas type, and direct current power during sputtering of the TiOx semiconductor layer. It was found that the performance of TiOx semiconductor-based TFTs including field-effect mobility (μFE), sub-threshold swing (SS), on current (Ion), off current (Ioff), on-to-off current ratio (Ion/off), and interface charge traps (Dit) were significantly influenced by such key parameters. Conductivity of the amorphous TiOx semiconductor layer and Ion values were critically dependent on the RTA temperature, whereas switching properties and Ioff values of the TiOx TFTs were influenced by the ambient gas type during the RTA process. At an RTA temperature of 500  °C under N2 flow, we achieved amorphous TiOx semiconductor based TFTs with a μFE of 0.29 cm2/V s, an SS of 2.08 V/decade, and a Dit of 7.32 × 1012 eV−1 cm−2.
Characterization of vertical Si nanowire p-n diodes fabricated by metal-assisted etching and AAO templates
Authors: Kwon Namyong , Kim Namkyu , Sung Sihyun , Kang Byungyun , Chung Ilsub
Published: July 2012

Vertical Si nanowire p-n diodes were fabricated utilizing both anodic aluminum oxide (AAO) templates and metal-assisted etching. AAO templates with different diameters were fabricated on a p(2.5 μm)-n junction substrate using a two-step anodization and pore widening process. The average diameters of the AAO templates were 36.3, 57.4, and 78.1 nm. Vertical Si nanowire p-n diodes were then fabricated by metal-assisted etching, with average diameters of 37.4, 53.3, and 62.8 nm. The lengths of the vertical Si nanowires were controlled by varying the etching times. For the fully etched (3 μm) Si nanowire, the p-n diodes with smaller diameters yielded higher current densities than those with larger diameters, due to mobility enhancement. However, such dependency was not observed for the partially etched (500 nm) Si nanowire p-n diodes. It was concluded that the recombination current is too dominant in the depletion region to improve mobility in one-dimensional transport.
F
detection by crosscorrelation with a comb function
Authors: Martin Ph.
Published: July 2012

Thanks to the development of fast digital hardware performing real-time spectral analysis on speech data, dependable pitch analysis can be obtained even in the presence of a large amount of noise through the use of new F0 measurement techniques. A new method is presented here, based on the crosscorrelation between the power spectrum of suitably windowed speech data F(ω) and a comb function C(ωp,ω): I(ωp) =  ∫ 0∝ F(ω)C(ωp,ω)dω. The comb function detects the possible harmonic structure in the spectrum, so that when C(ωp,ω) is carefully chosen, the crosscorrelation function I(ωp) shows maxima at values of ωp corresponding to the fundamental frequency of voiced speech. The appropriate design of the comb (with an amplitude varying with ω), leads to more appropriate and economical digital hardware compared to the general crosscorrelation approach.
Overexpression of
ShCYP51B
and
ShatrD
in Sclerotinia homoeocarpa Isolates Exhibiting Practical Field Resistance to a Demethylation Inhibitor Fungicide
Authors: Hulvey Jon , Popko James T. , Sang Hyunkyu , Berg Andrew , Jung Geunhwa
Published: July 2012

We investigated genetic factors that govern the reduced propiconazole sensitivity of
Sclerotinia homoeocarpa
field isolates collected during a 2-year field efficacy study on dollar spot disease of turf in five New England sites. These isolates displayed a >50-fold range of
in vitro
sensitivity to a sterol demethylation inhibitor (DMI) fungicide, propiconazole, making them ideal for investigations of genetic mechanisms of reduced DMI sensitivity. The
CYP51
gene homolog in
S. homoeocarpa
(
ShCYP51B
), encoding the enzyme target of DMIs, is likely a minor genetic factor for reduced propiconazole sensitivity, since there were no differences in constitutive relative expression (RE) values and only 2-fold-higher induced RE values for insensitive than for sensitive isolate groups. Next, we mined RNA-Seq transcriptome data for additional genetic factors and found evidence for the overexpression of a homolog of
Botrytis cinerea atrD
(
BcatrD
),
ShatrD
, a known efflux transporter of DMI fungicides. The
ShatrD
gene showed much higher constitutive and induced RE values for insensitive isolates. Several polymorphisms were found upstream of
ShatrD
but were not definitively linked to overexpression. The screening of constitutive RE values of
ShCYP51B
and
ShatrD
in isolates from two golf courses that exhibited practical field resistance to propiconazole uncovered evidence for significant population-specific overexpression of both genes. However, linear regression demonstrated that the RE of
ShatrD
displays a more significant relationship with propiconazole sensitivity than that of
ShCYP51B
. In summary, our results suggest that efflux is a major determinant of the reduced DMI sensitivity of
S. homoeocarpa
genotypes in New England, which may have implications for the emergence of practical field resistance in this important turfgrass pathogen.
Characterization of a Leuconostoc Bacteriophage Infecting Flavor Producers of Cheese Starter Cultures
Authors: Kleppen Hans Petter , Nes Ingolf F. , Holo Helge
Published: July 2012

Dairy siphovirus φLmd1, which infects starter culture isolate
Leuconostoc mesenteroides
subsp.
dextranicum
A1, showed resistance to pasteurization and was able to grow on 3 of the 4 commercial starter cultures tested. Its 26,201-bp genome was similar to that of
Leuconostoc
phage of vegetable origin but not to those of dairy phages infecting
Lactococcus
.
Identification of Soil Bacteria Susceptible to TiO
2
and ZnO Nanoparticles
Authors: Ge Yuan , Schimel Joshua P. , Holden Patricia A.
Published: July 2012

Because soil is expected to be a major sink for engineered nanoparticles (ENPs) released to the environment, the effects of ENPs on soil processes and the organisms that carry them out should be understood. DNA-based fingerprinting analyses have shown that ENPs alter soil bacterial communities, but specific taxon changes remain unknown. We used bar-coded pyrosequencing to explore the responses of diverse bacterial taxa to two widely used ENPs, nano-TiO
2
and nano-ZnO, at various doses (0, 0.5, 1.0, and 2.0 mg g
−1
soil for TiO
2
; 0.05, 0.1, and 0.5 mg g
−1
soil for ZnO) in incubated soil microcosms. These ENPs significantly altered the bacterial communities in a dose-dependent manner, with some taxa increasing as a proportion of the community, but more taxa decreasing, indicating that effects mostly reduced diversity. Some of the declining taxa are known to be associated with nitrogen fixation (
Rhizobiales
,
Bradyrhizobiaceae
, and
Bradyrhizobium
) and methane oxidation (
Methylobacteriaceae
), while some positively impacted taxa are known to be associated with the decomposition of recalcitrant organic pollutants (
Sphingomonadaceae
) and biopolymers including protein (
Streptomycetaceae
and
Streptomyces
), indicating potential consequences to ecosystem-scale processes. The latter was suggested by a positive correlation between protease activity and the relative abundance of
Streptomycetaceae
(
R
= 0.49,
P
= 0.000) and
Streptomyces
(
R
= 0.47,
P
= 0.000). Our results demonstrate that some metal oxide nanoparticles could affect soil bacterial communities and associated processes through effects on susceptible, narrow-function bacterial taxa.
Proximity-Dependent Inhibition of Growth of Mannheimia haemolytica by Pasteurella multocida
Authors: Bavananthasivam Jegarubee , Dassanayake Rohana P. , Kugadas Abirami , Shanthalingam Sudarvili , Call Douglas R. , Knowles Donald P. , Srikumaran Subramaniam
Published: July 2012

Mannheimia haemolytica
,
Pasteurella multocida
, and
Bibersteinia trehalosi
have been identified in the lungs of pneumonic bighorn sheep (BHS;
Ovis canadensis
). Of these pathogens,
M. haemolytica
has been shown to consistently cause fatal pneumonia in BHS under experimental conditions. However,
M. haemolytica
has been isolated by culture less frequently than the other bacteria. We hypothesized that the growth of
M. haemolytica
is inhibited by other bacteria in the lungs of BHS. The objective of this study was to determine whether
P. multocida
inhibits the growth of
M. haemolytica
. Although in monoculture both bacteria exhibited similar growth characteristics, in coculture with
P. multocida
there was a clear inhibition of growth of
M. haemolytica
. The inhibition was detected at mid-log phase and continued through the stationary phase. When cultured in the same medium, the growth of
M. haemolytica
was inhibited when both bacteria were separated by a membrane that allowed contact (pore size, 8.0 μm) but not when they were separated by a membrane that limited contact (pore size, 0.4 μm). Lytic bacteriophages or bactericidal compounds could not be detected in the culture supernatant fluid from monocultures of
P. multocida
or from
P. multocida
-
M. haemolytica
cocultures. These results indicate that
P. multocida
inhibits the growth of
M. haemolytica
by a contact- or proximity-dependent mechanism. If the inhibition of growth of
M. haemolytica
by
P. multocida
occurs
in vivo
as well, it could explain the inconsistent isolation of
M. haemolytica
from the lungs of pneumonic BHS.
Characterization of Staphylococcus aureus Strains Associated with Food Poisoning in Shenzhen, China
Authors: Yan Xiaomei , Wang Bing , Tao Xiaoxia , Hu Qinghua , Cui Zhigang , Zhang Jianzhong , Lin Yiman , You Yuanhai , Shi Xiaolu , Grundmann Hajo
Published: July 2012

To characterize isolates of
Staphylococcus aureus
that were associated with staphylococcal food poisoning between 2006 and 2009 in Shenzhen, Southern China, a total of 52
Staphylococcus aureus
isolates from 11 outbreaks were analyzed by using multilocus sequence typing (MLST),
spa
typing, and pulsed-field gel electrophoresis (PFGE). PCR analysis was used to analyze the staphylococcal enterotoxin (SE) genes
sea
to
sei
, and antimicrobial susceptibility testing was also performed. ST6 was the most dominant sequence type (ST), constituting 63.5% (34/52) of all of the isolates in 7 outbreaks. The next most common ST was ST943, which constituted 23.1% (12/52) of the isolates that were collected from 3 outbreaks. t701, t091, and t2360 were the most predominant
spa
types, constituting 67.3% (35/52) of the isolates that were collected from 11 outbreaks. Three PFGE types, (types A, B, and C) were the most frequently observed types, constituting 84.6% (44/52) of all of the isolates. The enterotoxin gene that we detected most frequently was
sea
(45/52; 86.5%). Four SE gene profiles were observed, including
sea
(
n
= 45),
sec-seh
(
n
= 3),
seb
(
n
= 2), and
seg-sei
(
n
= 2). With respect to antibiotic resistance, penicillin resistance was the most common (96.2%; 50/52), followed by resistance to tetracycline (28.8%; 15/52). Approximately 30.8% (16/52) of the isolates were resistant to at least two antibiotics, and 7.7% (4/52) of the isolates were resistant to three or more drugs. The two predominant
S. aureus
lineages, (i) PFGE types A and B with ST6 and (ii) PFGE type C with ST943, were identified in the outbreaks.
Proteomic Analysis of Survival of Rhodococcus jostii RHA1 during Carbon Starvation
Authors: Patrauchan Marianna A. , Miyazawa Daisuke , LeBlanc Justin C. , Aiga Carol , Florizone Christine , Dosanjh Manisha , Davies Julian , Eltis Lindsay D. , Mohn William W.
Published: July 2012

Rhodococcus jostii
RHA1, a catabolically diverse soil actinomycete, is highly resistant to long-term nutrient starvation. After 2 years of carbon starvation, 10% of the bacterial culture remained viable. To study the molecular basis of such resistance, we monitored the abundance of about 1,600 cytosolic proteins during a 2-week period of carbon source (benzoate) starvation. Hierarchical cluster analysis elucidated 17 major protein clusters and showed that most changes occurred during transition to stationary phase. We identified 196 proteins. A decrease in benzoate catabolic enzymes correlated with benzoate depletion, as did induction of catabolism of alternative substrates, both endogenous (lipids, carbohydrates, and proteins) and exogenous. Thus, we detected a transient 5-fold abundance increase for phthalate, phthalate ester, biphenyl, and ethyl benzene catabolic enzymes, which coincided with at least 4-fold increases in phthalate and biphenyl catabolic activities. Stationary-phase cells demonstrated an ∼250-fold increase in carbon monoxide dehydrogenase (CODH) concurrent with a 130-fold increase in CODH activity, suggesting a switch to CO or CO
2
utilization. We observed two phases of stress response: an initial response occurred during the transition to stationary phase, and a second response occurred after the cells had attained stationary phase. Although SigG synthesis was induced during starvation, a Δ
sigG
deletion mutant showed only minor changes in cell survival. Stationary-phase cells underwent reductive cell division. The extreme capacity of RHA1 to survive starvation does not appear to involve novel mechanisms; rather, it seems to be due to the coordinated combination of earlier-described mechanisms.
Toxigenic Clostridium difficile PCR Ribotypes from Wastewater Treatment Plants in Southern Switzerland
Authors: Romano Vincenza , Pasquale Vincenzo , Krovacek Karel , Mauri Federica , Demarta Antonella , Dumontet Stefano
Published: July 2012

The occurrence of
Clostridium difficile
in nine wastewater treatment plants in the Ticino Canton (southern Switzerland) was investigated. The samples were collected from raw sewage influents and from treated effluents. Forty-seven out of 55 characterized
C. difficile
strains belonged to 13 different reference PCR ribotypes (009, 010, 014, 015, 039, 052, 053, 066, 070, 078, 101, 106, and 117), whereas 8 strains did not match any of those available in our libraries. The most frequently isolated ribotype (40%) was 078, isolated from six wastewater treatment plants, whereas ribotype 066, a toxigenic emerging ribotype isolated from patients admitted to hospitals in Europe and Switzerland, was isolated from the outgoing effluent of one plant. The majority of the isolates (85%) were toxigenic. Forty-nine percent of them produced toxin A, toxin B, and the binary toxin (toxigenic profile A
+
B
+
CDT
+
), whereas 51% showed the profile A
+
B
+
CDT
−
. Interestingly, eight ribotypes (010, 014, 015, 039, 066, 078, 101, and 106) were among the riboprofiles isolated from symptomatic patients admitted to the hospitals of the Ticino Canton in 2010. Despite the limitation of sampling, this study highlights that toxigenic ribotypes of
C. difficile
involved in human infections may occur in both incoming and outgoing biological wastewater treatment plants. Such a finding raises concern about the possible contamination of water bodies that receive wastewater treatment plant effluents and about the safe reuse of treated wastewater.
Identification of a
p
-Coumarate Degradation Regulon in Rhodopseudomonas palustris by Xpression, an Integrated Tool for Prokaryotic RNA-Seq Data Processing
Authors: Phattarasukol Somsak , Radey Matthew C. , Lappala Colin R. , Oda Yasuhiro , Hirakawa Hidetada , Brittnacher Mitchell J. , Harwood Caroline S.
Published: July 2012

High-throughput sequencing of cDNA prepared from RNA, an approach known as RNA-seq, is coming into increasing use as a method for transcriptome analysis. Despite its many advantages, widespread adoption of the technique has been hampered by a lack of easy-to-use, integrated, open-source tools for analyzing the nucleotide sequence data that are generated. Here we describe Xpression, an integrated tool for processing prokaryotic RNA-seq data. The tool is easy to use and is fully automated. It performs all essential processing tasks, including nucleotide sequence extraction, alignment, quantification, normalization, and visualization. Importantly, Xpression processes multiplexed and strand-specific nucleotide sequence data. It extracts and trims specific sequences from files and separately quantifies sense and antisense reads in the final results. Outputs from the tool can also be conveniently used in downstream analysis. In this paper, we show the utility of Xpression to process strand-specific RNA-seq data to identify genes regulated by CouR, a transcription factor that controls
p
-coumarate degradation by the bacterium
Rhodopseudomonas palustris
.
Changes in Bowel Microbiota Induced by Feeding Weanlings Resistant Starch Stimulate Transcriptomic and Physiological Responses
Authors: Young Wayne , Roy Nicole C. , Lee Julian , Lawley Blair , Otter Don , Henderson Gemma , McCann Mark J. , Tannock Gerald W.
Published: July 2012

The ability to predictably engineer the composition of bowel microbial communities (microbiota) using dietary components is important because of the reported associations of altered microbiota composition with medical conditions. In a synecological study, weanling conventional Sprague-Dawley rats (21 days old) were fed a basal diet (BD) or a diet supplemented with resistant starch (RS) at 5%, 2.5%, or 1.25% for 28 days. Pyrosequencing of 16S rRNA genes and temporal temperature gradient electrophoresis (TTGE) profiles in the colonic digesta showed that rats fed RS had altered microbiota compositions due to blooms of
Bacteroidetes
and
Actinobacteria
. The altered microbiota was associated with changes in colonic short-chain fatty acid (SCFA) concentrations, colonic-tissue gene expression (
Gsta2
and
Ela1
), and host physiology (serum metabolite profiles and colonic goblet cell numbers). Comparisons between germ-free and conventional rats showed that transcriptional and serum metabolite differences were mediated by the microbiota and were not the direct result of diet composition. Altered transcriptomic and physiological responses may reflect the young host's attempts to maintain homeostasis as a consequence of exposure to a new collection of bacteria and their associated biochemistry.
Bioremediation and Tolerance of Humans to Heavy Metals through Microbial Processes: a Potential Role for Probiotics?
Authors: Monachese Marc , Burton Jeremy P. , Reid Gregor
Published: July 2012

The food and water we consume are often contaminated with a range of chemicals and heavy metals, such as lead, cadmium, arsenic, chromium, and mercury, that are associated with numerous diseases. Although heavy-metal exposure and contamination are not a recent phenomenon, the concentration of metals and the exposure to populations remain major issues despite efforts at remediation. The ability to prevent and manage this problem is still a subject of much debate, with many technologies ineffective and others too expensive for practical large-scale use, especially for developing nations where major pollution occurs. This has led researchers to seek alternative solutions for decontaminating environmental sites and humans themselves. A number of environmental microorganisms have long been known for their ability to bind metals, but less well appreciated are human gastrointestinal bacteria. Species such asLactobacillus, present in the human mouth, gut, and vagina and in fermented foods, have the ability to bind and detoxify some of these substances. This review examines the current understanding of detoxication mechanisms of lactobacilli and how, in the future, humans and animals might benefit from these organisms in remediating environmental contamination of food.
Intestinal Origin of Sourdough
Lactobacillus reuteri
Isolates as Revealed by Phylogenetic, Genetic, and Physiological Analysis
Authors: Su Marcia Shu-Wei , Oh Phaik Lyn , Walter Jens , Gänzle Michael G.
Published: July 2012

Lactobacillus reuteri
is both a gut symbiont and a stable member of sourdough microbiota. This study employed multilocus sequence analysis and an analysis of host-specific physiological and genetic traits to assign five sourdough isolates to rodent- or human-specific lineages. Comparative genome hybridization revealed that the model sourdough isolate LTH2584 had a genome content very similar to that of the model rodent isolate 100-23. These results demonstrate that sourdough isolates of
L. reuteri
are of intestinal origin.
Molecular Characterization of Commensal Escherichia coli Adapted to Different Compartments of the Porcine Gastrointestinal Tract
Authors: Abraham Sam , Gordon David M. , Chin James , Brouwers Huub J. M. , Njuguna Peter , Groves Mitchell D. , Zhang Ren , Chapman Toni A.
Published: July 2012

The role of
Escherichia coli
as a pathogen has been the focus of considerable study, while much less is known about it as a commensal and how it adapts to and colonizes different environmental niches within the mammalian gut. In this study, we characterize
Escherichia coli
organisms (
n
= 146) isolated from different regions of the intestinal tracts of eight pigs (dueodenum, ileum, colon, and feces). The isolates were typed using the method of random amplified polymorphic DNA (RAPD) and screened for the presence of bacteriocin genes and plasmid replicon types. Molecular analysis of variance using the RAPD data showed that
E. coli
isolates are nonrandomly distributed among different gut regions, and that gut region accounted for 25% (
P
< 0.001) of the observed variation among strains. Bacteriocin screening revealed that a bacteriocin gene was detected in 45% of the isolates, with 43% carrying colicin genes and 3% carrying microcin genes. Of the bacteriocins observed (H47, E3, E1, E2, E7, Ia/Ib, and B/M), the frequency with which they were detected varied with respect to gut region for the colicins E2, E7, Ia/Ib, and B/M. The plasmid replicon typing gave rise to 25 profiles from the 13 Inc types detected. Inc F types were detected most frequently, followed by Inc HI1 and N types. Of the Inc types detected, 7 were nonrandomly distributed among isolates from the different regions of the gut. The results of this study indicate that not only may the different regions of the gastrointestinal tract harbor different strains of
E. coli
but also that strains from different regions have different characteristics.
Rerouting Citrate Metabolism in Lactococcus lactis to Citrate-Driven Transamination
Authors: Pudlik Agata M. , Lolkema Juke S.
Published: July 2012

Oxaloacetate is an intermediate of the citrate fermentation pathway that accumulates in the cytoplasm of
Lactococcus lactis
ILCitM(pFL3) at a high concentration due to the inactivation of oxaloacetate decarboxylase. An excess of toxic oxaloacetate is excreted into the medium in exchange for citrate by the citrate transporter CitP (A. M. Pudlik and J. S. Lolkema, J. Bacteriol. 193:4049–4056, 2011). In this study, transamination of amino acids with oxaloacetate as the keto donor is described as an additional mechanism to relieve toxic stress. Redirection of the citrate metabolic pathway into the transamination route in the presence of the branched-chain amino acids Ile, Leu, and Val; the aromatic amino acids Phe, Trp, and Tyr; and Met resulted in the formation of aspartate and the corresponding α-keto acids. Cells grown in the presence of citrate showed 3.5 to 7 times higher transaminase activity in the cytoplasm than cells grown in the absence of citrate. The study demonstrates that transaminases of
L. lactis
accept oxaloacetate as a keto donor. A significant fraction of 2-keto-4-methylthiobutyrate formed from methionine by citrate-driven transamination
in vivo
was further metabolized, yielding the cheese aroma compounds 2-hydroxy-4-methylthiobutyrate and methyl-3-methylthiopropionate. Reducing equivalents required for the former compound were produced in the citrate fermentation pathway as NADH. Similarly, phenylpyruvate, the transamination product of phenylalanine, was reduced to phenyllactate, while the dehydrogenase activity was not observed for the branched-chain keto acids. Both α-keto acids and α-hydroxy acids are known substrates of CitP and may be excreted from the cell in exchange for citrate or oxaloacetate.
FlbD, a Myb Transcription Factor of Aspergillus nidulans, Is Uniquely Involved in both Asexual and Sexual Differentiation
Authors: Arratia-Quijada Jenny , Sánchez Olivia , Scazzocchio Claudio , Aguirre Jesús
Published: July 2012

In the fungus
Aspergillus nidulans
, inactivation of the
flbA
to
-E
,
fluG
,
fluF
, and
tmpA
genes results in similar phenotypes, characterized by a delay in conidiophore and asexual spore production.
flbB
to
-D
encode transcription factors needed for proper expression of the
brlA
gene, which is essential for asexual development. However, recent evidence indicates that FlbB and FlbE also have nontranscriptional functions. Here we show that
fluF1
is an allele of
flbD
which results in an R47P substitution. Amino acids C46 and R47 are highly conserved in FlbD and many other Myb proteins, and C46 has been proposed to mediate redox regulation. Comparison of Δ
flbD
and
flbD

R47P

mutants uncovered a new and specific role for
flbD
during sexual development. While
flbD

R47P

mutants retain partial function during conidiation, both
ΔflbD
and
flbD

R47P

mutants are unable to develop the peridium, a specialized external tissue that differentiates during fruiting body formation and ends up surrounding the sexual spores. This function, unique among other
fluffy
genes, does not affect the viability of the naked ascospores produced by mutant strains. Notably, ascospore development in these mutants is still dependent on the NADPH oxidase NoxA. We generated R47K, C46D, C46S, and C46A mutant alleles and evaluated their effects on asexual and sexual development. Conidiation defects were most severe in
ΔflbD
mutants and stronger in R47P, C46D, and C46S strains than in R47K strains. In contrast, mutants carrying the
flbD

C46A

allele exhibited conidiation defects in liquid culture only under nitrogen starvation conditions. The R47K, R47P, C46D, and C46S mutants failed to develop any peridial tissue, while the
flbD

C46A

strain showed normal peridium development and increased cleistothecium formation. Our results show that FlbD regulates both asexual and sexual differentiation, suggesting that both processes require FlbD DNA binding activity and that FlbD is involved in the response to nitrogen starvation.
A Detoxifying Oxygen Reductase in the Anaerobic Protozoan Entamoeba histolytica
Authors: Vicente João B. , Tran Vy , Pinto Liliana , Teixeira Miguel , Singh Upinder
Published: July 2012

We report the characterization of a bacterial-type oxygen reductase abundant in the cytoplasm of the anaerobic protozoan parasite
Entamoeba histolytica
. Upon host infection,
E. histolytica
is confronted with various oxygen tensions in the host intestine, as well as increased reactive oxygen and nitrogen species at the site of local tissue inflammation. Resistance to oxygen-derived stress thus plays an important role in the pathogenic potential of
E. histolytica
. The genome of
E. histolytica
has four genes that encode flavodiiron proteins, which are bacterial-type oxygen or nitric oxide reductases and were likely acquired by lateral gene transfer from prokaryotes. The
EhFdp1
gene has higher expression in virulent than in nonvirulent
Entamoeba
strains and species, hinting that the response to oxidative stress may be one correlate of virulence potential. We demonstrate that EhFdp1 is abundantly expressed in the cytoplasm of
E. histolytica
and that the protein levels are markedly increased (up to ∼5-fold) upon oxygen exposure. Additionally, we produced fully functional recombinant EhFdp1 and demonstrated that this enzyme is a specific and robust oxygen reductase but has poor nitric oxide reductase activity. This observation represents a new mechanism of oxygen resistance in the anaerobic protozoan pathogen
E. histolytica
.
Peroxide-Sensing Transcriptional Regulators in Bacteria
Authors: Dubbs James M. , Mongkolsuk Skorn
Published: July 2012

The ability to maintain intracellular concentrations of toxic reactive oxygen species (ROS) within safe limits is essential for all aerobic life forms. In bacteria, as well as other organisms, ROS are produced during the normal course of aerobic metabolism, necessitating the constitutive expression of ROS scavenging systems. However, bacteria can also experience transient high-level exposure to ROS derived either from external sources, such as the host defense response, or as a secondary effect of other seemingly unrelated environmental stresses. Consequently, transcriptional regulators have evolved to sense the levels of ROS and coordinate the appropriate oxidative stress response. Three well-studied examples of these are the peroxide responsive regulators OxyR, PerR, and OhrR. OxyR and PerR are sensors of primarily H
2
O
2
, while OhrR senses organic peroxide (ROOH) and sodium hypochlorite (NaOCl). OxyR and OhrR sense oxidants by means of the reversible oxidation of specific cysteine residues. In contrast, PerR senses H
2
O
2
via the Fe-catalyzed oxidation of histidine residues. These transcription regulators also influence complex biological phenomena, such as biofilm formation, the evasion of host immune responses, and antibiotic resistance via the direct regulation of specific proteins.
ThechbGGene of the Chitobiose (chb) Operon of Escherichia coli Encodes a Chitooligosaccharide Deacetylase
Authors: Verma Subhash Chandra , Mahadevan Subramony
Published: July 2012

Thechboperon ofEscherichia coliis involved in the utilization of the β-glucosides chitobiose and cellobiose. The function ofchbG(ydjC), the sixth open reading frame of the operon that codes for an evolutionarily conserved protein is unknown. We show thatchbGencodes a monodeacetylase that is essential for growth on the acetylated chitooligosaccharides chitobiose and chitotriose but is dispensable for growth on cellobiose and chitosan dimer, the deacetylated form of chitobiose. The predicted active site of the enzyme was validated by demonstrating loss of function upon substitution of its putative metal-binding residues that are conserved across the YdjC family of proteins. We show that activation of thechbpromoter by the regulatory protein ChbR is dependent on ChbG, suggesting that deacetylation of chitobiose-6-P and chitotriose-6-P is necessary for their recognition by ChbR as inducers. Strains carrying mutations inchbRconferring the ability to grow on both cellobiose and chitobiose are independent ofchbGfunction for induction, suggesting that gain of function mutations in ChbR allow it to recognize the acetylated form of the oligosaccharides. ChbR-independent expression of the permease and phospho-β-glucosidase from a heterologous promoter did not support growth on both chitobiose and chitotriose in the absence ofchbG, suggesting an additional role ofchbGin the hydrolysis of chitooligosaccharides. The homologs ofchbGin metazoans have been implicated in development and inflammatory diseases of the intestine, indicating that understanding the function ofE. colichbGhas a broader significance.
Convergent Molecular Evolution of Genomic Cores in Salmonella enterica and Escherichia coli
Authors: Chattopadhyay Sujay , Paul Sandip , Kisiela Dagmara I. , Linardopoulou Elena V. , Sokurenko Evgeni V.
Published: July 2012

One of the strongest signals of adaptive molecular evolution of proteins is the occurrence of convergent hot spot mutations: repeated changes in the same amino acid positions. We performed a comparative genome-wide analysis of mutation-driven evolution of core (omnipresent) genes in 17 strains ofSalmonella entericasubspecies I and 22 strains ofEscherichia coli. More than 20% of core genes in bothSalmonellaandE. coliaccumulated hot spot mutations, with a predominance of identical changes having recent evolutionary origin. There is a significant overlap in the functional categories of the adaptively evolving genes in both species, although mostly via separate molecular mechanisms. As a strong evidence of the link between adaptive mutations and virulence inSalmonella, two human-restricted serovars, Typhi and Paratyphi A, shared the highest number of genes with serovar-specific hot spot mutations. Many of the core genes affected by Typhi/Paratyphi A-specific mutations have known virulence functions. For each species, a list of nonrecombinant core genes (and the hot spot mutations therein) under positive selection is provided.
Chromosomal Replication Initiation Machinery of Low-G+C-Content Firmicutes
Authors: Briggs Geoffrey S. , Smits Wiep Klaas , Soultanas Panos
Published: July 2012

Much of our knowledge of the initiation of DNA replication comes from studies in the Gram-negative model organism
Escherichia coli
. However, the location and structure of the origin of replication within the
E. coli
genome and the identification and study of the proteins which constitute the
E. coli
initiation complex suggest that it might not be as universal as once thought. The archetypal low-G+C-content Gram-positive
Firmicutes
initiate DNA replication via a unique primosomal machinery, quite distinct from that seen in
E. coli
, and an examination of
oriC
in the
Firmicutes
species
Bacillus subtilis
indicates that it might provide a better model for the ancestral bacterial origin of replication. Therefore, the study of replication initiation in organisms other than
E. coli
, such as
B. subtilis
, will greatly advance our knowledge and understanding of these processes as a whole. In this minireview, we highlight the structure-function relationships of the
Firmicutes
primosomal proteins, discuss the significance of their
oriC
architecture, and present a model for replication initiation at
oriC
.
Inability To Catabolize Galactose Leads to Increased Ability To Compete for Nodule Occupancy in Sinorhizobium meliloti
Authors: Geddes Barney A. , Oresnik Ivan J.
Published: July 2012

A mutant unable to utilize galactose was isolated inSinorhizobium melilotistrain Rm1021. The mutation was found to be in a gene annotateddgoK1, a putative 2-keto-3-deoxygalactonokinase. The genetic region was isolated on a complementing cosmid and subsequently characterized. Based on genetic and bioinformatic evidence, the locus encodes all five enzymes (galD,dgoK,dgoA,SMc00883, andilvD1) involved in the De Ley-Doudoroff pathway for galactose catabolism. Although all five genes are present, genetic analysis suggests that the galactonase (SMc00883) and the dehydratase (ilvD1) are dispensable with respect to the ability to catabolize galactose. In addition, we show that the transport of galactose is partially facilitated by the arabinose transporter (AraABC) and that both glucose and galactose compete with arabinose for transport. Quantitative reverse transcription-PCR (qRT-PCR) data show that in adgoKbackground, the galactose locus is constitutively expressed, and the induction of thearalocus seems to be enhanced. Assays of competition for nodule occupancy show that the inability to catabolize galactose is correlated with an increased ability to compete for nodule occupancy.
Outcomes of hip arthroscopy. A prospective analysis and comparison between patients under 25 and over 25 years of age
Authors: Cooper Anthony Philip , Basheer Sheba Z , Maheshwari Rajan , Regan Laura , Madan Sanjeev S
Published: July 2012

Objective

To compare the results of hip arthroscopy in patients under the age of 25 with those over 25 years.

Design

From March 2006 until May 2010, data were collected on all patients who underwent hip arthroscopy for symptomatic intra-articular hip pathology. The patients were divided into two groups based on age (less than 25 years and over 25 years). Patients completed the modified Harris hip score (MHHS), non-arthritic hip score (NAHS) and hip dysfunction and osteoarthritis outcome score (HOOS) questionnaires at baseline then at 6 weeks, 6 months, 12 months and at latest follow-up.

Participants

88 patients who underwent 94 hip arthroscopies by the senior author. Mean age was 24.3 (range 11–57 years).

Results

The mean NAHS and HOOS subscales for pain and activities of daily living were worse at baseline in over 25 groups. Follow-up ranged from 9 to 68 months. 45 hips had greater than 3 year follow-up. The MHHS improved in both groups with a mean difference in the under-25 group of 16.22, and 20.88 in the over 25s. Improvements in the NAHS and HOOS subscales were also of a similar magnitude. There was no statistically significant difference between outcome scores of the two groups at the latest follow-up visit.

Conclusions

We found a comparable improvement in outcome between those patients under 25 years and those over 25 years. We propose that hip arthroscopy is of potential benefit to patients with symptoms of femoroacetabular impingement regardless of age.
Cystatin C in a composite risk score for mortality in patients with infective endocarditis: a cohort study
Authors: Bjurman Christian , Snygg-Martin Ulrika , Olaison Lars , Fu Michael L X , Hammarsten Ola
Published: July 2012

Objective

To develop a multimarker prognostic score for infective endocarditis (IE).

Design

Retrospective case–control.

Setting

Secondary care. Single centre.

Participants

125 patients with definite IE.

Primary outcome measures

90-day and 5-year mortality.

Results

Mean age was 62.7±17 years. The 90-day and 5-year mortality was 10.4% and 33.6%, respectively. CysC levels at admission and over 20% increases in CysC levels during 2 weeks of treatment were prognostic for 90-day and 5-year mortality independent of creatinine estimated glomerular filtration rate. In multivariate analyses, CysC (OR 5.42, 95% CI 1.90 to 15.5, p=0.002) and age (OR 1.06, 95% CI 1.02 to 1.10, p=0.002) remained prognostic for 5-year mortality. NT-proBNP, TnT, C reactive protein and interleukin 6 were also linked to prognosis. A composite risk scoring system using levels of CysC, NT-proBNP, age and presence of mitral valve insufficiency was able to separate a high-risk and a low-risk group.

Conclusions

CysC levels at admission and increase in CysC after 2 weeks of treatment were independent prognostic markers for both 90-day and 5-year mortality in patients with IE. A multimarker composite risk scoring system including CysC identified a high-risk group.
Dose–response effects of exercise training on the subjective sleep quality of postmenopausal women: exploratory analyses of a randomised controlled trial
Authors: Kline Christopher E , Sui Xuemei , Hall Martica H , Youngstedt Shawn D , Blair Steven N , Earnest Conrad P , Church Timothy S
Published: July 2012

Objective

To investigate whether a dose–response relationship existed between exercise and subjective sleep quality in postmenopausal women. This objective represents a post hoc assessment that was not previously considered.

Design

Parallel-group randomised controlled trial.

Setting

Clinical exercise physiology laboratory in Dallas, Texas.

Participants

437 sedentary overweight/obese postmenopausal women.

Intervention

Participants were randomised to one of four treatments, each of 6 months of duration: a non-exercise control treatment (n=92) or one of three dosages of moderate-intensity exercise (50% of VO2peak), designed to meet 50% (n=151), 100% (n=99) or 150% (n=95) of the National Institutes of Health Consensus Development Panel physical activity recommendations. Exercise dosages were structured to elicit energy expenditures of 4, 8 or 12 kilocalories per kilogram of body weight per week (KKW), respectively. Analyses were intent to treat.

Primary outcome measures

Continuous scores and odds of having significant sleep disturbance, as assessed by the Sleep Problems Index from the 6-item Medical Outcomes Study Sleep Scale. Outcome assessors were blinded to participant randomisation assignment.

Results

Change in the Medical Outcomes Study Sleep Problems Index score at 6 months significantly differed by treatment group (control: −2.09 (95% CI −4.58 to 0.40), 4 KKW: −3.93 (−5.87 to −1.99), 8 KKW: −4.06 (−6.45 to −1.67), 12 KKW: −6.22 (−8.68 to −3.77); p=0.04), with a significant dose–response trend observed (p=0.02). Exercise training participants had lower odds of having significant sleep disturbance at postintervention compared with control (4 KKW: OR 0.37 (95% CI 0.19 to 0.73), 8 KKW: 0.36 (0.17 to 0.77), 12 KKW: 0.34 (0.16 to 0.72)). The magnitude of weight loss did not differ between treatment conditions. Improvements in sleep quality were not related to changes in body weight, resting parasympathetic control or cardiorespiratory fitness.

Conclusion

Exercise training induced significant improvement in subjective sleep quality in postmenopausal women, with even a low dose of exercise resulting in greatly reduced odds of having significant sleep disturbance.

Trial registration number

clinicaltrials.govidentifier:NCT00011193.
Asthma and allergies in Jamaican children aged 2–17 years: a cross-sectional prevalence survey
Authors: Kahwa Eulalia K , Waldron Norman K , Younger Novie O , Edwards Nancy C , Knight-Madden Jennifer M , Bailey Kay A , Wint Yvonne B , Lewis-Bell Karen N
Published: July 2012

Objective

To determine the prevalence and severity of asthma and allergies as well as risk factors for asthma among Jamaican children aged 2–17 years.

Design

A cross-sectional, community-based prevalence survey using the International Study of Asthma and Allergies in Childhood questionnaire. The authors selected a representative sample of 2017 children using stratified, multistage cluster sampling design using enumeration districts as primary sampling units.

Setting

Jamaica, a Caribbean island with a total population of approximately 2.6 million, geographically divided into 14 parishes.

Participants

Children aged 2–17 years, who were resident in private households. Institutionalised children such as those in boarding schools and hospitals were excluded from the survey.

Primary and secondary outcome measures

The prevalence and severity of asthma and allergy symptoms, doctor-diagnosed asthma and risk factors for asthma.

Results

Almost a fifth (19.6%) of Jamaican children aged 2–17 years had current wheeze, while 16.7% had self-reported doctor-diagnosed asthma. Both were more common among males than among females. The prevalence of rhinitis, hay fever and eczema among children was 24.5%, 25% and 17.3%, respectively. Current wheeze was more common among children with rhinitis in the last 12 months (44.3% vs 12.6%, p<0.001), hay fever (36.8% vs 13.8%, p<0.001) and eczema (34.1% vs 16.4%, p<0.001). Independent risk factors for current wheeze (ORs, 95% CI) were chest infections in the first year of life 4.83 (3.00 to 7.77), parental asthma 4.19 (2.8 to 6.08), rhinitis in the last 12 months 6.92 (5.16 to 9.29), hay fever 4.82 (3.62 to 6.41), moulds in the home 2.25 (1.16 to 4.45), cat in the home 2.44 (1.66 to 3.58) and dog in the home 1.81 (1.18 to 2.78).

Conclusions

The prevalence of asthma and allergies in Jamaican children is high. Significant risk factors for asthma include chest infections in the first year of life, a history of asthma in the family, allergies, moulds and pets in the home.
Clinical practice patterns among native and immigrant doctors doing out-of-hours work in Norway: a registry-based observational study
Authors: Sandvik Hogne , Hunskaar Steinar , Diaz Esperanza
Published: July 2012

Objectives

To evaluate whether immigrant and native Norwegian doctors differ in their practice patterns.

Design

Observational study.

Setting

Out-of-hours (OOH) emergency primary healthcare in Norway, 2008.

Participants

All primary care physicians doing OOH work, altogether 4165 physicians.

Main outcome measures

Number of patient contacts per doctor. Use of laboratory tests, minor surgery, sickness certification and length of consultations. Use of diagnoses related to psychiatric and sexual health. Choice of management strategy with psychiatric patients (psychotherapy or hospitalisation).

Results

21.4% of the physicians were immigrants, and they had 30.6% of the patient contacts. Immigrant doctors from Asia, Africa and Latin America had most patient contacts, 633 (95% CI 549 to 716), while native Norwegian doctors had 306 (95% CI 288 to 325). In multivariate analyses, immigrant physicians did not differ significantly from native Norwegians regarding use of laboratory tests, minor surgery or length of consultations, but immigrant doctors wrote more sickness certificates, OR 1.75 (95% CI 1.24 to 2.47) for immigrant doctors from Europe, North America and Oceania versus native Norwegian doctors and OR 1.56 (95% CI 1.15 to 2.11) for immigrant doctors from Asia, Africa and Latin America versus native Norwegians. Immigrant physicians from Europe, North America and Oceania used more diagnoses related to pregnancy, family planning and female genitals, OR 1.55 (95% CI 1.11 to 2.16), versus native Norwegian physicians. Immigrant doctors from Asia, Africa and Latin America used less psychiatric diagnoses, OR 0.71 (95% CI 0.53 to 0.95), versus native Norwegian doctors but did not differ significantly in their management of recognised psychiatric illness.

Conclusions

Immigrant doctors make an important contribution to OOH emergency primary healthcare in Norway. The authors found only modest evidence that their clinical practice patterns are different from that of native Norwegian doctors.