bluuebunny/crossref_metadata_2025 huggingface dataset:
Allelematch: an R package for identifying unique multilocus genotypes where genotyping error and missing data may be present
Authors: GALPERN PAUL , MANSEAU MICHELINE , HETTINGA PETER , SMITH KAREN , WILSON PAUL
Published: March 2012

We presentallelematch, an R package, to automate the identification of unique multilocus genotypes in data sets where the number of individuals is unknown, and where genotyping error and missing data may be present. Such conditions commonly occur in noninvasive sampling protocols. Output from the software enables a comparison of unique genotypes and their matches, and facilitates the review of differences between profiles. The software has a variety of applications in molecular ecology, and may be valuable where a large number of samples must be processed, unique genotypes identified, and repeated observations made over space and time. We used simulations to assess the performance ofallelematchand found that it can reliably and accurately determine the correct number of unique genotypes (±3%) across a broad range of data set properties. We found that the software performs with highest accuracy when genotyping error is below 4%. The R package is available from the Comprehensive R Archive Network (http://cran.r‐project.org/). Supplementary documentation and tutorials are provided.
Factors responsible for the discrepancy between IL28B polymorphism prediction and the viral response to peginterferon plus ribavirin therapy in Japanese chronic hepatitis C patients
Authors: Saito Hiroaki , Ito Kiyoaki , Sugiyama Masaya , Matsui Teppei , Aoki Yoshihiko , Imamura Masatoshi , Murata Kazumoto , Masaki Naohiko , Nomura Hideyuki , Adachi Hiroshi , Hige Shuhei , Enomoto Nobuyuki , Sakamoto Naoya , Kurosaki Masayuki , Mizokami Masashi , Watanabe Sumio
Published: March 2012

Aim:  IL28B polymorphisms serve to predict response to pegylated interferon plus ribavirin therapy (PEG IFN/RBV) in Japanese patients with chronic hepatitis C (CHC) very reliably. However, the prediction by the IL28B polymorphism contradicted the virological response to PEG IFN/RBV in some patients. Here, we aimed to investigate the factors responsible for the discrepancy between the IL28B polymorphism prediction and virological responses.

Methods:  CHC patients with genotype 1b and high viral load were enrolled in this study. In a case–control study, clinical and virological factors were analyzed for 130 patients with rs8099917 TT genotype and 96 patients with rs8099917 TG or GG genotype who were matched according to sex, age, hemoglobin level and platelet count.

Results:  Higher low‐density lipoprotein (LDL) cholesterol, lower γ‐glutamyltransferase and the percentage of wild‐type phenotype at amino acids 70 and 91 were significantly associated with the rs8099917 TT genotype. Multivariate analysis showed that rs8099917 TG or GG genotype, older age and lower LDL cholesterol were independently associated with the non‐virological responder (NVR) phenotype. In patients with rs8099917 TT genotype (predicted as virological responder [VR]), multivariate analysis showed that older age was independently associated with NVR. In patients with rs8099917 TG or GG genotype (predicted as NVR), multivariate analysis showed that younger age was independently associated with VR.

Conclusion:  Patient age gave rise to the discrepancy between the prediction by IL28B polymorphism and the virological responses, suggesting that patients should be treated at a younger age.
Inventory Management in China: An Empirical Study
Authors: Shan Jun , Zhu Kaijie
Published: March 2012

With the outsourcing of manufacturing activities from Western countries, China has gradually become the global manufacturing hub. In the presence of increased competition from both inside and outside of China, many Chinese manufacturers have turned to scientific management approaches and implemented various enterprise systems. In academia, there has been a growing interest in quantifying the impacts of such efforts on the corporate performance of Chinese firms, and research has been carried out in areas such as finance and accounting. However, due to limited visibility of operational decisions and data, there seems to be a lack of investigation into the impacts on the firms’ operational performance in the literature. In this article, we apply an empirical method to investigate the inventories of 1286 firms listed on the two stock exchanges in China, the Shanghai Stock Exchange and the Shenzhen Stock Exchange. We find that on average the inventory levels have declined over time and that the firm‐level data is consistent with several implications derived from classical inventory models.
A Sales Forecast Model for Short‐Life‐Cycle Products: New Releases at Blockbuster
Authors: Chung Casey , Niu Shun‐Chen , Sriskandarajah Chelliah
Published: March 2012

We develop, in this article, a sales model for movie and game products at Blockbuster. The model assumes that there are three sales components: the first is from consumers who have already committed to purchasing (or renting) a product (e.g., based on promotion of, or exposure to, the product prior to its launch); the second comes from consumers who are potential buyers of the product; and the third comes from either a networking effect on closely tied (as in a social group) potential buyers from previous buyers (in the case of movie rental and all retail products) or re‐rents (in the case of game rental). In addition, we explicitly formulate into our model dynamic interactions between these sales components, both within and across sales periods. This important feature is motivated by realism, and it significantly contributes to the accuracy of our model. The model is thoroughly tested against sales data for rental and retail products from Blockbuster. Our empirical results show that the model offers excellent fit to actual sales activity. We also demonstrate that the model is capable of delivering reasonable sales forecasts based solely on environmental data (e.g., theatrical sales, studio, genre, MPAA ratings, etc.) and actual first‐period sales. Accurate sales forecasts can lead to significant cost savings. In particular, it can improve the retail operations at Blockbuster by determining appropriate order quantities of products, which is critical in effective inventory management (i.e., it can reduce the extent of over‐stocking and under‐stocking). While our model is developed specifically for product sales at Blockbuster, we believe that with context‐dependent modifications, our modeling approach could also provide a reasonable basis for the study of sales for other short‐Life‐Cycle products.
Role of the Porphyromonas gingivalis extracytoplasmic function sigma factor, SigH
Authors: Yanamandra S.S. , Sarrafee S.S. , Anaya‐Bergman C. , Jones K. , Lewis J.P.
Published: March 2012

Little is known about the regulatory mechanisms that allow Porphyromonas gingivalis to survive in the oral cavity. Here we characterize the sigma (σ) factor SigH, one of six extracytoplasmic function (ECF) σ factors encoded in the P. gingivalis genome. Our results indicate that sigH expression is upregulated by exposure to molecular oxygen, suggesting that sigH plays a role in adaptation of P. gingivalis to oxygen. Furthermore, several genes involved in oxidative stress protection, such as sod, trx, tpx, ftn, feoB2 and the hemin uptake hmu locus, are downregulated in a mutant deficient in SigH designated as V2948. ECF σ consensus sequences were identified upstream of the transcriptional start sites of these genes, consistent with the SigH‐dependent regulation of these genes. Growth of V2948 was inhibited in the presence of 6% oxygen when compared with the wild‐type W83 strain, whereas in anaerobic conditions both strains were able to grow. In addition, reduced growth of V2948 was observed in the presence of peroxide and the thiol‐oxidizing reagent diamide when compared with the W83 strain. The SigH‐deficient strain V2948 also exhibited reduced hemin uptake, consistent with the observed reduced expression of genes involved in hemin uptake. Finally, survival of V2948 was reduced in the presence of host cells compared with the wild‐type W83 strain. Collectively, our studies demonstrate that SigH is a positive regulator of gene expression required for survival of the bacterium in the presence of oxygen and oxidative stress, hemin uptake and virulence.
Food restriction and refeeding induces changes in lipid pathways and fat deposition in the adipose and hepatic tissues in rats with diet‐induced obesity
Authors: Duarte Fernanda Oliveira , Sene‐Fiorese Marcela , Cheik Nadia Carla , Maria Adriana Simone Lopes Santa , de Aquino Antônio Eduardo , Oishi Jorge Camargo , Rossi Elizeu Antônio , Garcia de Oliveira Duarte Ana Cláudia , Dâmaso Ana Raimunda
Published: March 2012

The aim of this study was to determine the effects of successive cycles of a moderately restrictive diet and refeeding with a high‐fat diet on the metabolism of the adipose and hepatic tissues of obese rats. Rats were assigned to the following groups: a chow diet; a high‐fat diet; a moderate caloric restriction; or a moderate caloric restriction plus refeeding. Some animals in each group were given [1‐14C]triolein intragastrically, while others received an intraperitoneal injection of 3 mCi 3H2O. All animals were killed by decapitation. The retroperitoneal, visceral epididymal and omental white adipose tissues, brown adipose tissue, liver and blood were immediately removed. The lipid uptake from the diet, in vivo rate of lipogenesis, percentage of fat, lipid profile and leptin concentration were analysed. The high‐fat diet promoted an increase in fatty liver (P≤ 0.05), adiposity mass (P≤ 0.05) and the plasma concentration of leptin (P≤ 0.05) and a decreased lipid uptake in white adipose tissue depots (P≤ 0.05) in relation to the chow diet. The moderate caloric restriction did not reverse the changes promoted by the high‐fat diet but induced a small decrease in adiposity, which was reversed after refeeding, and the animals maintained a dyslipidaemic profile and high fat deposition in the liver. We can conclude that the high‐fat diet and subsequent moderate caloric restriction plus refeeding increased the risks of developing visceral obesity, dyslipidaemia and non‐alcoholic fatty liver disease, which suggests that this type of experimental protocol can be used to study mechanisms related to the metabolic syndrome.
Anterograde and retrograde blood velocity profiles in the intact human cardiovascular system
Authors: Ade C. J. , Broxterman R. M. , Wong B. J. , Barstow T. J.
Published: March 2012

Current assessments of the effects of shear patterns on vascular function assume that a parabolic velocity profile is always present. Any substantial deviation in the profile away from this may result in misinterpretation of the importance that shear patterns have on vascular function. The present investigation tested the hypothesis that anterograde and retrograde blood flow would have a parabolic velocity profile at rest, during cold pressor test and exercise. Eight healthy subjects completed a cold pressor test and a graded knee‐extension exercise test. Doppler ultrasound was used to determine time‐averaged mean velocity (Vmean) and time‐averaged peak velocity (Vpeak) for both anterograde and retrograde flow in the femoral artery (FA) and brachial artery (BA). The Vmean/Vpeak ratio was used to interpret the shape of the blood velocity profile (parabolic, Vmean/Vpeak= 0.5; plug‐like, Vmean/Vpeak= 1.0). At rest, BA and FA Vmean/Vpeak ratios of anterograde and retrograde flow were not significantly different from 0.5. During cold pressor test, anterograde Vmean/Vpeak in the BA (0.56 ± 0.02) and FA (0.58 ± 0.03) were significantly greater than 0.5. During peak exercise, the Vmean/Vpeak ratio of anterograde flow in the FA (0.53 ± 0.04) was not significantly different from 0.5. In all conditions, the retrograde Vmean/Vpeak ratio was lower than anterograde. These data demonstrate that blood flow through two different conduit arteries during two different physiological stressors maintains a velocity profile that resembles a slightly blunted parabolic velocity profile.
Actomyosin kinetics of pure fast and slow rat myosin isoforms studied by in vitro motility assay approach
Authors: Canepari Monica , Maffei Manuela , Longa Emanuela , Geeves Michael , Bottinelli Roberto
Published: March 2012

An in vitro motility assay approach was used to investigate the mechanisms of the functional differences between myosin isoforms, by studying the effect of MgATP and MgADP on actin sliding velocity (Vf) of pure slow and fast rat skeletal myosin at different temperatures. The value of Vf depended on [MgATP] according to Michaelis–Menten kinetics, with an apparent constant (Km) of 54.2, 64.4 and 200 μm for the fast isoform and 18.6, 36.5 and 45.5 μm for the slow isoform at 20, 25 and 35°C, respectively. The presence of 2 mm MgADP decreased Vf and yielded an inhibition constant (Ki) of 377, 463 and 533 μm for the fast isoform at 20, 25 and 35°C, respectively, and 120 and 355 μm for the slow isoform at 25 and 35°C, respectively. The analysis of Km and Ki suggested that slow and fast isoforms differ in the kinetics limiting Vf. Moreover, the higher sensitivity of the fast myosin isoform to a drop in [MgATP] is consistent with the higher fatigability of fast fibres than slow fibres. From the Michaelis–Menten relation in the absence of MgADP, we calculated the rate of actomyosin dissociation by MgATP (k+ATP) and the rate of MgADP release (k‐ADP). We found values of k+ATP of 4.8 × 106, 6.5 × 106 and 6.6 × 106m−1 s−1 for the fast isoform and 3.3 × 106, 2.9 × 106 and 6.7 × 106m−1 s−1 for the slow isoform and values of k‐ADP of 263, 420 and 1320 s−1 for the fast isoform and 62, 107 and 306 s−1 for the slow isoform at 20, 25 and 35°C, respectively. The results suggest that k‐ADP could be the major determinant of functional differences between the fast and slow myosin isoforms at physiological temperatures.
Isolation of Legionella pneumophila from Pluvial Floods by Amoebal Coculture
Authors: Schalk J. A. C. , Docters van Leeuwen A. E. , Lodder W. J. , de Man H. , Euser S. , den Boer J. W. , de Roda Husman A. M.
Published: March 2012

Viable
Legionella pneumophila
bacteria were isolated by amoebal coculture from pluvial floods after intense rainfall and from water collected at sewage treatment plants. Several isolated
L. pneumophila
strains belonged to sequence types that have been previously identified in patients.
Efficacy of Octenidine Hydrochloride for Reducing Escherichia coli O157:H7, Salmonella spp., and Listeria monocytogenes on Cattle Hides
Authors: Ananda Baskaran Sangeetha , Upadhyay Abhinav , Upadhyaya Indu , Bhattaram Varunkumar , Venkitanarayanan Kumar
Published: March 2012

The efficacy of octenidine hydrochloride (OH; 0.025, 0.15, and 0.25%) for inactivating
Escherichia coli
O157:H7,
Salmonella
spp., and
Listeria monocytogenes
on cattle hides was investigated at 23°C in the presence and absence of bovine feces. All tested concentrations of OH were effective in decreasing more than 5.0 log CFU of bacteria/cm
2
in 5 min (
P
< 0.01). The results suggest that OH could be used to decontaminate cattle hides; however, further studies under commercial settings are necessary to validate these results.
High-Throughput Sequence-Based Analysis of the Intestinal Microbiota of Weanling Pigs Fed Genetically Modified MON810 Maize Expressing Bacillus thuringiensis Cry1Ab (Bt Maize) for 31 Days
Authors: Buzoianu Stefan G. , Walsh Maria C. , Rea Mary C. , O'Sullivan Orla , Cotter Paul D. , Ross R. Paul , Gardiner Gillian E. , Lawlor Peadar G.
Published: March 2012

The objective of this study was to investigate if feeding genetically modified (GM) MON810 maize expressing the
Bacillus thuringiensis
insecticidal protein (Bt maize) had any effects on the porcine intestinal microbiota. Eighteen pigs were weaned at ∼28 days and, following a 6-day acclimatization period, were assigned to diets containing either GM (Bt MON810) maize or non-GM isogenic parent line maize for 31 days (
n
= 9/treatment). Effects on the porcine intestinal microbiota were assessed through culture-dependent and -independent approaches. Fecal, cecal, and ileal counts of total anaerobes,
Enterobacteriaceae
, and
Lactobacillus
were not significantly different between pigs fed the isogenic or Bt maize-based diets. Furthermore, high-throughput 16S rRNA gene sequencing revealed few differences in the compositions of the cecal microbiotas. The only differences were that pigs fed the Bt maize diet had higher cecal abundance of
Enterococcaceae
(0.06 versus 0%;
P
< 0.05),
Erysipelotrichaceae
(1.28 versus 1.17%;
P
< 0.05), and
Bifidobacterium
(0.04 versus 0%;
P
< 0.05) and lower abundance of
Blautia
(0.23 versus 0.40%;
P
< 0.05) than pigs fed the isogenic maize diet. A lower enzyme-resistant starch content in the Bt maize, which is most likely a result of normal variation and not due to the genetic modification, may account for some of the differences observed within the cecal microbiotas. These results indicate that Bt maize is well tolerated by the porcine intestinal microbiota and provide additional data for safety assessment of Bt maize. Furthermore, these data can potentially be extrapolated to humans, considering the suitability of pigs as a human model.
Biofilm Growth and Near-Infrared Radiation-Driven Photosynthesis of the Chlorophyll
d
-Containing Cyanobacterium Acaryochloris marina
Authors: Behrendt Lars , Schrameyer Verena , Qvortrup Klaus , Lundin Luisa , Sørensen Søren J. , Larkum Anthony W. D. , Kühl Michael
Published: March 2012

The cyanobacterium
Acaryochloris marina
is the only known phototroph harboring chlorophyll (Chl)
d
. It is easy to cultivate it in a planktonic growth mode, and
A. marina
cultures have been subject to detailed biochemical and biophysical characterization. In natural situations,
A. marina
is mainly found associated with surfaces, but this growth mode has not been studied yet. Here, we show that the
A. marina
type strain MBIC11017 inoculated into alginate beads forms dense biofilm-like cell clusters, as in natural
A. marina
biofilms, characterized by strong O
2
concentration gradients that change with irradiance. Biofilm growth under both visible radiation (VIS, 400 to 700 nm) and near-infrared radiation (NIR, ∼700 to 730 nm) yielded maximal cell-specific growth rates of 0.38 per day and 0.64 per day, respectively. The population doubling times were 1.09 and 1.82 days for NIR and visible light, respectively. The photosynthesis versus irradiance curves showed saturation at a photon irradiance of
E

k

(saturating irradiance) >250 μmol photons m
−2
s
−1
for blue light but no clear saturation at 365 μmol photons m
−2
s
−1
for NIR. The maximal gross photosynthesis rates in the aggregates were ∼1,272 μmol O
2
mg Chl
d
−1
h
−1
(NIR) and ∼1,128 μmol O
2
mg Chl
d
−1
h
−1
(VIS). The photosynthetic efficiency (α) values were higher in NIR-irradiated cells [(268 ± 0.29) × 10
−6
m
2
mg Chl
d
−1
(mean ± standard deviation)] than under blue light [(231 ± 0.22) × 10
−6
m
2
mg Chl
d
−1
].
A. marina
is well adapted to a biofilm growth mode under both visible and NIR irradiance and under O
2
conditions ranging from anoxia to hyperoxia, explaining its presence in natural niches with similar environmental conditions.
Diversity of Integron- and Culture-Associated Antibiotic Resistance Genes in Freshwater Floc
Authors: Drudge Christopher N. , Elliott Amy V. C. , Plach Janina M. , Ejim Linda J. , Wright Gerard D. , Droppo Ian G. , Warren Lesley A.
Published: March 2012

Clinically important antibiotic resistance genes were detected in culturable bacteria and class 1 integron gene cassettes recovered from suspended floc, a significant aquatic repository for microorganisms and trace elements, across freshwater systems variably impacted by anthropogenic activities. Antibiotic resistance gene cassettes in floc total community DNA differed appreciably in number and type from genes detected in bacteria cultured from floc. The number of floc antibiotic resistance gene cassette types detected across sites was positively correlated with total (the sum of Ag, As, Cu, and Pb) trace element concentrations in aqueous solution and in a component of floc readily accessible to bacteria. In particular, concentrations of Cu and Pb in the floc component were positively correlated with floc resistance gene cassette diversity. Collectively, these results identify suspended floc as an important reservoir, distinct from bulk water and bed sediment, for antibiotic resistance in aquatic environments ranging from heavily impacted urban sites to remote areas of nature reserves and indicate that trace elements, particularly Cu and Pb, are geochemical markers of resistance diversity in this environmental reservoir. The increase in contamination of global water supplies suggests that aquatic environments will become an even more important reservoir of clinically important antibiotic resistance in the future.
Transcriptional and Enzymatic Profiling of Pleurotus ostreatus Laccase Genes in Submerged and Solid-State Fermentation Cultures
Authors: Castanera Raúl , Pérez Gúmer , Omarini Alejandra , Alfaro Manuel , Pisabarro Antonio G. , Faraco Vincenza , Amore Antonella , Ramírez Lucía
Published: March 2012

The genome of the white rot basidiomycete
Pleurotus ostreatus
includes 12 phenol oxidase (laccase) genes. In this study, we examined their expression profiles in different fungal strains under different culture conditions (submerged and solid cultures) and in the presence of a wheat straw extract, which was used as an inducer of the laccase gene family. We used a reverse transcription-quantitative PCR (RT-qPCR)-based approach and focused on determining the reaction parameters (in particular, the reference gene set for the normalization and reaction efficiency determinations) used to achieve an accurate estimation of the relative gene expression values. The results suggested that (i) laccase gene transcription is upregulated in the induced submerged fermentation (iSmF) cultures but downregulated in the solid fermentation (SSF) cultures, (ii) the
Lacc2
and
Lacc10
genes are the main sources of laccase activity in the iSmF cultures upon induction with water-soluble wheat straw extracts, and (iii) an additional, as-yet-uncharacterized activity (Unk1) is specifically induced in SSF cultures that complements the activity of Lacc2 and Lacc10. Moreover, both the enzymatic laccase activities and the
Lacc
gene family transcription profiles greatly differ between closely related strains. These differences can be targeted for biotechnological breeding programs for enzyme production in submerged fermentation reactors.
Stringent Response Regulation of Biofilm Formation in Vibrio cholerae
Authors: He Huajun , Cooper Jennifer N. , Mishra Arunima , Raskin David M.
Published: March 2012

Biofilm formation is a key factor in
Vibrio cholerae
environmental survival and host colonization. Production of biofilm enables
V. cholerae
to survive and persist in aquatic environments and aids in the passage through the gastric acid barrier to allow access to the small intestine. The genes involved in biofilm formation are regulated by the transcriptional activators
vpsR
and
vpsT
, which are in turn transcriptionally regulated by a number of environmental signals. In this study, the role of the stringent response in biofilm formation was examined.
V. cholerae
mutants deficient in stringent response had a reduced ability to form biofilms, although they were not completely deficient in biofilm formation. There are three (p)ppGpp synthases in
V. cholerae
: RelA, SpoT, and RelV. All three synthases were necessary for
vpsR
transcription, with RelV showing the strongest effect. RelA was the only synthase that was necessary for
vpsT
expression. Stringent response regulation of
vpsR
and
vpsT
was shown to partially occur through
rpoS
. Biofilm formation in
V. cholerae
is controlled by a complex regulatory apparatus, with negative regulators of biofilm gene expression, such as quorum sensing, and positive regulators of biofilm genes, including stringent response, interacting to ensure that biofilm formation is coordinated with the environment.
Analysis of the CtrA Pathway in Magnetospirillum Reveals an Ancestral Role in Motility in Alphaproteobacteria
Authors: Greene Shannon E. , Brilli Matteo , Biondi Emanuele G. , Komeili Arash
Published: March 2012

Developmental events across the prokaryotic life cycle are highly regulated at the transcriptional and posttranslational levels. Key elements of a few regulatory networks are conserved among phylogenetic groups of bacteria, although the features controlled by these conserved systems are as diverse as the organisms encoding them. In this work, we probed the role of the CtrA regulatory network, conserved throughout the
Alphaproteobacteria
, in the magnetotactic bacterium
Magnetospirillum magneticum
strain AMB-1, which possesses unique intracellular organization and compartmentalization. While we have shown that CtrA in AMB-1 is not essential for viability, it is required for motility, and its putative phosphorylation state dictates the ability of CtrA to activate the flagellar biosynthesis gene cascade. Gene expression analysis of strains expressing active and inactive CtrA alleles points to the composition of the extended CtrA regulon, including both direct and indirect targets. These results, combined with a bioinformatic study of the AMB-1 genome, enabled the prediction of an AMB-1-specific CtrA binding site. Further, phylogenetic studies comparing CtrA sequences from alphaproteobacteria in which the role of CtrA has been experimentally examined reveal an ancestral role of CtrA in the regulation of motility and suggest that its essential functions in other alphaproteobacteria were acquired subsequently.
Characterization of the Two-Component Monooxygenase System AlnT/AlnH Reveals Early Timing of Quinone Formation in Alnumycin Biosynthesis
Authors: Grocholski Thadée , Oja Terhi , Humphrey Laurence , Mäntsälä Pekka , Niemi Jarmo , Metsä-Ketelä Mikko
Published: March 2012

Alnumycin A is an aromatic polyketide with a strong resemblance to related benzoisochromanequinone (BIQ) antibiotics, such as the model antibiotic actinorhodin. One intriguing difference between these metabolites is that the positions of the benzene and quinone rings are reversed in alnumycin A in comparison to the BIQ polyketides. In this paper we demonstrate that inactivation of either the monooxygenase
alnT
gene or the flavin reductase
alnH
gene results in the accumulation of a novel nonquinoid metabolite, thalnumycin A (ThA), in the culture medium. Additionally, two other previously characterized metabolites, K1115 A and 1,6-dihydroxy-8-propylanthraquinone (DHPA), were identified, which had oxidized into quinones putatively nonenzymatically at the incorrect position in the central ring. None of the compounds isolated contained correctly formed pyran rings, which suggests that on the alnumycin pathway quinone biosynthesis occurs prior to third ring cyclization. The regiochemistry of the two-component monooxygenase system AlnT/AlnH was finally confirmed
in vitro
by using ThA, FMN, and NADH in enzymatic synthesis, where the reaction product, thalnumycin B (ThB), was verified to contain the expected
p
-hydroquinone structure in the lateral ring.
Environment-Mediated Accumulation of Diacyl Lipoproteins over Their Triacyl Counterparts in Staphylococcus aureus
Authors: Kurokawa Kenji , Kim Min-Su , Ichikawa Rie , Ryu Kyoung-Hwa , Dohmae Naoshi , Nakayama Hiroshi , Lee Bok Luel
Published: March 2012

Bacterial lipoproteins are believed to exist in only one specific lipid-modified structure, such as the diacyl form or the triacyl form, in each bacterium. In the case ofStaphylococcus aureus, recent extensive matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry analysis revealed thatS. aureuslipoproteins exist in the α-aminoacylated triacyl form. Here, we discovered conditions that induce the accumulation of diacyl lipoproteins that lack α-aminoacylation inS. aureus. The accumulation of diacyl lipoproteins required a combination of conditions, including acidic pH and a post-logarithmic-growth phase. High temperatures and high salt concentrations additively accelerated the accumulation of the diacyl lipoprotein form. Following a post-logarithmic-growth phase whereS. aureusMW2 cells were grown at pH 6, SitC lipoprotein was found almost exclusively in its diacyl structure rather than in its triacyl structure. This is the first report showing that the environment mediates lipid-modified structural alterations of bacterial lipoproteins.
Incident user cohort study of risk for gastrointestinal bleed and stroke in individuals with major depressive disorder treated with antidepressants
Authors: Castro Victor M , Gallagher Patience J , Clements Caitlin C , Murphy Shawn N , Gainer Vivian S , Fava Maurizio , Weilburg Jeffrey B , Churchill Susanne E , Kohane Isaac S , Iosifescu Dan V , Smoller Jordan W , Perlis Roy H
Published: March 2012

Objective

To examine the association between exposure to newer antidepressants and risk of gastrointestinal (GI) and other bleeding complications among individuals with major depressive disorder (MDD).

Design

This study uses an incident user cohort design to compare associations between incidence of vascular/bleeding events and the relative affinity (low, moderate or high) of the antidepressant for the serotonin transporter during an exposure risk period for each patient.

Setting

New England healthcare system electronic medical record database.

Participants

36 389 individuals with a diagnosis of MDD and monotherapy with a selective serotonin reuptake inhibitor, serotonin–norepinephrine reuptake inhibitor or other new-generation antidepressant were identified from among 3.1 million patients in a New England healthcare system.

Primary and secondary outcome measures

Rates of bleeding or other vascular complications, including acute liver failure, acute renal failure, asthma, breast cancer and hip fractures.

Results

601 GI bleeds were observed in the 21 462 subjects in the high-affinity group versus 333 among the 14 927 subjects in the lower affinity group (adjusted RR: 1.17, 95% CI 1.02 to 1.34). Similarly, 776 strokes were observed in the high-affinity group versus 434 in the lower affinity treatment group (adjusted RR: 1.18, 95% CI 1.06 to 1.32). No significant association with risk for a priori negative control outcomes, including acute liver failure, acute renal failure, asthma, breast cancer and hip fractures, was identified.

Conclusions

Use of antidepressants with high affinity for the serotonin transporter may confer modestly elevated risk for GI and other bleeding complications. While multiple methodologic limitations must be considered, these results suggest that antidepressants with lower serotonin receptor affinity may be preferred in patients at greater risk for such complications.
Imaging in children presenting with acute neurological deficit: paediatric stroke mimics
Authors: Rasalkar Darshana D , Chu Winnie C W
Published: March 2012

Stroke mimics refer to conditions manifesting with neurologic deficits without underlying cerebrovascular diseases. Major causes in the paediatric population under this category include infections, inflammation, demyelination, neoplasm, drug related, phacomatosis, and miscellaneous disorders. These conditions and their respective imaging findings are briefly discussed here.
Anaphylaxis: current state of knowledge for the modern physician
Authors: Rutkowski Krzysztof , Dua Shelley , Nasser Shuaib
Published: March 2012

Anaphylaxis is a severe, potentially fatal, hypersensitivity reaction of rapid onset. It may trigger life-threatening cardiopulmonary compromise, often with skin and mucosal changes such as urticaria and angioedema. The prevalence of anaphylaxis is increasing and the number of cases of fatal anaphylaxis appears to be rising. Food, insect stings, and drugs are the most common triggers. Novel triggers are increasingly seen and include delayed anaphylaxis to red meat, food-dependent exercise-induced reactions and anaphylaxis to monoclonal antibodies. Anaphylaxis is usually IgE mediated, but other mechanisms also play a role for example direct mast cells activation. Differential diagnosis is discussed including asthma, syncope and shock; excessive endogenous histamine, food related syndromes, and some rare diagnoses. Intramuscular epinephrine is first line treatment. The role of other drugs is reviewed. Timed and serial serum tryptase measurements help to confirm the diagnosis. Long-term management is necessary to minimise the risk of recurrence and includes identification of the trigger(s), management of risk factors, education on avoidance and a formalised treatment plan with an epinephrine auto-injector if appropriate. Every patient who has experienced anaphylaxis should be referred to an allergy clinic for appropriate management. This is endorsed by many national guidelines (eg, UK NICE). Anaphylaxis is often misdiagnosed or miscoded as, for example, asthma or food allergy. Most doctors will encounter a patient with anaphylaxis in their career and should to be familiar with the clinical features, management and mechanisms of this potentially fatal condition.
Acute inhibition of GSK causes mitochondrial remodeling
Authors: Nguyen Tiffany , Wong Renee , Wang Guanghui , Gucek Marjan , Steenbergen Charles , Murphy Elizabeth
Published: March 2012

Recent data have shown that cardioprotection can result in the import of specific proteins into the mitochondria in a process that involves heat shock protein 90 (HSP90) and is blocked by geldanamycin (GD), a HSP90 inhibitor. To test the hypothesis that an alteration in mitochondrial import is a more widespread feature of cardioprotection, in this study, we used a broad-based proteomics approach to investigate changes in the mitochondrial proteome following cardioprotection induced by inhibition of glycogen synthase kinase (GSK)-3. Mitochondria were isolated from control hearts, and hearts were perfused with the GSK inhibitor SB 216763 (SB) for 15 min before isolation of mitochondria. Mitochondrial extracts from control and SB-perfused hearts were labeled with isotope tags for relative and absolute quantification (iTRAQ), and differences in mitochondrial protein levels were determined by mass spectrometry. To test for the role of HSP90-mediated protein import, hearts were perfused in the presence and absence of GD for 15 min before perfusion with SB followed by mitochondrial isolation and iTRAQ labeling. We confirmed that treatment with GD blocked the protection afforded by SB treatment in a protocol of 20 min of ischemia and 40 min of reperfusion. We found 16 proteins that showed an apparent increase in the mitochondrial fraction following SB treatment. GD treatment significantly blocked the SB-mediated increase in mitochondrial association for five of these proteins, which included annexin A6, vinculin, and pyruvate kinase. We also found that SB treatment resulted in a decrease in mitochondrial content of eight proteins, of which all but two are established mitochondrial proteins. To confirm a role for mitochondrial import versus a change in protein synthesis and/or degradation, we measured changes in these proteins in whole cell extracts. Taken together, these data show that SB leads to a remodeling of the mitochondrial proteome that is partially GD sensitive.
Increases in intracellular sodium activate transcription and gene expression via the salt-inducible kinase 1 network in an atrial myocyte cell line
Authors: Popov Sergej , Venetsanou Kyriaki , Chedrese P. Jorge , Pinto Vanda , Takemori Hiroshi , Franco-Cereceda Anders , Eriksson Per , Mochizuki Naoki , Soares-da-Silva Patricio , Bertorello Alejandro M.
Published: March 2012

Cardiac hypertrophy (CH) generally occurs as the result of the sustained mechanical stress caused by elevated systemic arterial blood pressure (BP). However, in animal models, elevated salt intake is associated with CH even in the absence of significant increases in BP. We hypothesize that CH is not exclusively the consequence of mechanical stress but also of other factors associated with elevated BP such as abnormal cell sodium homeostasis. We examined the effect of small increases in intracellular sodium concentration ([Na+]i) on transcription factors and genes associated with CH in a cardiac cell line. Increases in [Na+]iled to a time-dependent increase in the expression levels of mRNA for natriuretic peptide and myosin heavy chain genes and also increased myocyte enhancer factor (MEF)2/nuclear factor of activated T cell (NFAT) transcriptional activity. Increases in [Na+]iare associated with activation of salt-inducible kinase 1 (snflk-1, SIK1), a kinase known to be critical for cardiac development. Moreover, increases in [Na+]iresulted in increased SIK1 expression. Sodium did not increase MEF2/NFAT activity or gene expression in cells expressing a SIK1 that lacked kinase activity. The mechanism by which SIK1 activated MEF2 involved phosphorylation of HDAC5. Increases in [Na+]iactivate SIK1 and MEF2 via a parallel increase in intracellular calcium through the reverse mode of Na+/Ca2+-exchanger and activation of CaMK1. These data obtained in a cardiac cell line suggest that increases in intracellular sodium could influence myocardial growth by controlling transcriptional activation and gene expression throughout the activation of the SIK1 network.
Effects of increased preload on the force-frequency response and contractile kinetics in early stages of cardiac muscle hypertrophy
Authors: Haizlip Kaylan M. , Bupha-Intr Tepmanas , Biesiadecki Brandon J. , Janssen Paul M. L.
Published: March 2012

Numerous studies have aimed to elucidate markers for the onset of decompensatory hypertrophy and heart failure in vivo and in vitro. Alterations in the force-frequency relationship are commonly used as markers for heart failure with a negative staircase being a hallmark of decompensated cardiac function. Here we aim to determine the functional and molecular alterations in the very early stages of compensatory hypertrophy through analysis of the force-frequency relationship, using a novel isolated muscle culture system that allows assessment of force-frequency relationship during the development of hypertrophy. New Zealand white male rabbit trabeculae excised from the right ventricular free wall were utilized for all experiments. Briefly, muscles held at constant preload and contracting isometrically were stimulated to contract in culture for 24 h, and in a subset up to 48 h. We found that, upon an increase in the preload and maintaining the muscles in culture for up to 24 h, there was an increase in baseline force produced by isolated trabeculae over time. This suggests a gradual compensatory response to the impact of increased preload. Temporal analysis of the force-frequency response during this progression revealed a significant blunting (at 12 h) and then reversal of the positive staircase as culture time increased (at 24 h). Phosphorylation analysis revealed a significant decrease in desmin and troponin (Tn)I phosphorylation from 12 to 24 h in culture. These results show that even very early on in the compensatory hypertrophy state, the force-frequency relationship is already affected. This effect on force-frequency relationship may, in addition to protein expression changes, be partially attributed to the alterations in myofilament protein phosphorylation.
Contractile parameters and occurrence of alternans in isolated rat myocardium at supra-physiological stimulation frequency
Authors: Slabaugh Jessica L. , Brunello Lucia , Gyorke Sandor , Janssen Paul M. L.
Published: March 2012

The cardiac refractory period prevents the heart from tetanic activation that is typically used in noncardiac striated muscle tissue. To what extent the refractory period prevents successive action potentials to activate the excitation-contraction coupling process and contractile machinery at supra-physiological rates, such as those present during ventricular fibrillation, is unknown. Using multicellular trabeculae isolated from rat hearts, we studied amplitude and kinetics of contraction at rates well above the normal in vivo rat heart range. We show that even at twice the maximal heart rate of the rat, little or no mechanical instability is observed; twitch contractions are at steady state, albeit with an elevated active diastolic force. Although the amplitude of contraction increased within in vivo heart rates (positive force-frequency response), at frequencies beyond the maximal heart rate (10–30 Hz) a steady decline of contractile amplitude is observed. Not until 30 Hz do the majority of the isolated muscle preparations show mechanical alternans, where strong and weak beats alternate. Interestingly, unlike striated limb skeletal muscle, fusing of twitch contractions did not cause a continuous increase in peak force: at frequencies of 10 Hz and above, systolic force declines with relatively little elevation in diastolic force. Contractile kinetics continued to accelerate, from 1 Hz up to 30 Hz, whereas the relative speed of contraction and relaxation remained closely coupled, reflected by a singular linear relationship between the maximal and minimal derivative of force (dF/d t). We conclude that cardiac muscle can produce mechanically stable steady-state contractions at supra-physiological pacing rates, while these contractions continue to decline in amplitude and increase in diastolic force past maximal heart rate.
Hyperoxia alters the mechanical properties of alveolar epithelial cells
Authors: Roan Esra , Wilhelm Kristina , Bada Alex , Makena Patrudu S. , Gorantla Vijay K. , Sinclair Scott E. , Waters Christopher M.
Published: March 2012

Patients with severe acute lung injury are frequently administered high concentrations of oxygen (>50%) during mechanical ventilation. Long-term exposure to high levels of oxygen can cause lung injury in the absence of mechanical ventilation, but the combination of the two accelerates and increases injury. Hyperoxia causes injury to cells through the generation of excessive reactive oxygen species. However, the precise mechanisms that lead to epithelial injury and the reasons for increased injury caused by mechanical ventilation are not well understood. We hypothesized that alveolar epithelial cells (AECs) may be more susceptible to injury caused by mechanical ventilation if hyperoxia alters the mechanical properties of the cells causing them to resist deformation. To test this hypothesis, we used atomic force microscopy in the indentation mode to measure the mechanical properties of cultured AECs. Exposure of AECs to hyperoxia for 24 to 48 h caused a significant increase in the elastic modulus (a measure of resistance to deformation) of both primary rat type II AECs and a cell line of mouse AECs (MLE-12). Hyperoxia also caused remodeling of both actin and microtubules. The increase in elastic modulus was blocked by treatment with cytochalasin D. Using finite element analysis, we showed that the increase in elastic modulus can lead to increased stress near the cell perimeter in the presence of stretch. We then demonstrated that cyclic stretch of hyperoxia-treated cells caused significant cell detachment. Our results suggest that exposure to hyperoxia causes structural remodeling of AECs that leads to decreased cell deformability.
Characterization of Selective Antibacterial Peptides by Polarity Index
Authors: Polanco C. , Samaniego J. L. , Buhse T. , Mosqueira F. G. , Negron-Mendoza A. , Ramos-Bernal S. , Castanon-Gonzalez J. A.
Published: April 2012

In the recent decades, antibacterial peptides have occupied a strategic position for pharmaceutical drug applications and became subject of intense research activities since they are used to strengthen the immune system of all living organisms by protecting them from pathogenic bacteria. This work proposes a simple and easy statistical/computational method through a peptide polarity index measure by which an antibacterial peptide subgroup can be efficiently identified, that is, characterized by a high toxicity to bacterial membranes but presents a low toxicity to mammal cells. These peptides also have the feature not to adopt to an alpha-helicoidal structure in aqueous solution. The double-blind test carried out to the whole Antimicrobial Peptide Database (November 2011) showed an accuracy of 90% applying the polarity index method for the identification of such antibacterial peptide groups.
The Effects of Chemotherapy on Cognitive Function in a Mouse Model: A Prospective Study
Authors: Winocur Gordon , Henkelman Mark , Wojtowicz J. Martin , Zhang Haibo , Binns Malcolm A. , Tannock Ian F.
Published: March 2012

Purpose: Clinical studies indicate that up to 70% of patients with cancer who receive chemotherapy experience cognitive impairment. The present study used a prospective longitudinal design to assess short- and long-term effects of commonly used anticancer drugs on cognitive performance in a mouse model.

Experimental Design: Normal mice received three weekly injections of a combination of methotrexate + 5-fluorouracil (CHEMO group) or an equal volume of saline (SAL group). Cognitive tests, measuring different aspects of learning and memory, were administered before treatment, immediately after treatment, and three months later. Structural MRI scanning was conducted at each stage of cognitive testing.

Results: The CHEMO group exhibited deficits on cognitive tasks acquired pretreatment [spatial memory, nonmatching-to-sample (NMTS) learning, and delayed NMTS], as well as impaired new learning on two tasks (conditional associative learning, discrimination learning) introduced posttreatment. Consistent with clinical evidence, cognitive deficits were pronounced on tests that are sensitive to hippocampal and frontal lobe dysfunction, but the CHEMO group's poor performance on the discrimination learning problem suggests that impairment is more widespread than previously thought. Cognitive deficits persisted for at least three months after treatment but some recovery was noted, particularly on tests thought to be under frontal lobe control. The MRI tests did not detect brain changes that could be attributed to treatment.

Conclusions: Chemotherapeutic agents can have adverse effects on information acquired pretreatment as well as new learning and memory and, despite some recovery, impairment is long lasting. Clin Cancer Res; 18(11); 3112–21. ©2012 AACR.