bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure-Activity Relationship of Synthetic Variants of the Milk-Derived Antimicrobial Peptide α
s2
-Casein f(183–207)
Authors: Alvarez-Ordóñez Avelino , Begley Máire , Clifford Tanya , Deasy Thérèse , Considine Kiera , Hill Colin
Published: June 2013

Template-based studies on antimicrobial peptide (AMP) derivatives obtained through manipulation of the amino acid sequence are helpful to identify properties or residues that are important for biological activity. The present study sheds light on the importance of specific amino acids of the milk-derived α
s2
-casein f(183–207) peptide to its antibacterial activity against the food-borne pathogens
Listeria monocytogenes
and
Cronobacter sakazakii
. Trimming of the peptide revealed that residues at the C-terminal end of the peptide are important for activity. Removal of the last 5 amino acids at the C-terminal end and replacement of the Arg at position 23 of the peptide sequence by an Ala residue significantly decreased activity. These findings suggest that Arg23 is very important for optimal activity of the peptide. Substitution of the also positively charged Lys residues at positions 15 and 17 of the α
s2
-casein f(183–207) peptide also caused a significant reduction of the effectiveness against
C. sakazakii
, which points toward the importance of the positive charge of the peptide for its biological activity. Indeed, simultaneous replacement of various positively charged amino acids was linked to a loss of bactericidal activity. On the other hand, replacement of Pro residues at positions 14 and 20 resulted in a significantly increased antibacterial potency, and hydrophobic end tagging of α
s2
-casein f(193–203) and α
s2
-casein f(197–207) peptides with multiple Trp or Phe residues significantly increased their potency against
L. monocytogenes
. Finally, the effect of pH (4.5 to 7.4), temperature (4°C to 37°C), and addition of sodium and calcium salts (1% to 3%) on the activity of the 15-amino-acid α
s2
-casein f(193–207) peptide was also determined, and its biological activity was shown to be completely abolished in high-saline environments.
Longitudinal Study of Distributions of Similar Antimicrobial-Resistant Salmonella Serovars in Pigs and Their Environment in Two Distinct Swine Production Systems
Authors: Keelara Shivaramu , Scott H. Morgan , Morrow William M. , Gebreyes Wondwossen A. , Correa Maria , Nayak Rajesh , Stefanova Rossina , Thakur Siddhartha
Published: June 2013

The aim of this longitudinal study was to determine and compare the prevalences and genotypic profiles of antimicrobial-resistant (AR)Salmonellaisolates from pigs reared in antimicrobial-free (ABF) and conventional production systems at farm, at slaughter, and in their environment. We collected 2,889 pig fecal and 2,122 environmental (feed, water, soil, lagoon, truck, and floor swabs) samples from 10 conventional and eight ABF longitudinal cohorts at different stages of production (farrowing, nursery, finishing) and slaughter (postevisceration, postchill, and mesenteric lymph nodes [MLN]). In addition, we collected 1,363 carcass swabs and 205 lairage and truck samples at slaughter. A total of 1,090Salmonellaisolates were recovered from the samples; these were isolated with a significantly higher prevalence in conventionally reared pigs (4.0%;n= 66) and their environment (11.7%;n= 156) than in ABF pigs (0.2%;n= 2) and their environment (0.6%;n= 5) (P< 0.001).Salmonellawas isolated from all stages at slaughter, including the postchill step, in the two production systems.Salmonellaprevalence was significantly higher in MLN extracted from conventional carcasses than those extracted from ABF carcasses (P< 0.001). We identified a total of 24 different serotypes, withSalmonella entericaserovar Typhimurium,Salmonella entericaserovar Anatum,Salmonella entericaserovar Infantis, andSalmonella entericaserovar Derby being predominant. The highest frequencies of antimicrobial resistance (AR) were exhibited to tetracycline (71%), sulfisoxazole (42%), and streptomycin (17%). Multidrug resistance (resistance to ≥3 antimicrobials; MDR) was detected in 27% (n= 254) of theSalmonellaisolates from the conventional system. Our study reports a low prevalence ofSalmonellain both production systems in pigs on farms, while a higher prevalence was detected among the carcasses at slaughter. The dynamics ofSalmonellaprevalence in pigs and carcasses were reciprocated in the farm and slaughter environment, clearly indicating an exchange of this pathogen between the pigs and their surroundings. Furthermore, the phenotypic and genotypic fingerprint profile results underscore the potential role played by environmental factors in dissemination of ARSalmonellato pigs.
Polysaccharide-Degrading Thermophiles Generated by Heterologous Gene Expression in Geobacillus kaustophilus HTA426
Authors: Suzuki Hirokazu , Yoshida Ken-ichi , Ohshima Toshihisa
Published: June 2013

Thermophiles have important advantages over mesophiles as host organisms for high-temperature bioprocesses, functional production of thermostable enzymes, and efficient expression of enzymatic activitiesin vivo. To capitalize on these advantages of thermophiles, we describe here a new inducible gene expression system in the thermophileGeobacillus kaustophilusHTA426. Six promoter regions in the HTA426 genome were identified and analyzed for expression profiles using β-galactosidase reporter assay. This analysis identified a promoter region upstream of a putative amylose-metabolizing gene cluster that directed high-level expression of the reporter gene. The expression was >280-fold that without a promoter and was further enhanced 12-fold by maltose addition. In association with a multicopy plasmid, this promoter region was used to express heterologous genes. Several genes, including a gene whose product was insoluble when expressed inEscherichia coli, were successfully expressed as soluble proteins, with yields of 0.16 to 59 mg/liter, and conferred new functions toG. kaustophilusstrains. Remarkably, cellulase and α-amylase genes conferred the ability to degrade cellulose paper and insoluble starch at high temperatures, respectively, generating thermophiles with the potential to degrade plant biomass. Our results demonstrate that this novel expression system expands the potential applications ofG. kaustophilus.
Characterization of a Feruloyl Esterase from Lactobacillus plantarum
Authors: Esteban-Torres María , Reverón Inés , Mancheño José Miguel , de las Rivas Blanca , Muñoz Rosario
Published: June 2013

Lactobacillus plantarum
is frequently found in the fermentation of plant-derived food products, where hydroxycinnamoyl esters are abundant.
L. plantarum
WCFS1 cultures were unable to hydrolyze hydroxycinnamoyl esters; however, cell extracts from the strain partially hydrolyze methyl ferulate and methyl
p
-coumarate. In order to discover whether the protein Lp_0796 is the enzyme responsible for this hydrolytic activity, it was recombinantly overproduced and enzymatically characterized. Lp_0796 is an esterase that, among other substrates, is able to efficiently hydrolyze the four model substrates for feruloyl esterases (methyl ferulate, methyl caffeate, methyl
p
-coumarate, and methyl sinapinate). A screening test for the detection of the gene encoding feruloyl esterase Lp_0796 revealed that it is generally present among
L. plantarum
strains. The present study constitutes the description of feruloyl esterase activity in
L. plantarum
and provides new insights into the metabolism of hydroxycinnamic compounds in this bacterial species.
Novel, Oxygen-Insensitive Group 5 [NiFe]-Hydrogenase in Ralstonia eutropha
Authors: Schäfer Caspar , Friedrich Bärbel , Lenz Oliver
Published: June 2013

Recently, a novel group of [NiFe]-hydrogenases has been defined that appear to have a great impact in the global hydrogen cycle. This so-called group 5 [NiFe]-hydrogenase is widespread in soil-living actinobacteria and can oxidize molecular hydrogen at atmospheric levels, which suggests a high affinity of the enzyme toward H
2
. Here, we provide a biochemical characterization of a group 5 hydrogenase from the betaproteobacterium
Ralstonia eutropha
H16. The hydrogenase was designated an actinobacterial hydrogenase (AH) and is catalytically active, as shown by the
in vivo
H
2
uptake and by activity staining in native gels. However, the enzyme does not sustain autotrophic growth on H
2
. The AH was purified to homogeneity by affinity chromatography and consists of two subunits with molecular masses of 65 and 37 kDa. Among the electron acceptors tested, nitroblue tetrazolium chloride was reduced by the AH at highest rates. At 30°C and pH 8, the specific activity of the enzyme was 0.3 μmol of H
2
per min and mg of protein. However, an unexpectedly high Michaelis constant (

K
m

) for H
2
of 3.6 ± 0.5 μM was determined, which is in contrast to the previously proposed low

K
m

of group 5 hydrogenases and makes atmospheric H
2
uptake by
R. eutropha
most unlikely. Amperometric activity measurements revealed that the AH maintains full H
2
oxidation activity even at atmospheric oxygen concentrations, showing that the enzyme is insensitive toward O
2
.
Exploring Environmental Control of Cyclic di-GMP Signaling in Vibrio cholerae by Using theEx VivoLysate Cyclic di-GMP Assay (TELCA)
Authors: Koestler Benjamin J. , Waters Christopher M.
Published: June 2013

Vibrio choleraesenses its environment, including the surrounding bacterial community, using both the second messenger cyclic di-GMP (c-di-GMP) and quorum sensing (QS) to regulate biofilm formation and other bacterial behaviors. Cyclic di-GMP is synthesized by diguanylate cyclase (DGC) enzymes and degraded by phosphodiesterase (PDE) enzymes.V. choleraeencodes a complex network of 61 enzymes predicted to mediate changes to the levels of c-di-GMP in response to extracellular signals, and the transcription of many of these enzymes is influenced by QS. Because of the complexity of the c-di-GMP signaling system inV. cholerae, it is difficult to determine if modulation of intracellular c-di-GMP in response to different stimuli is driven primarily by changes in c-di-GMP synthesis or hydrolysis. Here, we describe a novel method, named theex vivolysate c-di-GMP assay (TELCA), that systematically measures total DGC and PDE cellular activity. We show thatV. choleraegrown in different environments exhibits significantly different intracellular levels of c-di-GMP, and we used TELCA to determine that these differences correspond to changes in both c-di-GMP synthesis and hydrolysis. Furthermore, we show that the increased concentration of c-di-GMP at low cell density is primarily due to increased DGC activity due to the DGC CdgA. Our findings highlight the idea that modulation of both total DGC and PDE activity alters the intracellular concentration of c-di-GMP, and we present a new method that is widely applicable to the systematic analysis of complex c-di-GMP signaling networks.
Tracking Down Biotransformation to the Genetic Level: Identification of a Highly Flexible Glycosyltransferase from Saccharothrix espanaensis
Authors: Strobel Tina , Schmidt Yvonne , Linnenbrink Anton , Luzhetskyy Andriy , Luzhetska Marta , Taguchi Takaaki , Brötz Elke , Paululat Thomas , Stasevych Maryna , Stanko Oleg , Novikov Volodymyr , Bechthold Andreas
Published: June 2013

Saccharothrix espanaensis
is a member of the order
Actinomycetales
. The genome of the strain has been sequenced recently, revealing 106 glycosyltransferase genes. In this paper, we report the detection of a glycosyltransferase from
Saccharothrix espanaensis
which is able to rhamnosylate different phenolic compounds targeting different positions of the molecules. The gene encoding the flexible glycosyltransferase is not located close to a natural product biosynthetic gene cluster. Therefore, the native function of this enzyme might be not the biosynthesis of a secondary metabolite but the glycosylation of internal and external natural products as part of a defense mechanism.
Population Structure of Salmonella enterica Serovar 4,[5],12:b:− Strains and Likely Sources of Human Infection
Authors: Toboldt Anne , Tietze Erhard , Helmuth Reiner , Junker Ernst , Fruth Angelika , Malorny Burkhard
Published: June 2013

Salmonella enterica
serovar 4,[5],12:b:− is a monophasic serovar not able to express the second-phase flagellar antigen (H2 antigen). In Germany, the serovar is occasionally isolated from poultry, reptiles, fish, food, and humans. In this study, a selection of 67 epidemiologically unrelated
Salmonella enterica
serovar 4,[5],12:b:− strains isolated in Germany between 2000 and 2011 from the environment, animal, food, and humans was investigated by phenotypic and genotypic methods to better understand the population structure and to identify potential sources of human infections. Strains of this monophasic serovar were highly diverse. Within the 67 strains analyzed, we identified 52 different pulsed-field gel electrophoresis XbaI profiles, 12 different multilocus sequence types (STs), and 18 different pathogenicity array types. The relatedness of strains based on the pathogenicity gene repertoire (102 markers tested) was in good agreement with grouping by MLST.
S. enterica
serovar 4,[5],12:b:− is distributed across multiple unrelated eBurst groups and consequently is highly polyphyletic. Two sequence types (ST88 and ST127) were linked to
S. enterica
serovar Paratyphi B (
d
-tartrate positive), two single-locus variants of ST1583 were linked to
S. enterica
serovar Abony, and one sequence type (ST1484) was associated with
S. enterica
serovar Mygdal, a recently defined, new serovar. From the characterization of clinical isolates and those of nonhuman origin, it can be concluded that the potential sources of sporadic human infections with
S. enterica
serovar 4,[5],12:b:− most likely are mushrooms, shellfish/fish, and poultry.
Active Hydrocarbon Biosynthesis and Accumulation in a Green Alga, Botryococcus braunii (Race A)
Authors: Hirose Mana , Mukaida Fukiko , Okada Sigeru , Noguchi Tetsuko
Published: June 2013

Among oleaginous microalgae, the colonial green alga
Botryococcus braunii
accumulates especially large quantities of hydrocarbons. This accumulation may be achieved more by storage of lipids in the extracellular space rather than in the cytoplasm, as is the case for all other examined oleaginous microalgae. The stage of hydrocarbon synthesis during the cell cycle was determined by autoradiography. The cell cycle of
B. braunii
race A was synchronized by aminouracil treatment, and cells were taken at various stages in the cell cycle and cultured in a medium containing [
14
C]acetate. Incorporation of
14
C into hydrocarbons was detected. The highest labeling occurred just after septum formation, when it was about 2.6 times the rate during interphase. Fluorescent and electron microscopy revealed that new lipid accumulation on the cell surface occurred during at least two different growth stages and sites of cells. Lipid bodies in the cytoplasm were not prominent in interphase cells. These lipid bodies then increased in number, size, and inclusions, reaching maximum values just before the first lipid accumulation on the cell surface at the cell apex. Most of them disappeared from the cytoplasm concomitant with the second new accumulation at the basolateral region, where extracellular lipids continuously accumulated. The rough endoplasmic reticulum near the plasma membrane is prominent in
B. braunii
, and the endoplasmic reticulum was often in contact with both a chloroplast and lipid bodies in cells with increasing numbers of lipid bodies. We discuss the transport pathway of precursors of extracellular hydrocarbons in race A.
Mutual Cross Talk between the Regulators Hac1 of the Unfolded Protein Response and Gcn4 of the General Amino Acid Control of Saccharomyces cerevisiae
Authors: Herzog Britta , Popova Blagovesta , Jakobshagen Antonia , Shahpasandzadeh Hedieh , Braus Gerhard H.
Published: June 2013

Hac1 is the activator of the cellular response to the accumulation of unfolded proteins in the endoplasmic reticulum. Hac1 function requires the activity of Gcn4, which mainly acts as a regulator of the general amino acid control network providing
Saccharomyces cerevisiae
cells with amino acids. Here, we demonstrate novel functions of Hac1 and describe a mutual connection between Hac1 and Gcn4. Hac1 is required for induction of Gcn4-responsive promoter elements in haploid as well as diploid cells and therefore participates in the cellular amino acid supply. Furthermore, Hac1 and Gcn4 mutually influence their mRNA expression levels. Hac1 is also involved in
FLO11
expression and adhesion upon amino acid starvation. Hac1 and Gcn4 act through the same promoter regions of the
FLO11
flocculin. The results indicate an indirect effect of both transcription factors on
FLO11
expression. Our data suggest a complex mutual cross talk between the Hac1- and Gcn4-controlled networks.
Unisexual Reproduction Enhances Fungal Competitiveness by Promoting Habitat Exploration via Hyphal Growth and Sporulation
Authors: Phadke Sujal S. , Feretzaki Marianna , Heitman Joseph
Published: June 2013

Unisexual reproduction is a novel homothallic sexual cycle recently discovered in both ascomycetous and basidiomycetous pathogenic fungi. It is a form of selfing that induces the yeast-to-hyphal dimorphic transition in isolates of the α mating type of the human fungal pathogen
Cryptococcus neoformans
. Unisexual reproduction may benefit the pathogen by facilitating sexual reproduction in the absence of the opposite
a
mating type and by generating infectious propagules called basidiospores. Here, we report an independent potential selective advantage of unisexual reproduction beyond genetic exchange and recombination. We competed a wild-type strain capable of undergoing unisexual reproduction with mutants defective in this developmental pathway and found that unisexual reproduction provides a considerable dispersal advantage through hyphal growth and sporulation. Our results show that unisexual reproduction may serve to facilitate access to both nutrients and potential mating partners and may provide a means to maintain the capacity for dimorphic transitions in the environment.
Genome Sequence of the Bacillus subtilis Biofilm-Forming Transformable Strain PS216
Authors: Durrett Russell , Miras Mathieu , Mirouze Nicolas , Narechania Apurva , Mandic-Mulec Ines , Dubnau David
Published: June 2013

Bacillus subtilis
PS216, a strain isolated in Slovenia, has been sequenced. PS216 is transformable and forms robust biofilms, making it useful for the study of competence regulation in an undomesticated bacterium.
Draft Genome Sequences for Ten Salmonella enterica Serovar Typhimurium Phage Type 135 Variants
Authors: Hogg Geoff , Dimovski Karolina , Hiley Lester , Holt Kathryn E.
Published: June 2013

Salmonella enterica
serovar Typhimurium (
S
. Typhimurium) is a common cause of gastroenteritis in humans. Here, we report the draft genome sequences of 10 isolates of an
S
. Typhimurium phage type 135 variant that is linked to egg-associated outbreaks in Tasmania, Australia.
Complete Genome Sequences of Azotobacter vinelandii Wild-Type Strain CA and Tungsten-Tolerant Mutant Strain CA6
Authors: Noar Jesse D. , Bruno-Bárcena José M.
Published: June 2013

We report the complete genome sequences of
Azotobacter vinelandii
mutant strain CA6 and its parent wild-type strain, CA. When fixing nitrogen, strain CA6 displays slow growth and impaired molybdate uptake, tolerance to tungstates, and production of hydrogen gas, compared to results for strain CA. Comparing these genome sequences may provide a genetic basis for these mutant phenotypes.
Genome Sequences of a Novel HIV-1 Circulating Recombinant Form (CRF59_01B) Identified among Men Who Have Sex with Men in Northeastern China
Authors: Han Xiaoxu , An Minghui , Zhang Weiqing , Zhao Bin , Chu Zhenxing , Takebe Yutaka , Shang Hong
Published: June 2013

We report here a novel HIV-1 circulating recombinant form (CRF) (CRF59_01B) comprised of CRF01_AE and subtype B, with two recombination breakpoints in the
pol
and
vpu-env
regions, respectively. CRF59_01B was identified from three epidemiologically unlinked men who have sex with men (MSM) in northeast China. This represents the second CRF identified in the MSM population in China.
Draft Genome Sequence for
Ralstonia
sp. Strain OR214, a Bacterium with Potential for Bioremediation
Authors: Utturkar Sagar M. , Bollmann Annette , Brzoska Ryann M. , Klingeman Dawn M. , Epstein Slava E. , Palumbo Anthony V. , Brown Steven D.
Published: June 2013

Ralstonia
sp. strain OR214 belongs to the class
Betaproteobacteria
and was isolated from subsurface sediments in Oak Ridge, TN. A member of this genus has been described as a potential bioremediation agent. Strain OR214 is tolerant to various heavy metals, such as uranium, nickel, cobalt, and cadmium. We present its draft genome sequence here.
Draft Genome Sequence for
Caulobacter
sp. Strain OR37, a Bacterium Tolerant to Heavy Metals
Authors: Utturkar Sagar M. , Bollmann Annette , Brzoska Ryann M. , Klingeman Dawn M. , Epstein Slava E. , Palumbo Anthony V. , Brown Steven D.
Published: June 2013

Caulobacter
sp. strain OR37 belongs to the class
Alphaproteobacteria
and was isolated from subsurface sediments in Oak Ridge, TN. Strain OR37 is noteworthy due to its tolerance to high concentrations of heavy metals, such as uranium, nickel, cobalt, and cadmium, and we present its draft genome sequence here.
Genome Sequences of Industrially Relevant Saccharomyces cerevisiae Strain M3707, Isolated from a Sample of Distillers Yeast and Four Haploid Derivatives
Authors: Brown Steven D. , Klingeman Dawn M. , Johnson Courtney M. , Clum Alicia , Aerts Andrea , Salamov Asaf , Sharma Aditi , Zane Matthew , Barry Kerrie , Grigoriev Igor V. , Davison Brian H. , Lynd Lee R. , Gilna Paul , Hau Heidi , Hogsett David A. , Froehlich Allan C.
Published: June 2013

Saccharomyces cerevisiae
strain M3707 was isolated from a sample of commercial distillers yeast, and its genome sequence together with the genome sequences for the four derived haploid strains M3836, M3837, M3838, and M3839 has been determined. Yeasts have potential for consolidated bioprocessing (CBP) for biofuel production, and access to these genome sequences will facilitate their development.
Draft Genome Sequence of
Leucobacter
sp. Strain UCD-THU (Phylum
Actinobacteria
)
Authors: Holland-Moritz Hannah E. , Bevans Dakota R. , Lang Jenna M. , Darling Aaron E. , Eisen Jonathan A. , Coil David A.
Published: June 2013

Here we present the draft genome of
Leucobacter
sp. strain UCD-THU. The genome contains 3,317,267 bp in 11 scaffolds. This strain was isolated from a residential toilet as part of an undergraduate project to sequence reference genomes of microbes from the built environment.
Genome Sequence of Proteus mirabilis Strain PR03, Isolated from a Local Hospital in Malaysia
Authors: Khalid M. I. H. , Teh L. K. , Lee L. S. , Zakaria Z. A. , Salleh M. Z.
Published: June 2013

Proteus mirabilis
is one of the pathogenic agents that commonly causes urinary tract infections among elderly individuals and long-term catheterized patients. Here, we report a draft genome sequence of
Proteus mirabilis
strain PR03 (3,932,623 bp, with a G+C content of 38.6%) isolated from a local hospital in Malaysia.
New Volvovirus Isolates from
Acheta domesticus
(Japan) and
Gryllus assimilis
(United States)
Authors: Pham Hanh T. , Iwao Hajime , Bergoin Max , Tijssen Peter
Published: June 2013

A novel circular single-stranded DNA (ssDNA) virus, volvovirus, from the house cricket has been described recently. Here, we report the isolation of volvoviruses from
Acheta domesticus
in Japan and
Gryllus assimilis
in the United States. These
Acheta domesticus
volvovirus (AdVVV) isolates have genomes of 2,517 and 2,516 nucleotides (nt) and 4 large open reading frames (ORFs).
Draft Genome Sequence of the Aeromonas diversa Type Strain
Authors: Farfán Maribel , Spataro Nino , Sanglas Ariadna , Albarral Vicenta , Lorén J. Gaspar , Bosch Elena , Fusté M. Carmen
Published: June 2013

We present here the first genome sequence of the
Aeromonas diversa
type strain (CECT 4254
T
). This strain was isolated from the leg wound of a patient in New Orleans (Louisiana) and was originally described as enteric group 501 and distinguished from
A. schubertii
by DNA-DNA hybridization and phenotypical characterization.
Complete Genome Sequence of Staphylococcus aureus Strain M1, a Unique t024-ST8-IVa Danish Methicillin-Resistant S. aureus Clone
Authors: Larner-Svensson Hanna , Worning Peder , Bartels Mette D. , Hestbjerg Hansen Lars , Boye Kit , Westh Henrik
Published: June 2013

We report the genome sequence, in five contigs, of a methicillin-resistant
Staphylococcus aureus
isolate designated M1. This clinical isolate was from the index patient of a methicillin-resistant
Staphylococcus aureus
(MRSA) outbreak in Copenhagen, Denmark, that started in 2003. This strain is sequence type 8 (ST8),
spa
type t024, and staphylococcal cassette chromosome
mec
element (SCC
mec
) type IVa.
Complete Genome Sequence of Propionibacterium avidum Strain 44067, Isolated from a Human Skin Abscess
Authors: Ördögh Lilla , Hunyadkürti Judit , Vörös Andrea , Horváth Balázs , Szűcs Attila , Urbán Edit , Kereszt Attila , Kondorosi Éva , Nagy István
Published: June 2013

Propionibacterium avidum
is an anaerobic Gram-positive bacterium that forms part of the normal human cutaneous microbiota, colonizing moist areas such as the vestibule of the nose, axilla, and perineum. Here we present the complete genome sequence of
P. avidum
strain 44067, which was isolated from a carbuncle of the trunk.
Complete Genome Sequence of the Feline Calicivirus 2280 Strain from the American Tissue Culture Collection
Authors: Oka Tomoichiro , Takagi Hirotaka , Saif Linda J. , Wang Qiuhong
Published: June 2013

Feline calicivirus (FCV) is a highly contagious pathogen of cats that can be grown in cultured cells. FCV is used as a model to study nonculturable caliciviruses, such as noroviruses. We determined the complete genome sequence of the FCV 2280 strain from the American Tissue Culture Collection.
Complete Genome Sequence of Probiotic Strain Lactobacillus acidophilus La-14
Authors: Stahl Buffy , Barrangou Rodolphe
Published: June 2013

We present the 1,991,830-bp complete genome sequence of
Lactobacillus acidophilus
strain La-14 (SD-5212). Comparative genomic analysis revealed 99.98% similarity overall to the
L. acidophilus
NCFM genome. Globally, 111 single nucleotide polymorphisms (SNPs) (95 SNPs, 16 indels) were observed throughout the genome. Also, a 416-bp deletion in the LA14_1146 sugar ABC transporter was identified.
Draft Genome Sequence of a Benzothiophene-Desulfurizing Bacterium,
Gordona terrae
Strain C-6
Authors: Wang Wei , Ma Ting , Ren Yi , Li Guoqiang
Published: June 2013

Gordona terrae
strain C-6 was isolated from oil-contaminated soil and is capable of desulfurizing benzothiophene (BT). Here we report the draft genome sequence of
G. terrae
strain C-6, which may help to reveal the genetic basis of the BT biodesulfurization pathway.
Evolutionary Dynamics of the Prokaryotic Adaptive Immunity System CRISPR-Cas in an Explicit Ecological Context
Authors: Iranzo Jaime , Lobkovsky Alexander E. , Wolf Yuri I. , Koonin Eugene V.
Published: June 2013

A stochastic, agent-based mathematical model of the coevolution of the archaeal and bacterial adaptive immunity system, CRISPR-Cas, and lytic viruses shows that CRISPR-Cas immunity can stabilize the virus-host coexistence rather than leading to the extinction of the virus. In the model, CRISPR-Cas immunity does not specifically promote viral diversity, presumably because the selection pressure on each single proto-spacer is too weak. However, the overall virus diversity in the presence of CRISPR-Cas grows due to the increase of the host and, accordingly, the virus population size. Above a threshold value of total viral diversity, which is proportional to the viral mutation rate and population size, the CRISPR-Cas system becomes ineffective and is lost due to the associated fitness cost. Our previous modeling study has suggested that the ubiquity of CRISPR-Cas in hyperthermophiles, which contrasts its comparative low prevalence in mesophiles, is due to lower rates of mutation fixation in thermal habitats. The present findings offer a complementary, simpler perspective on this contrast through the larger population sizes of mesophiles compared to hyperthermophiles, because of which CRISPR-Cas can become ineffective in mesophiles. The efficacy of CRISPR-Cas sharply increases with the number of proto-spacers per viral genome, potentially explaining the low information content of the proto-spacer-associated motif (PAM) that is required for spacer acquisition by CRISPR-Cas because a higher specificity would restrict the number of spacers available to CRISPR-Cas, thus hampering immunity. The very existence of the PAM might reflect the tradeoff between the requirement of diverse spacers for efficient immunity and avoidance of autoimmunity.
Teaching Acupuncture to Medical Students: The Experience of Rio Preto Medical School (Famerp), Brazil
Authors: da Silva João Bosco Guerreiro , Saidah Rassen , Megid Cecília Baccili Cury , Ramos Neil Alvimar
Published: June 2013

Complementary and alternative medicine, and in particular acupuncture, has been practised and taught in recent years in many universities in the Western world. Here, we relate our experiences since 1997 in teaching acupuncture to medical students at Rio Preto Medical School (Faculty of Medicine of São José do Rio Preto (FAMERP)), Brazil. Classes are given in the third and fifth years. The main goals of understanding the mechanisms of action and being able to recognise patients who may benefit from treatment and referring them have been well achieved, scoring 3.6 and 4.1, respectively, on a scale of 1–5. Also using that scale, medical students believe that acupuncture is important in the curriculum (4.6), course time is not sufficient (2.7) and they would like more information (4.6). To overcome these concerns, many students join an undergraduate study group (Acupuncture League) where they have more time to learn. We also describe the presence of foreign medical students who, since 2000, have enrolled in a course of 150 h in an exchange programme.
Acupuncture for Primary Hyperhidrosis: Case Series
Authors: Cayir Yasemin , Engin Yasemin
Published: June 2013

Three cases of primary hyperhidrosis of no known cause, with excess sweating day and night, were treated using the same acupuncture points. The patients reported that their sweating decreased and that they felt better after the treatment.
Realising the potential for an Olympic legacy; teaching medical students about sport and exercise medicine and exercise prescribing
Authors: Jones Paul R , Brooks John H M , Wylie Ann
Published: June 2013

Background

Physicians are increasingly being called upon to promote physical activity (PA) among patients. However, a paucity of exercise medicine teaching in the UK undergraduate medical curricula prevents students from acquiring the necessary knowledge and skills to do so. To address this issue, King's College London School of Medicine introduced an exercise medicine strand of teaching. This study evaluated the acceptability of exercise promotion behaviour change lectures and explored the knowledge and attitudes of the students who received it.

Methods

Students were invited to complete a 6-item online questionnaire prior to and after exercise medicine lectures. The questionnaire assessed beliefs regarding the importance of PA in disease prevention and management, in addition to their confidence in advising patients on PA recommendations. A focus group (n=7) explored students’ attitudes towards and knowledge of PA promotion and exercise prescribing.

Results

In total, 121 (15%) first-year and second-year MBBS students completed the questionnaire. Students’ beliefs regarding the importance of PA in managing disease and their confidence in PA promotion among patients increased after the teaching (p<0.001). More students were able to correctly identify the Chief Medical Officer recommended adult PA guidelines (p<0.05). Students were enthusiastic about the exercise medicine teaching, strongly supportive of its continued inclusion in the curriculum and advocated its importance for patients and themselves as future doctors.

Conclusions

Behaviour change teaching successfully improved students’ knowledge of and confidence regarding PA promotion. These improvements are a step forward and may increase the rates and success of physician PA counselling in the future.
The use of glucosamine for chronic low back pain: a systematic review of randomised control trials
Authors: Sodha Reena , Sivanadarajah Naveethan , Alam Mahbub
Published: June 2013

Objectives

To ascertain whether the use of oral glucosamine influences symptoms or functional outcomes in patients with chronic low back pain (LBP) thought to be related to spinal osteoarthritis (OA).

Design

Systematic review of randomised control trials. Searches were performed up to March 2011 on Medline, AMED, CINHAL, Cochrane and EMBASE with subsequent reference screening of retrieved studies. In addition, the grey literature was searched via opensigle. Included studies were required to incorporate at least one of the Cochrane Back Pain Review Group's outcome measures as part of their design. Trials with participants over 18 years with a minimum of 12 weeks of back pain, in combination with radiographic changes of OA in the spine, were included. Studies were rated for risk-of-bias and graded for quality.

Results

148 studies were identified after screening and meeting eligibility requirements, and three randomised controlled trials (n=309) were included in the quantitative synthesis. The review found that there was low quality but generally no evidence of an effect from glucosamine on function, with no change in the Roland-Morris Disability Questionnaire score in all studies. Conflicting evidence was demonstrated with pain scores with two studies showing no difference and one study with a high risk-of-bias showing both a statistically and clinically significant improvement from taking glucosamine.

Conclusions

On the basis of the current research, any clinical benefit of oral glucosamine for patients with chronic LBP and radiographic changes of spinal OA can neither be demonstrated nor excluded based on insufficient data and the low quality of existing studies.
Psychometric properties of the WHO Violence Against Women instrument in a female population-based sample in Sweden: a cross-sectional survey
Authors: Nybergh Lotta , Taft Charles , Krantz Gunilla
Published: June 2013

Objective

To explore psychometric properties of the Violence Against Women instrument in a randomly selected national sample of women (N=573) aged 18–65 years and residing in Sweden.

Design

Cross-sectional survey study.

Setting

Sweden.

Participants

A postal survey was sent to 1006 women between January and March 2009, during which 624 women (62%) returned the questionnaire. 51 women who did not answer any of the violence items were excluded from the analyses, resulting in a final sample of 573 women.

Primary and secondary outcome measures

Self-reported exposure to psychological, physical and sexual intimate partner violence.

Results

Cronbach's α coefficients were 0.79 (psychological scale), 0.80 (physical scale), 0.72 (sexual scale) and 0.88 (total scale). A predetermined three-component solution largely replicated the explored three component conceptual model of the Violence Against Women instrument. The instrument was able to discriminate between groups known from previous studies to differ in exposure to physical and/or sexual violence, that is, respondents with poor versus good self-rated health and witnessed versus not witnessed physical violence at home when growing up. Past-year prevalence of physical (8.1%; 95% CI 5.9 to 10.3) and sexual (3%; 1.6 to 4.4) violence was similar to that reported in other Nordic studies; however, earlier-in-life prevalence was lower in the current study (14.3%; 95% CI 11.4 to 17.2 and 9.2%; 95% CI 6.8 to 11.6, respectively). Reported exposure rates were higher than those obtained from a concurrently administered instrument (NorVold Abuse Questionnaire).

Conclusions

The Violence Against Women instrument demonstrated good construct validity and internal reliability in an adult female population in Sweden. However, further studies examining these and other psychometric properties need to be conducted in other countries.
Bed sharing when parents do not smoke: is there a risk of SIDS? An individual level analysis of five major case–control studies
Authors: Carpenter Robert , McGarvey Cliona , Mitchell Edwin A , Tappin David M , Vennemann Mechtild M , Smuk Melanie , Carpenter James R
Published: June 2013

Objective

To resolve uncertainty as to the risk of Sudden Infant Death Syndrome (SIDS) associated with sleeping in bed with your baby if neither parent smokes and the baby is breastfed.

Design

Bed sharing was defined as sleeping with a baby in the parents’ bed; room sharing as baby sleeping in the parents’ room. Frequency of bed sharing during last sleep was compared between babies who died of SIDS and living control infants. Five large SIDS case–control datasets were combined. Missing data were imputed. Random effects logistic regression controlled for confounding factors.

Setting

Home sleeping arrangements of infants in 19 studies across the UK, Europe and Australasia.

Participants

1472 SIDS cases, and 4679 controls. Each study effectively included all cases, by standard criteria. Controls were randomly selected normal infants of similar age, time and place.

Results

In the combined dataset, 22.2% of cases and 9.6% of controls were bed sharing, adjusted OR (AOR) for all ages 2.7; 95% CI (1.4 to 5.3). Bed sharing risk decreased with increasing infant age. When neither parent smoked, and the baby was less than 3 months, breastfed and had no other risk factors, the AOR for bed sharing versus room sharing was 5.1 (2.3 to 11.4) and estimated absolute risk for these room sharing infants was very low (0.08 (0.05 to 0.14)/1000 live-births). This increased to 0.23 (0.11 to 0.43)/1000 when bed sharing. Smoking and alcohol use greatly increased bed sharing risk.

Conclusions

Bed sharing for sleep when the parents do not smoke or take alcohol or drugs increases the risk of SIDS. Risks associated with bed sharing are greatly increased when combined with parental smoking, maternal alcohol consumption and/or drug use. A substantial reduction of SIDS rates could be achieved if parents avoided bed sharing.
INterpreting the Processes of the UMPIRE Trial (INPUT): protocol for a qualitative process evaluation study of a fixed-dose combination (FDC) strategy to improve adherence to cardiovascular medications
Authors: Salam Abdul , Stewart Frances , Singh Kavita , Thom Simon , Williams Hilarie Jane , Patel Anushka , Jan Stephen , Laba Tracey , Prabhakaran Dorairaj , Maulik Pallab , Day Sophie , Ward Helen
Published: June 2013

Introduction

This paper describes a planned process evaluation of the Use of a Multidrug Pill In Reducing Cardiovascular Events (UMPIRE) trial, one of several randomised clinical trials taking place globally to assess the potential of cardiovascular drugs as a fixed-dose combination (polypill) in cardiovascular disease prevention. A fixed-dose combination may be a promising strategy for promoting adherence to medication; alleviating pill burden through simplifying regimens and reducing cost. This process evaluation will complement the UMPIRE trial by using qualitative research methods to inform understanding of the complex interplay of factors that underpin trial outcomes.

Methods

A series of semistructured, in-depth interviews with local health professionals and UMPIRE trial participants in India and the UK will be undertaken. The aim is to understand their views and experiences of the trial context and of day-to-day use of medications more generally. The grounded theory approach will be used to analyse data and help inform the processes of the UMPIRE trial.

Ethics and dissemination

The study has received ethical approval for all sites in the UK and India where trial participant interviews will be undertaken. The process evaluation will help inform and enhance the understanding of the UMPIRE trial results and its applicability to clinical practice as well as shaping policy regarding strategies for improving cardiovascular medication adherence.
GenotypingChlamydia trachomatisstrains among men who have sex with men from a Northern Spain region: a cohort study
Authors: Mejuto P , Boga J A , Junquera M , Torreblanca A , Leiva P S
Published: June 2013

Objectives

To determine the prevalence of anorectalChlamydia trachomatisserovars in a group of men who have sex with men (MSM) with high risk sexual behaviour, attendees at a sexually transmitted infection (STI) unit from a region in Northwest Spain.

Design

Retrospective and descriptive study of all swabs obtained from all MSM attendees at an STI unit, from 2007 to 2011.Retrospective ethical approval was granted by the Ethical Regional Committee of Clinical Investigation of the Principality of Asturias.

Setting

The STI clinic in Oviedo, Spain, offers screening and free-of-charge treatment to about 3646 patients per year.

Participants

303 symptomatic and asymptomatic consecutive and unselected MSM patients (mean age 36.7 and range 21–55 years) were evaluated for anorectal chlamydial infection.

Main outcome measures

C trachomatisDNA extraction and detection in all rectal and in 36 urethral swabs. Characterisation ofC trachomatisgenotypes through sequencing ofompAgene amplicons and further phylogenetic tree analysis.

Results

We found 40 (13. 2%) positive rectal samples. The distribution of genotypes was E (37. 5%) followed by G (25%), D (12. 5%), J (10%) and L2b (5%).25 (62.5%, 95% CI 46.2 to 78.7) of the chlamydia-infected MSM showed clinical manifestations while 15 (37.5%, 95% CI 21.25 to 53.75) reported no symptoms. Concurrent infection with other STIs was documented in 27 (67.5%, 95% CI 51.7 to 83.2) patients. The most frequently reported clinical symptom was anal ulcer (7 cases, 17.5%; 95% CI 4.47 to 30.52). E genotype was mostly detected in asymptomatic patients. There were non-E genotypes detected in 21 (84%, 95% CI 63.9 to 95.5) of 25 symptomatic patients (p<0.001).

Conclusions

The first two confirmed cases of lymphogranuloma venereum (LGV) in MSM in Asturias are reported, probably indicating the increase of this infection. The SpanishC trachomatislaboratory-based surveillance system may underlie an underestimated number of chlamydial infections. Whenever mild and atypical symptoms exist, laboratory evaluation would contribute to the early implementation of appropriate therapy and prevent LGV dissemination.
Confidence in the future, health-related behaviour and psychological distress: results from a web-based cross-sectional study of 101 257 Finns
Authors: Joutsenniemi Kaisla , Härkänen Tommi , Pankakoski Maiju , Langinvainio Heimo , Mattila Antti S , Saarelma Osmo , Lönnqvist Jouko , Mustonen Pekka
Published: June 2013

Objectives

To investigate the role of socioeconomic status and psychological stress to potential associations between confidence in the future and a wide range of health-related behaviours.

Design

Web-based cross-sectional study including an ‘Electronic Health Check’ at the Finnish Happiness-Flourishing Study website linked to a TV programme on happiness and depression.

Setting

The Finnish population with access to the internet.

Participants

101 257 Finns aged 18 and above (21 365 men; 79 892 women). Participants who were under the age of 18 and who did not provide information about their gender were excluded.

Primary outcome measures

As planned, we assessed smoking, weekly alcohol consumption and binge drinking, daily intake of fruits and vegetables and regular exercise.

Results

Compared with participants with low confidence in the future, those with high confidence were less likely to be daily smokers (men OR 0.58, 95% CI 0.52 to 0.65; women 0.57, 95% CI 0.53 to 0.61) and binge drinkers (men 0.57; 0.52 to 0.63; women 0.54; 0.50 to 0.57). Participants with high confidence in the future were more likely to exercise regularly (men OR 2.82, 95% CI 2.55 to 3.13; women 2.57, 95% CI 2.44 to 2.71) and consume vegetables (men OR 2.48, 95% CI 2.25 to 2.74; women 2.13, 95% CI 2.03 to 2.24) and fruits (men OR 2.09, 95% CI 1.86 to 2.35; women 1.83, 95% CI 1.74 to 1.93) daily. Adjustment for current psychological distress and satisfaction for income attenuated the results.

Conclusions

Having confidence in the future is strongly associated with a healthy lifestyle, as assessed by a healthy diet, physical exercise and substance abuse. Health-related interventions may benefit from tailoring interventions according to the target population's level of confidence in the future as well as their level of psychological distress.
Error rates in a clinical data repository: lessons from the transition to electronic data transfer—a descriptive study
Authors: Hong Matthew K H , Yao Henry H I , Pedersen John S , Peters Justin S , Costello Anthony J , Murphy Declan G , Hovens Christopher M , Corcoran Niall M
Published: June 2013

Objective

Data errors are a well-documented part of clinical datasets as is their potential to confound downstream analysis. In this study, we explore the reliability of manually transcribed data across different pathology fields in a prostate cancer database and also measure error rates attributable to the source data.

Design

Descriptive study.

Setting

Specialist urology service at a single centre in metropolitan Victoria in Australia.

Participants

Between 2004 and 2011, 1471 patients underwent radical prostatectomy at our institution. In a large proportion of these cases, clinicopathological variables were recorded by manual data-entry. In 2011, we obtained electronic versions of the same printed pathology reports for our cohort. The data were electronically imported in parallel to any existing manual entry record enabling direct comparison between them.

Outcome measures

Error rates of manually entered data compared with electronically imported data across clinicopathological fields.

Results

421 patients had at least 10 comparable pathology fields between the electronic import and manual records and were selected for study. 320 patients had concordant data between manually entered and electronically populated fields in a median of 12 pathology fields (range 10–13), indicating an outright accuracy in manually entered pathology data in 76% of patients. Across all fields, the error rate was 2.8%, while individual field error ranges from 0.5% to 6.4%. Fields in text formats were significantly more error-prone than those with direct measurements or involving numerical figures (p<0.001). 971 cases were available for review of error within the source data, with figures of 0.1–0.9%.

Conclusions

While the overall rate of error was low in manually entered data, individual pathology fields were variably prone to error. High-quality pathology data can be obtained for both prospective and retrospective parts of our data repository and the electronic checking of source pathology data for error is feasible.