bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Antimicrobial Dosage Regimen onSalmonellaandEscherichia coliIsolates from Feeder Swine
Authors: Wagner Bruce A. , Straw Barbara E. , Fedorka-Cray Paula J. , Dargatz David A. 
Published: January 2008

ABSTRACTA body of evidence exists that suggests that antimicrobial use in food animals leads to resistance in both pathogenic and commensal bacteria. This study focused on the impact of three different antimicrobial regimes (low-level continuous, pulse, and no antimicrobial) for two antimicrobials (chlortetracycline and tylosin) on the presence ofSalmonellaspp. and on the prevalence of antimicrobial resistance of bothSalmonellaspp. and nonspecificEscherichia coliin fecal samples from feeder swine. The prevalence of fecal samples positive forSalmonellaspp. significantly decreased between the samples taken at feeder placement compared to samples taken when the animals were close to market weight. Differences in resistance ofSalmonellaspp. did not appear to be influenced by dosing treatment including the control. Analysis of antimicrobial resistance examining both susceptibility and resistance, as well as MIC outcomes, demonstrated that only resistance to cephalothin increased inE. coliunder the pulse chlortetracycline treatment. These results suggest that the dosing regimes examined in this study did not lead to an increase in either the prevalence ofSalmonellaspp. or the prevalence of antimicrobial resistance in isolates ofSalmonellaspp. orE. coli.
Mucin Degradation by
Bifidobacterium
Strains Isolated from the Human Intestinal Microbiota
Authors: Ruas-Madiedo Patricia , Gueimonde Miguel , Fernández-García María , de los Reyes-Gavilán Clara G. , Margolles Abelardo 
Published: January 2008

ABSTRACT

The presence of the genes
engBF
(
endo
-α-
N
-acetylgalactosaminidase) and
afcA
(1,2-α-
l
-fucosidase) was detected in several intestinal
Bifidobacterium
isolates. Two strains of
Bifidobacterium bifidum
contained both genes, and they were able to degrade high-molecular weight porcine mucin in vitro. The expression of both genes was highly induced in the presence of mucin.
Genetic Modulation of the Overexpression of Tailoring Genes
eryK
and
eryG
Leading to the Improvement of Erythromycin A Purity and Production in
Saccharopolyspora erythraea
Fermentation
Authors: Chen Yun , Deng Wei , Wu Jiequn , Qian Jiangchao , Chu Ju , Zhuang Yingping , Zhang Siliang , Liu Wen 
Published: January 2008

ABSTRACT

Erythromycin A (Er-A) is the most potent and clinically important member in the Er family produced by
Saccharopolyspora erythraea
. Er-B and Er-C, which are biologically much less active and cause greater side effects than Er-A, serve as the intermediates for Er-A biosynthesis and impurities in fermentation processes of many industrial strains. In this study, systematical modulation of the amounts of tailoring enzymes EryK (a P450 hydroxylase) and EryG (an
S
-adenosylmethionine-dependent
O
-methyltransferase) was carried out by genetic engineering in
S. erythraea
, including alterations of gene copy number ratio and organization and integrating the locus on the chromosome by homologous recombination. Introduction of additional
eryK
and
eryG
genes into
S. erythraea
showed significant impacts on their transcription levels and enhanced the biotransformation process from Er-D to Er-A with gene dose effects. At the
eryK
/
eryG
copy number ratio of 3:2 as well as their resultant transcript ratio of around 2.5:1 to 3.0:1, Er-B and Er-C were nearly completely eliminated and accordingly converted to Er-A, and the Er titer was improved by around 25% in the recombinant strain ZL1004 (genotype
PermK*-K-K-G
+
PermE*-K
+
PermA*-G
) and ZL1007 (genotype
PermK*-K-G-K
+
PermE*-K
+
PermA*-G
). This study may contribute to the continuous efforts toward further evaluation of the Er-producing system, with the aims of improving Er-A purity and production at the fermentation stage and lowering the production costs and environmental concerns in industry.
Bacillus thuringiensis
Cry1Ac Toxin-Binding and Pore-Forming Activity in Brush Border Membrane Vesicles Prepared from Anterior and Posterior Midgut Regions of Lepidopteran Larvae
Authors: Rodrigo-Simón Ana , Caccia Silvia , Ferré Juan 
Published: January 2008

ABSTRACT

It is generally accepted that
Bacillus thuringiensis
Cry toxins insert into the apical membrane of the larval midgut after binding to specific receptors, and there is evidence that the distribution of binding molecules along the midgut is not uniform. By use of the voltage-sensitive dye DiSC
3
(5) and
125
I-labeled Cry1Ac, we have measured the effect of Cry1Ac in terms of permeabilization capacity and of binding parameters on brush border membrane vesicles (BBMV) prepared from the anterior and the posterior regions of the larval midgut from two insect species,
Manduca sexta
and
Helicoverpa armigera
. The permeabilizing activity was significantly higher with BBMV from the posterior region than with the one observed in the anterior region in both insect species. Instead,
125
I-Cry1Ac bound specifically to BBMV from the two midgut regions, with no significant differences in the binding parameters between the anterior and posterior regions within an insect species.
N
-acetylgalactosamine inhibition patterns on pore formation and binding differed between anterior and posterior midgut regions and between species, providing evidence of a multifaceted involvement of the sugar in the Cry1Ac mode of action. The analysis of binding and pore formation in different midgut regions could be an effective method to study differences in the mode of action of Cry1Ac toxin in different species.
Eighty Years after Its Discovery, Fleming's
Penicillium
Strain Discloses the Secret of Its Sex
Authors: Hoff Birgit , Pöggeler Stefanie , Kück Ulrich 
Published: January 2008

ABSTRACT

Eighty years ago, Alexander Fleming discovered antibacterial activity in the asexual mold
Penicillium
, and the strain he studied later was replaced by an overproducing isolate still used for penicillin production today. Using a heterologous PCR approach, we show that these strains are of opposite mating types and that both have retained transcriptionally expressed pheromone and pheromone receptor genes required for sexual reproduction. This discovery extends options for industrial strain improvement programs using conventional genetical approaches.
Genetic Diversity of Heat-Labile Toxin Expressed by Enterotoxigenic
Escherichia coli
Strains Isolated from Humans
Authors: Lasaro M. A. , Rodrigues J. F. , Mathias-Santos C. , Guth B. E. C. , Balan A. , Sbrogio-Almeida M. E. , Ferreira L. C. S. 
Published: January 2008

ABSTRACT

The natural diversity of the
elt
operons, encoding the heat-labile toxin LT-I (LT), carried by enterotoxigenic
Escherichia coli
(ETEC) strains isolated from humans was investigated. For many years, LT was supposed to be represented by a rather conserved toxin, and one derivative, produced by the reference H10407 strain, was intensively studied either as a virulence factor or as a vaccine adjuvant. Amplicons encompassing the two LT-encoding genes (
eltA
and
eltB
) of 51 human-derived ETEC strains, either LT
+
(25 strains) only or LT
+
/ST
+
(26 strains), isolated from asymptomatic (24 strains) or diarrheic (27 strains) subjects, were subjected to restriction fragment length polymorphism (RFLP) analysis and DNA sequencing. Seven polymorphic RFLP types of the H10407 strain were detected with six (BsaI, DdeI, HhaI, HincII, HphI, and MspI) restriction enzymes. Additionally, the single-nucleotide polymorphic analysis revealed 50 base changes in the
elt
operon, including 21 polymorphic sites at
eltA
and 9 at
eltB
. Based on the deduced amino acid sequences, 16 LT types were identified, including LT1, expressed by the H10407 strain and 23 other strains belonging to seven different serotypes, and LT2, expressed by 11 strains of six different serotypes. In vitro experiments carried out with purified toxins indicated that no significant differences in GM1-binding affinity could be detected among LT1, LT2, and LT4. However, LT4, but not other toxin types, showed reduced toxic activities measured either in vitro with cultured cells (Y-1 cells) or in vivo in rabbit ligated ileal loops. Collectively, these results indicate that the natural diversity of LTs produced by wild-type ETEC strains isolated from human hosts is considerably larger than previously assumed and may impact the pathogeneses of the strains and the epidemiology of the disease.
Regulation of Swarming Motility andflhDCSmExpression by RssAB Signaling inSerratia marcescens
Authors: Soo Po-Chi , Horng Yu-Tze , Wei Jun-Rong , Shu Jwu-Ching , Lu Chia-Chen , Lai Hsin-Chih 
Published: January 2008

ABSTRACTSerratia marcescenscells swarm at 30°C but not at 37°C, and the underlying mechanism is not characterized. Our previous studies had shown that a temperature upshift from 30 to 37°C reduced the expression levels offlhDCSmandhagSminS. marcescensCH-1. Mutation inrssAorrssB, cognate genes that comprise a two-component system, also resulted in precocious swarming phenotypes at 37°C. To further characterize the underlying mechanism, in the present study, we report that expression offlhDCSmand synthesis of flagella are significantly increased in therssAmutant strain at 37°C. Primer extension analysis for determination of the transcriptional start site(s) offlhDCSmrevealed two transcriptional start sites, P1 and P2, inS. marcescensCH-1. Characterization of the phosphorylated RssB (RssB∼P) binding site by an electrophoretic mobility shift assay showed direct interaction of RssB∼P, but not unphosphorylated RssB [RssB(D51E)], with the P2 promoter region. A DNase I footprinting assay using a capillary electrophoresis approach further determined that the RssB∼P binding site is located between base pair positions −341 and −364 from the translation start codon ATG in theflhDCSmpromoter region. The binding site overlaps with the P2 “−35” promoter region. A modified chromatin immunoprecipitation assay was subsequently performed to confirm that RssB∼P binds to theflhDCSmpromoter region in vivo. In conclusion, our results indicated that activated RssA-RssB signaling directly inhibitsflhDCSmpromoter activity at 37°C. This inhibitory effect was comparatively alleviated at 30°C. This finding might explain, at least in part, the phenomenon of inhibition ofS. marcescensswarming at 37°C.
A ViableBacillus subtilisStrain without Functional Extracytoplasmic Function Sigma Genes
Authors: Asai Kei , Ishiwata Keisuke , Matsuzaki Kunihiko , Sadaie Yoshito 
Published: January 2008

ABSTRACTWe constructed aBacillus subtilisMarburg strain that harbors deletion mutations in all seven extracytoplasmic function (ECF) sigma genes. The strain shows wild-type growth at 37°C both in a complex and in a synthetic medium and exhibits wild-type sporulation. ECF sigma genes ofB. subtilisare dispensable as long as no stress is imposed, although they seem to be required for quick response to stresses.
Escherichia coli
Peptidase A, B, or N Can Process Translation Inhibitor Microcin C
Authors: Kazakov Teymur , Vondenhoff Gaston H. , Datsenko Kirill A. , Novikova Maria , Metlitskaya Anastasia , Wanner Barry L. , Severinov Konstantin 
Published: January 2008

ABSTRACT

The heptapeptide-nucleotide microcin C (McC) targets aspartyl-tRNA synthetase. Upon its entry into a susceptible cell, McC is processed to release a nonhydrolyzable aspartyl-adenylate that inhibits aspartyl-tRNA synthetase, leading to the cessation of translation and cell growth. Here, we surveyed
Escherichia coli
cells with singly, doubly, and triply disrupted broad-specificity peptidase genes to show that any of three nonspecific oligopeptidases (PepA, PepB, or PepN) can effectively process McC. We also show that the rate-limiting step of McC processing in vitro is deformylation of the first methionine residue of McC.
B7-H1 is a ubiquitous antiapoptotic receptor on cancer cells
Authors: Azuma Takeshi , Yao Sheng , Zhu Gefeng , Flies Andrew S. , Flies Sarah J. , Chen Lieping 
Published: January 2008

AbstractB7-H1 is an immunoglobulin-like immune suppressive molecule broadly detectable on the majority of human and rodent cancers, and its functions have been attributed to delivering an inhibitory signal to its counter-receptor programmed death-1 (PD-1) on T cells. Here we report that B7-H1 on cancer cells receives a signal from PD-1 to rapidly induce resistance against T cell–mediated killing because crippling signaling capacity of B7-H1 but not PD-1 ablates this resistance. Importantly, loss of B7-H1 signaling is accompanied by increased susceptibility to immune-mediated tumoricidal activity. In addition to resistance against T-cell destruction, B7-H1+ cancer cells also become refractory to apoptosis induced by Fas ligation or the protein kinase inhibitor Staurosporine. Our study reveals a new mechanism by which cancer cells use a receptor on immune cells as a ligand to induce resistance to therapy.
CD8+ but not CD4+ T cells require cognate interactions with target tissues to mediate GVHD across only minor H antigens, whereas both CD4+ and CD8+ T cells require direct leukemic contact to mediate GVL
Authors: Matte-Martone Catherine , Liu Jinli , Jain Dhanpat , McNiff Jennifer , Shlomchik Warren D. 
Published: January 2008

AbstractWhether T-cell antigen receptors (TCR) on donor T cells require direct interactions with major histocompatibility complex class I or class II (MHCI/MHCII) molecules on target cells to mediate graft-versus-host disease (GVHD) and graft-versus-leukemia (GVL) is a fundamental question in allogeneic stem-cell transplantation (alloSCT). In MHC-mismatched mouse models, these contacts were not required for GVHD. However, this conclusion may not apply to MHC-matched, multiple minor histocompatibility antigen-mismatched alloSCT, the most common type performed clinically. To address this, we used wild-type (wt)→MHCI−/− or wt→MHCII−/− bone marrow chimeras as recipients in GVHD experiments. For GVL experiments, we used MHCI−/− or MHCII−/− chronic-phase CML cells created by expressing the BCR-ABL cDNA in bone marrow from MHCI−/− or MHCII−/− mice. TCR/MHCI contact was obligatory for both CD8-mediated GVHD and GVL. In contrast, CD4 cells induced GVHD in wt→MHCII−/− chimeras, whereas MHCII−/− mCP-CML was GVL-resistant. Donor CD4 cells infiltrated affected skin and bowel in wt→MHCII−/− recipients, indicating that they mediated GVHD by acting locally. Thus, CD4 cells use distinct effector mechanisms in GVHD and GVL: direct cytolytic action is required for GVL but not for GVHD. If these noncytolytic pathways can be inhibited, then GVHD might be ameliorated while preserving GVL.
Should adjustment for covariates be used in prevalence estimations?
Authors: Li Wenjun , Stanek Edward J , Bertone-Johnson Elizabeth R 
Published: January 2008

Abstract
Background
Adjustment for covariates (also called auxiliary variables in survey sampling literature) is commonly applied in health surveys to reduce the variances of the prevalence estimators. In theory, adjusted prevalence estimators are more accurate when variance components are known. In practice, variance components needed to achieve the adjustment are unknown and their sample estimators are used instead. The uncertainty introduced by estimating variance components may overshadow the reduction in the variance of the prevalence estimators due to adjustment. We present empirical guidelines indicating when adjusted prevalence estimators should be considered, using gender adjusted and unadjusted smoking prevalence as an illustration.

Methods
We compare the accuracy of adjusted and unadjusted prevalence estimators via simulation. We simulate simple random samples from hypothetical populations with the proportion of males ranging from 30% to 70%, the smoking prevalence ranging from 15% to 35%, and the ratio of male to female smoking prevalence ranging from 1 to 4. The ranges of gender proportions and smoking prevalences reflect the conditions in 1999–2003 Behavioral Risk Factors Surveillance System (BRFSS) data for Massachusetts. From each population, 10,000 samples are selected and the ratios of the variance of the adjusted prevalence estimators to the variance of the unadjusted (crude) ones are computed and plotted against the proportion of males by population prevalence, as well as by population and sample sizes. The prevalence ratio thresholds, above which adjusted prevalence estimators have smaller variances, are determined graphically.

Results
In many practical settings, gender adjustment results in less accuracy. Whether or not there is better accuracy with adjustment depends on sample sizes, gender proportions and ratios between male and female prevalences. In populations with equal number of males and females and smoking prevalence of 20%, the adjusted prevalence estimators are more accurate when the ratios of male to female prevalences are above 2.4, 1.8, 1.6, 1.4 and 1.3 for sample sizes of 25, 50, 100, 150 and 200, respectively.

Conclusion
Adjustment for covariates will not result in more accurate prevalence estimator when ratio of male to female prevalences is close to one, sample size is small and risk factor prevalence is low. For example, when reporting smoking prevalence based on simple random sampling, gender adjustment is recommended only when sample size is greater than 200.
Old Dispersions and Scenes for the Production of Public Space The Constructive Margins of Secondarity
Authors: de Meulder Bruno 
Published: January 2008

AbstractThe density of development in Belgium is such that the entire country has become an open city, with little sense of where one metropolitan area begins and another ends. Bruno De Meulder describes the underlying logic of this unbroken urbanscape, and the opportunity it affords for re‐editing and reinserting informal social spaces in areas of wasted land. Copyright © 2008 John Wiley & Sons, Ltd.
Reinvigorating Childhood
Authors: Watson Howard 
Published: January 2008

AbstractHoward Watson is uplifted by the ‘brave, graceful subtlety’ of Caruso St John's redevelopment of the Bethnal Green Museum of Childhood in east London. He finds the pared‐down spaces of the interior surprisingly in accord with the original Victorian structure, drawing their inspiration from ‘the regimented order of grand Victorian museology’. Copyright © 2008 John Wiley & Sons, Ltd.
Natural Methods of Interaction Or Natural Interaction in the Everyday Digital World
Authors: Croci Valentina 
Published: January 2008

AbstractComputers, mobiles and automatised machines are so omnipresent that the means by which we interact with digital devices is now generally regarded as a given. Italian practice iO Agency, though, questions our use of mechanised interfaces and the language that they require us to learn. Valentina Croci explains how iO Agency has developed more natural ways for people to interact with digital environments through physical or tactile ‘triggers’. Copyright © 2008 John Wiley & Sons, Ltd.
On the energy transfer between the electromagnetic field and nanomachines for biological applications
Authors: Bellizzi G. , Bucci O. M. , Capozzoli A. 
Published: January 2008

AbstractThe article presents a simple expression of the power transferred from the electromagnetic field (EMF) to a biological nanomachine (NM) embedded in a background medium (BM). The expression is useful to analyse the interaction mechanism and test the hypothesis on its nature. Furthermore, it should represent a helpful tool to design remotely controlled NMs for bio‐medical applications and the relative electromagnetic control apparatuses. Finally, to show its practical usefulness, we used it to discuss the hypothesis on the energy transfer mechanism proposed in the literature to explain intriguing experimental phenomena referring to the remotely controlled dehybridization of DNA molecules attached to gold nanocrystals. Bioelectromagnetics 29:331–339, 2008. © 2008 Wiley‐Liss, Inc.
Improvement of student understanding of how kinetic data facilitates the determination of amino acid catalytic function through an alkaline phosphatase structure/mechanism bioinformatics exercise
Authors: Grunwald Sandra K. , Krueger Katherine J. 
Published: January 2008

AbstractLaboratory exercises, which utilize alkaline phosphatase as a model enzyme, have been developed and used extensively in undergraduate biochemistry courses to illustrate enzyme steady‐state kinetics. A bioinformatics laboratory exercise for the biochemistry laboratory, which complements the traditional alkaline phosphatase kinetics exercise, was developed and implemented. In this exercise, students examine the structure of alkaline phosphatase using the free, on‐line bioinformatics protein‐modeling program Protein Explorer. Specifically, students examine the active site residues of alkaline phosphatase and propose functions for these residues. Furthermore, by examining the mechanism of alkaline phosphatase and by using the published kinetic data, students propose specific roles for several active‐site residues. Paired t‐test analysis of pre‐ versus postexercise assessment data shows that the completion of the exercise improves student's ability to use kinetic data correctly thereby determining a probable catalytic function for an active site amino acid.
Interactive computer simulations of genetics, biochemistry, and molecular biology
Authors: White Brian T. , Bolker Ethan D. 
Published: January 2008

AbstractThis article describes three interactive software simulations targeted to key domains of modern molecular genetics: genetics, biochemistry, and molecular biology. These simulations allow students to deepen their understanding of key principles in these domains by setting up crosses, designing proteins, and designing genes; the simulations then apply these principles to produce results that the students can interpret. Using this software, students can confront their misconceptions and connect these disciplines in a way that is difficult if not impossible without an interactive environment. We present lab exercises that guide the students as they use the software in a series of activities that begin by introducing the tools and build towards more open inquiry. Preliminary evaluation shows that students enjoy the software and that it promotes active engagement and application of the material. The open‐source Java software and the relevant lab manuals are available free of charge on line.