bluuebunny/crossref_metadata_2025 huggingface dataset:
Analytical modeling of third party service provider selection in lead logistics provider environments
Authors: Singh Bhatti Rajbir , Kumar Pradeep , Kumar Dinesh
Published: November 2010

Purpose

The purpose of this paper is to model the choice parameters for selection of third party logistics service providers in global lead logistics provider (LLP) environments.

Design/methodology/approach

Analytical hierarchy process (AHP) modeling has been carried out after questionnaire‐based survey, results of which were moderated with inputs from experts from industry and academics.

Findings

The findings of this study revealed the under lying sub‐parameters which come into play while rating/choosing or evaluating service providers in the global LLP situations of today.

Research limitations/implications

The number of service providers, selection criteria and the number of members of the AHP assessment team have been identified as some of the limitations of the present work.

Practical implications

The study has significant practical implications for the service providers and for the organizations which have to choose them. The fourth party logistics scenario entails this choice to be made by the LLP.

Originality/value

This paper deals with inputs from the Indian LLPs and the Indian service providers. With India emerging as the second most important outsourcing destination after China, the assessment of parameters specific to this country while modeling is of practical importance to LLPs beyond the political boundaries of India also.
Construction project selection using fuzzy TOPSIS approach
Authors: Tan Yong‐tao , Shen Li‐yin , Langston Craig , Liu Yan
Published: November 2010

Purpose

The purpose of this paper is to introduce a quantitative method for assisting contractors to select appropriate projects for bidding by considering multiple attributes and integrating decision group member opinions.

Design/methodology/approach

The fuzzy technique for order preference by similarity to ideal solution (TOPSIS) method is used to help contractors make decision on project selection and the linguistic terms are defined for representing the triangular fuzzy numbers for ratings of alternatives and weights of criteria.

Findings

The selection of appropriate projects for bidding is a multiple attribute group decision‐making exercise. In a real decision process, there are many uncertainties and ambiguities, and time limitations mean that decision makers cannot always make precise judgments. The numerical example demonstrates that the fuzzy TOPSIS approach can be used to simulate the decision process in project selection, and the results provide contractors with valuable insight into the project selection problem.

Originality/value

Selecting appropriate projects for bidding is to use a contractor's limited resources more efficiently and increase the probability of winning contracts. Therefore, there is a need for a quantitative method to help contractors make better decision on project selection. That leads to the formulation of this paper. The fuzzy TOPSIS method can assist contractors to make better decisions in bidding.
When in Britain, do as the British do: if anyone knows what that means
Authors: Wilson Jonathan A.J.
Published: November 2010

Purpose

Multiculturalism and diversity are both evident and encouraged in the UK. However, this paper highlights evidence pointing towards the passive and sporadic transmission of unifying values – especially prevalent when interacting with individuals across cultures, or in culturally diverse settings. The aim is to stimulate debate surrounding day‐to‐day practices and accountability, at an operational level.

Design/methodology/approach

Reflective practitioner‐based commentary, using inductive reasoning as a basis for critical discourse analysis. Evidence gathered from literature reviews – supported by anecdotal evidence, personal observations and experiences.

Findings

The position held is that critical to the future long‐term successes of business education, students and lecturers should adopt a two‐way bottom‐up approach which prioritises the implementation of the following: an appreciation and participative study of culture, followed by active encouragement towards embracing further multiculturalism, and finally the preservation and transmission of tacit knowledge within a cultural paradigm – between host and surrogate cultures. Without this, business schools and the study of business are hampered. Using the analogy of an orchestra conductor, the suggestion is that lecturers as facilitator conductors should increase their efforts towards championing culture, embedding them within the formative aspects of their duties. To this end, they should be nurtured and supported as such.

Practical implications

Furthermore, lecturers require resources and recognition from institutions, beyond mere compliance with human resource legislation and the pursuit of institutional commercial gains.

Originality/value

The paper presents a proposed innovative approach – centred on cultural diffusion innovation, convergence continuum and hybridisation.
Maintenance strategy in Malaysian manufacturing companies: a total productive maintenance (TPM) approach
Authors: Mad Lazim Halim , Ramayah T.
Published: November 2010

Purpose

The paper aims to investigate the extent of TPM practices in Malaysian manufacturing companies, as TPM practices have been shown to lead to better performance.

Design/methodology/approach

A survey was conducted in Malaysian manufacturing companies to examine the extent of TPM practices. The correlations among TPM practices were also evaluated accordingly.

Findings

Correlation analysis was carried out and the results show that there is a positive relationship among TPM practices. In general, TPM practices, for instance autonomous maintenance, planned maintenance and TPM strategy, show positive and significant correlations among this sample of Malaysian manufacturing companies.

Research limitation/implications

Since the sample was rather small, caution is required when making generalizations.

Practical implications

The study highlights the need to improve the collaboration between the maintenance function and other functions in organizations. TPM can be established as an aggressive strategy to face stiff competitive environments that require zero breakdowns, stoppages, and failures of equipment.

Originality/value

The achievements of Malaysian manufacturing companies through TPM practices are evaluated and important TPM practices are identified for enhancing the effectiveness of TPM implementation programs in the Malaysian context.
Product innovation among ICT technopreneurs in Malaysia
Authors: Khin Sabai , Hazlina Ahmad Noor , Ramayah T.
Published: November 2010

Purpose

The first purpose of this study is to discuss a brief review of the literature in product innovation, innovation strategies and resources. The second purpose is to present qualitative findings related to product innovation as well as their strategies and resources among ICT (information and communication technology) technopreneurs in the software sector of Malaysia.

Design/methodology/approach

This qualitative study is a preliminary study to a larger empirical study. Semi‐structured interviews were conducted with five ICT technopreneurs in Malaysia.

Findings

The findings generate insights into the kind of market that ICT technopreneurs are in, the problems they are facing, their practices and opinions towards product innovation, and their strategies as well as the resources required.

Research limitations/implications

One limitation of the work could be related to the small sample size.

Practical implications

The findings imply that resource constraints, market factors such as market need, and strategic orientation towards customer and market needs may play a part in product innovation practices among ICT technopreneurs. Practitioners should pay attention to these factors to achieve innovative advantage.

Originality/value

This study adds knowledge regarding product innovation among software firms by shedding light on ICT technopreneurs in terms of product innovation and the factors associated with it. The implications provide an impetus for further research in related areas.
Organisational change and innovation in small accounting practices: evidence from the field
Authors: Alam Manzurul , Nandan Ruvendra
Published: November 2010

Purpose

The purpose of this paper is to explore the nature of context specific issues and challenges facing small accounting practices (SAPs) in Australian regional and rural centres. It is argued that these firms face a dynamic and continuously changing environment which requires strategic responses on the part of SAP owners. The paper explores how SAPs accommodate and respond to their contextual environment, and in turn, shape that environment.

Design/methodology/approach

This paper adopts a qualitative case study research approach involving the review and analysis of the prior literature and relevant archival documents, and semi‐structured interviews with the key SAP owner/managers.

Findings

The findings suggest that SAPs adopt innovative strategies and structures. The SAPs in this study were generally found to be resilient and dynamic in responding to the changes in their contextual environment. Significant differences between SAPs were also found, particularly on how they addressed contextual uncertainties.

Research limitations/implications

This is a case study research on SAPs in rural and regional centres. Any generalization of the conclusions from this study should be undertaken with care, even though there are similarities between SAPs operating in rural and regional centres and those operating in large metropolitan areas.

Originality/value

This paper makes an important contribution by highlighting the SAPs' responses depending on their contextual environment.
Analysis ofven3andven6reticulate mutants reveals the importance of arginine biosynthesis in Arabidopsis leaf development
Authors: Mollá‐Morales Almudena , Sarmiento‐Mañús Raquel , Robles Pedro , Quesada Víctor , Pérez‐Pérez José M. , González‐Bayón Rebeca , Hannah Matthew A. , Willmitzer Lothar , Ponce María R. , Micol José L.
Published: November 2010

Arabidopsis thalianareticulate mutants exhibit differential pigmentation of the veinal and interveinal leaf regions, a visible phenotype that often indicates impaired mesophyll development. We performed a metabolomic analysis of oneven6(venosa6) and threeven3reticulate mutants that revealed altered levels of arginine precursors, namely increased ornithine and reduced citrulline levels. In addition, the mutants were more sensitive than the wild‐type to exogenous ornithine, and leaf reticulation and mesophyll defects of these mutants were completely rescued by exogenous citrulline. Taken together, these results indicate thatven3andven6mutants experience a blockage of the conversion of ornithine into citrulline in the arginine pathway. Consistent with the participation of VEN3 and VEN6 in the same pathway, the morphological phenotype ofven3 ven6double mutants was synergistic. Map‐based cloning showed that theVEN3andVEN6genes encode subunits of Arabidopsis carbamoyl phosphate synthetase (CPS), which is assumed to be required for the conversion of ornithine into citrulline in arginine biosynthesis. Heterologous expression of the ArabidopsisVEN3andVEN6genes in a CPS‐deficientEscherichia colistrain fully restored bacterial growth in minimal medium, demonstrating the enzymatic activity of the VEN3 and VEN6 proteins, and indicating a conserved role for CPS in these distinct and distant species. Detailed study of the reticulate leaf phenotype in theven3andven6mutants revealed that mesophyll development is highly sensitive to impaired arginine biosynthesis.
Perceptions of insulin therapy amongst Asian patients with diabetes in Singapore
Authors: Wong S. , Lee J. , Ko Y. , Chong M. F. , Lam C. K. , Tang W. E.
Published: November 2010

Diabet. Med. 28, 206–211 (2011)

Aims  The objective of this study was to determine the prevalence of insulin refusal amongst Singaporean patients with Type 2 diabetes mellitus, to compare perceptions regarding insulin therapy use between patients who were willing to use insulin and those who were not and to identify demographic factors that might predict insulin refusal.

Methods  A cross‐sectional interviewer‐administered survey incorporating demographic variables and 17 perceptions regarding insulin use (14 negative and three positive) was conducted among a sample of 265 patients attending a public primary healthcare centre.

Results  Seven of every 10 patients expressed unwillingness to use insulin therapy (70.6%). The greatest differences in perceptions between patients willing to use insulin therapy and those who were not included fear of not being able to inject insulin correctly (47.4 vs. 70.6%), fear of pain (44.9 vs. 65.8%), belief that insulin therapy would make it difficult to fulfil responsibilities at work and home (46.2 vs. 66.8%) and belief that insulin therapy improved diabetes control (82.1 vs. 58.3%). A tertiary level of education was associated with willingness to use insulin (odds ratio 3.3, confidence interval 1.8–6.1), and significant differences in perceptions were present in patients with different educational levels.

Conclusions  Insulin refusal is an important problem amongst our patients with Type 2 diabetes mellitus. Findings of this study suggest that interventions aimed at increasing insulin therapy use should focus on injection‐related concerns, perceived lifestyle adaptations and correction of misconceptions. Different interventions may also be required for patients of different educational groups.
Alterations of tendons in patients with diabetes mellitus: a systematic review
Authors: de Oliveira R. R. , Lemos A. , de Castro Silveira P. V. , da Silva R. J. , de Moraes S. R. A.
Published: November 2010

Diabet. Med. 28, 886–895 (2011)

Aims  To perform a systematic review of observational studies which analyse tendon alterations in patients with diabetes mellitus compared with healthy individuals.

Methods  Data collection was performed, with no language restriction, using the databases of PubMed/Medline, BIREME, CINAHL, LILACS and Cochrane, as well as the references found in these studies. Three reviewers performed independent extractions of articles. Subsequently, these reviewers analysed the articles, focusing on their methodological quality, using the appropriate scale to evaluate observational studies from the Agency for Healthcare Research and Quality.

Results  Six articles were included in the analysis. Of these, four had used ultrasonographic diagnostics, one computed tomography and one magnetic resonance imaging. The patient pool comprised 396 individuals. All the articles evaluated tendon thickness and presented heterogeneous results. Two articles stated thickening or increased volume of the tendons in diabetic people, one article did not report any alteration, the fourth failed to determine any alterations and the fifth showed thinning of the tendons. The arrangement of collagen fibrils and the presence of calcification were analysed in only one article (n = 80), showing that 88.10% (n = 68) of individuals with diabetes presented disorientation of collagen fibril arrangement, while only 10% (n = 1) of healthy individuals presented this condition. Regarding tendon calcification, the article showed diabetic individuals with higher values than healthy individuals.

Conclusions  All the articles indicated some relation between diabetes mellitus and tendon alterations in human beings, but due to methodological drawbacks, this association could not be sustained.
Effect of LKB1 deficiency on mitochondrial content, fibre type and muscle performance in the mouse diaphragm
Authors: Brown J. D. , Hancock C. R. , Mongillo A. D. , Benjamin Barton J. , DiGiovanni R. A. , Parcell A. C. , Winder W. W. , Thomson D. M.
Published: November 2010

Aim:  The liver kinase B1 (LKB1)/AMP‐activated protein kinase (AMPK) signalling pathway is a major regulator of skeletal muscle metabolic processes. During exercise, LKB1‐mediated phosphorylation of AMPK leads to its activation, promoting mitochondrial biogenesis and glucose transport, among other effects. The roles of LKB1 and AMPK have not been fully characterized in the diaphragm.

Methods:  Two methods of AMPK activation were used to characterize LKB1/AMPK signalling in diaphragms from muscle‐specific LKB1 knockout (KO) and littermate control mice: (1) acute injection of 5‐aminoimidazole‐4‐carboxamide ribonucleoside (AICAR) and (2) 5‐min direct electrical stimulation of the diaphragm. Diaphragms were excised 60 min post‐AICAR injection and immediately after electrical stimulation.

Results:  AMPK phosphorylation increased with AICAR and electrical stimulation in control but not KO mice. Acetyl CoA carboxylase phosphorylation increased with AICAR in control but not KO mice, but increased in both genotypes with electrical stimulation. While the majority of mitochondrial protein levels were lower in KO diaphragms, uncoupling protein 3, complex I and cytochrome oxidase IV protein levels were not different between genotypes. KO diaphragms have a lower percentage of IIx fibres and an elevated percentage of IIb fibres when compared with control diaphragms. While in vitro peak force generation was similar between genotypes, KO diaphragms fatigued more quickly and had an impaired ability to recover.

Conclusion:  LKB1 regulates AMPK phosphorylation, mitochondrial protein expression, fibre type distribution, as well as recovery of the diaphragm from fatigue.
Differential Protein Expression in
Streptococcus uberis
under Planktonic and Biofilm Growth Conditions
Authors: Crowley R. C. , Leigh J. A. , Ward P. N. , Lappin-Scott H. M. , Bowler L. D.
Published: November 2010

The bovine pathogen
Streptococcus uberis
was assessed for biofilm growth. The transition from planktonic to biofilm growth in strain 0140J correlated with an upregulation of several gene products that have been shown to be important for pathogenesis, including a glutamine ABC transporter (SUB1152) and a lactoferrin binding protein (gene
lbp
; protein SUB0145).
Tangential-Flow Ultrafiltration with Integrated Inhibition Detection for Recovery of Surrogates and Human Pathogens from Large-Volume Source Water and Finished Drinking Water
Authors: Gibson Kristen E. , Schwab Kellogg J.
Published: November 2010

Tangential-flow ultrafiltration was optimized for the recovery of
Escherichia coli
,
Enterococcus faecalis
,
Clostridium perfringens
spores, bacteriophages MS2 and PRD1, murine norovirus, and poliovirus seeded into 100-liter surface water (SW) and drinking water (DW) samples. SW and DW collected from two drinking water treatment plants were then evaluated for human enteric viruses.
Respiration Response Imaging for Real-Time Detection of Microbial Function at the Single-Cell Level
Authors: Konopka M. C. , Strovas T. J. , Ojala David S. , Chistoserdova L. , Lidstrom M. E. , Kalyuzhnaya M. G.
Published: November 2010

The ability to detect specific functions of uncultured microbial cells in complex natural communities remains one of the most difficult tasks of environmental microbiology. Here we present respiration response imaging (RRI) as a novel fluorescence microscopy-based approach for the identification of microbial function, such as the ability to use C
1
substrates, at a single-cell level. We demonstrate that RRI could be used for the investigation of heterogeneity of a single microbial population or for functional profiling of microbial cells from complex environmental communities, such as freshwater lake sediment.
Dynamic Analysis of the
Lactococcus lactis
Transcriptome in Cheeses Made from Milk Concentrated by Ultrafiltration Reveals Multiple Strategies of Adaptation to Stresses
Authors: Cretenet Marina , Laroute Valérie , Ulvé Vincent , Jeanson Sophie , Nouaille Sébastien , Even Sergine , Piot Michel , Girbal Laurence , Le Loir Yves , Loubière Pascal , Lortal Sylvie , Cocaign-Bousquet Muriel
Published: November 2010

Lactococcus lactis
is used extensively for the production of various cheeses. At every stage of cheese fabrication,
L. lactis
has to face several stress-generating conditions that result from its own modification of the environment as well as externally imposed conditions. We present here the first
in situ
global gene expression profile of
L. lactis
in cheeses made from milk concentrated by ultrafiltration (UF-cheeses), a key economical cheese model. The transcriptomic response of
L. lactis
was analyzed directly in a cheese matrix, starting from as early as 2 h and continuing for 7 days. The growth of
L. lactis
stopped after 24 h, but metabolic activity was maintained for 7 days. Conservation of its viability relied on an efficient proteolytic activity measured by an increasing, quantified number of free amino acids in the absence of cell lysis. Extensive downregulation of genes under CodY repression was found at day 7.
L. lactis
developed multiple strategies of adaptation to stressful modifications of the cheese matrix. In particular, expression of genes involved in acidic- and oxidative-stress responses was induced.
L. lactis
underwent unexpected carbon limitation characterized by an upregulation of genes involved in carbon starvation, principally due to the release of the CcpA control. We report for the first time that in spite of only moderately stressful conditions, lactococci phage is repressed under UF-cheese conditions.
Diversity of Phytoplankton Nitrate Transporter Sequences from Isolated Single Cells and Mixed Samples from the East China Sea and mRNA Quantification
Authors: Kang Lee-Kuo , Wang Hsuan-Fan , Chang Jeng
Published: November 2010

The transcript abundances of nitrate transporter genes (
Nrt2
) were proposed as potential markers for nitrogen deficiency in marine diatoms. To correctly quantify diatom
Nrt2
mRNA in the East China Sea (ECS), we utilized both mixed-species sequencing and single-cell PCR to expand the sequence database for this region. Using the single-cell method of PCR, 9 new diatom
Nrt2
sequences belonging to 5 genera, the
Nrt2
sequences of which have never been reported before, were obtained. On the other hand, 291 sequences homologous to
Nrt2
were retrieved from mixed-species sequencing using degenerate primers, and these sequences were clustered into 12 major groups according to a phylogenetic analysis. Based on sequence alignments, 11 pairs of group-specific PCR primers were designed to detect
Nrt2
mRNA levels in the ECS, and 3 of these primer pairs showed high specificity to target species. In ECS phytoplankton samples, environmental RNA was amplified via antisense RNA amplification followed by cDNA production. Subsequently,
Nrt2
transcript levels were readily detected using quantitative PCR. Our results indicated that investigating sequence diversity followed by careful primer design and evaluation is a good strategy to quantify the expression of genes of ecologically important phytoplankton.
Detection of Bacterial Indicators and Human and Bovine Enteric Viruses in Surface Water and Groundwater Sources Potentially Impacted by Animal and Human Wastes in Lower Yakima Valley, Washington
Authors: Gibson Kristen E. , Schwab Kellogg J.
Published: November 2010

Tangential flow ultrafiltration (UF) was used to concentrate and recover bacterial indicators and enteric viruses from 100 liters of groundwater (GW;
n
= 10) and surface water (SW;
n
= 11) samples collected in Lower Yakima Valley, WA. Human and bovine enteric viruses were analyzed in SW and GW concentrates by real-time PCR by using integrated inhibition detection.
Colonization of Tomato Plants by
Salmonella enterica
Is Cultivar Dependent, and Type 1 Trichomes Are Preferred Colonization Sites
Authors: Barak Jeri D. , Kramer Lara C. , Hao Ling-yun
Published: November 2010

Nontyphoid salmonellosis caused by
Salmonella enterica
is the most common bacterial food-borne illness in humans, and fresh produce, including tomatoes, is a common vehicle. Accumulating data indicate that human enteric pathogenic bacteria, including
S. enterica
, interact actively with plants. Tomato plants were inoculated with
S. enterica
to evaluate plausible contamination routes and to determine if the tomato cultivar affects
S. enterica
colonization.
S. enterica
population levels on tomato leaves were cultivar dependent.
S. enterica
levels on
Solanum pimpinellifolium
(West Virginia 700 [WVa700]) were lower than on
S. lycopersicum
cultivars.
S. enterica
preferentially colonized type 1 trichomes and rarely interacted with stomata, unlike what has been reported for cut lettuce leaves. Early
S. enterica
leaf colonization led to contamination of all fruit, with levels as high as 10
5
CFU per fruit. Reduced bacterial speck lesion formation correlated with reduced
S. enterica
populations in the phyllosphere. Tomato pedicels and calyxes also harbored large
S. enterica
populations following inoculation via contaminated water postharvest. WVa700 green fruit harbored significantly smaller
S. enterica
populations than did red fruit or
S. lycopersicum
fruit. We found that plants irrigated with contaminated water had larger
S. enterica
populations than plants grown from seeds planted in infested soil. However, both routes of contamination resulted in detectable
S. enterica
populations in the phyllosphere. Phyllosphere
S. enterica
populations pose a risk of fruit contamination and subsequent human disease. Restricting
S. enterica
phyllosphere populations may result in reduced fruit contamination. We have identified WVa700 as a tomato cultivar that can restrict
S. enterica
survival in the phyllosphere.
Real-Time PCR Assay To Differentiate Listeriolysin S-Positive and -Negative Strains ofListeria monocytogenes
Authors: Clayton Evelyn M. , Hill Colin , Cotter Paul D. , Ross R. Paul
Published: November 2010

Due to the severity of the food-borne infection listeriosis, strict legislation governs the detectable and permissible limits at whichListeria monocytogenesis permitted in foods. These requirements, coupled with the ubiquitous nature ofL. monocytogenesstrains and the potential for epidemic outbreaks, mean that the pathogen can devastate affected sectors of the food industry. Although almost allL. monocytogenesstrains have the potential to cause listeriosis, those implicated in the vast majority of epidemics belong to a subset of strains belonging to evolutionary lineage I. It has been established that a significant proportion of these strains, including those implicated in the majority of outbreaks, produce an additional hemolysin, designated listeriolysin S (LLS), which may be responsible for the enhanced virulence of these strains. In order to ultimately establish this definitively, it is important to first be able to rapidly discriminate between LLS-positive and -negative strains. Here, after essential genes within the LLS-encoding cluster,Listeriapathogenicity island 3, were identified by deletion mutagenesis, a real-time PCR assay which targets one such gene,llsX, was developed as a means of identifying LLS-positiveL. monocytogenes. The specificity of the assay was validated against a panel of 40L. monocytogenesstrains (20 of which were LLS positive) and 25 strains representative of otherListeriaspecies. Furthermore, 1 CFU of an LLS-positive strain per 25 g/ml of spiked foods was detected in less than 30 h when the assay was coupled with culture enrichment. The detection limit of this assay was 10 genome equivalents.
Engineered Biosynthesis of Gilvocarcin Analogues with Altered Deoxyhexopyranose Moieties
Authors: Shepherd Micah D. , Liu Tao , Méndez Carmen , Salas Jose A. , Rohr Jürgen
Published: November 2010

A combinatorial biosynthetic approach was used to interrogate the donor substrate flexibility of GilGT, the glycosyltransferase involved in
C
-glycosylation during gilvocarcin biosynthesis. Complementation of gilvocarcin mutant
Streptomyces lividans
TK24 (cosG9B3-U
−
), in which the biosynthesis of the natural sugar donor substrate was compromised, with various deoxysugar plasmids led to the generation of six gilvocarcin analogues with altered saccharide moieties. Characterization of the isolated gilvocarcin derivatives revealed five new compounds, including 4-β-
C
-
d
-olivosyl-gilvocarcin V (
d
-olivosyl GV), 4-β-
C
-
d
-olivosyl-gilvocarcin M (
d
-olivosyl GM), 4-β-
C
-
d
-olivosyl-gilvocarcin E (
d
-olivosyl GE), 4-α-
C
-
l
-rhamnosyl-gilvocarcin M (polycarcin M), 4-α-
C
-
l
-rhamnosyl-gilvocarcin E (polycarcin E), and the recently characterized 4-α-
C
-
l
-rhamnosyl-gilvocarcin V (polycarcin V). Preliminary anticancer assays showed that
d
-olivosyl-gilvocarcin and polycarcin V exhibit antitumor activities comparable to that of their parent drug congener, gilvocarcin V, against human lung cancer (H460), murine lung cancer (LL/2), and breast cancer (MCF-7) cell lines. Our findings demonstrate GilGT to be a moderately flexible
C
-glycosyltransferase able to transfer both
d
- and
l
-hexopyranose moieties to the unique angucyclinone-derived benzo[
d
]naphtho[1,2
b
]pyran-6-one backbone of the gilvocarcins.
Domain Organization and Evolution of Multifunctional Autoprocessing Repeats-in-Toxin (MARTX) Toxin in
Vibrio vulnificus
Authors: Roig Francisco J. , González-Candelas Fernando , Amaro Carmen
Published: November 2010

The objective of this study was to analyze multifunctional autoprocessing repeats-in-toxin (MARTX) toxin domain organization within the aquatic species
Vibrio vulnificus
as well as to study the evolution of the
rtxA1
gene. The species is subdivided into three biotypes that differ in host range and geographical distribution. We have found three different types (I, II, and III) of
V. vulnificus
MARTX (MARTX
Vv
) toxins with common domains (an autocatalytic cysteine protease domain [CPD], an α
/
β-hydrolase domain, and a domain resembling that of the LifA protein of
Escherichia coli
O127:H6 E2348/69 [Efa/LifA]) and specific domains (a Rho-GTPase inactivation domain [RID], a domain of unknown function [DUF],a domain resembling that of the
rtxA
protein of
Photorhabdus asymbiotica
[
rtxA
PA
], and an actin cross-linking domain [ACD]). Biotype 1 isolates harbor MARTX
Vv
toxin types I and II, biotype 2 isolates carry MARTX
Vv
toxin type III, and biotype 3 isolates have MARTX
Vv
toxin type II. The analyzed biotype 2 isolates harbor two identical copies of
rtxA1
, one chromosomal and the other plasmidic. The evolutionary history of the gene demonstrates that MARTX
Vv
toxins are mosaics, comprising pieces with different evolutionary histories, some of which have been acquired by intra- or interspecific horizontal gene transfer. Finally, we have found evidence that the evolutionary history of the
rtxA1
gene for biotype 2 differs totally from the gene history of biotypes 1 and 3.
Randomized Soil Survey of the Distribution of
Burkholderia pseudomallei
in Rice Fields in Laos
Authors: Rattanavong Sayaphet , Wuthiekanun Vanaporn , Langla Sayan , Amornchai Premjit , Sirisouk Joy , Phetsouvanh Rattanaphone , Moore Catrin E. , Peacock Sharon J. , Buisson Yves , Newton Paul N.
Published: November 2010

Melioidosis is a major cause of morbidity and mortality in Southeast Asia, where the causative organism (
Burkholderia pseudomallei
) is present in the soil. In the Lao People's Democratic Republic (Laos),
B. pseudomallei
is a significant cause of sepsis around the capital, Vientiane, and has been isolated in soil near the city, adjacent to the Mekong River. We explored whether
B. pseudomallei
occurs in Lao soil distant from the Mekong River, drawing three axes across northwest, northeast, and southern Laos to create nine sampling areas in six provinces. Within each sampling area, a random rice field site containing a grid of 100 sampling points each 5 m apart was selected. Soil was obtained from a depth of 30 cm and cultured for
B. pseudomallei
. Four of nine sites (44%) were positive for
B. pseudomallei
, including all three sites in Saravane Province, southern Laos. The highest isolation frequency was in east Saravane, where 94% of soil samples were
B. pseudomallei
positive with a geometric mean concentration of 464 CFU/g soil (95% confidence interval, 372 to 579 CFU/g soil; range, 25 to 10,850 CFU/g soil). At one site in northwest Laos (Luangnamtha), only one sample (1%) was positive for
B. pseudomallei
, at a concentration of 80 CFU/g soil. Therefore,
B. pseudomallei
occurs in Lao soils beyond the immediate vicinity of the Mekong River, alerting physicians to the likelihood of melioidosis in these areas. Further studies are needed to investigate potential climatic, soil, and biological determinants of this heterogeneity.
Phylogeographical Patterns among Mediterranean Sepiolid Squids and TheirVibrioSymbionts: Environment Drives Specificity among Sympatric Species
Authors: Zamborsky D. J. , Nishiguchi M. K.
Published: November 2010

Bobtail squid from the generaSepiolaandRondeletiola(Cephalopoda: Sepiolidae) form mutualistic associations with luminous Gram-negative bacteria (Gammaproteobacteria:Vibrionaceae) from the generaVibrioandPhotobacterium. Symbiotic bacteria proliferate inside a bilobed light organ until they are actively expelled by the host into the surrounding environment on a diel basis. This event results in a dynamic symbiont population with the potential to establish the symbiosis with newly hatched sterile (axenic) juvenile sepiolids. In this study, we examined the genetic diversity found in populations of sympatric sepiolid squid species and their symbionts by the use of nested clade analysis with multiple gene analyses. Variation found in the distribution of different species of symbiotic bacteria suggests a strong influence of abiotic factors in the local environment, affecting bacterial distribution among sympatric populations of hosts. These abiotic factors include temperature differences incurred by a shallow thermocline, as well as a lack of strong coastal water movement accompanied by seasonal temperature changes in overlapping niches. Host populations are stable and do not appear to have a significant role in the formation of symbiont populations relative to their distribution across the Mediterranean Sea. Additionally, all squid species examined (Sepiola affinis,S. robusta,S. ligulata,S. intermedia, andRondeletiola minor) are genetically distinct from one another regardless of location and demonstrate very little intraspecific variation within species. These findings suggest that physical boundaries and distance in relation to population size, and not host specificity, are important factors in limiting or defining gene flow within sympatric marine squids and their associated bacterial symbionts in the Mediterranean Sea.
Isolation of Oligotrophic Denitrifiers Carrying Previously Uncharacterized Functional Gene Sequences
Authors: Ishii Satoshi , Ashida Naoaki , Otsuka Shigeto , Senoo Keishi
Published: November 2010

Oligotrophic denitrifying bacteria, including those belonging to the genera
Herbaspirillum
,
Azospirillum
, and
Bradyrhizobium
, were obtained using a single-cell isolation technique. The taxonomic composition of the denitrifier population was similar to those assessed by previous culture-independent studies. The sequencing of nitrite reductase and N
2
O reductase genes of these strains revealed previously unknown links between 16S rRNA and the denitrification-functional gene phylogenies. In particular, we identified
Bradyrhizobium
strains that harbor
nirS
sequences previously detected only in culture-independent studies.
Comparative Genomics and the Evolution of Pathogenicity in Human Pathogenic Fungi
Authors: Moran Gary P. , Coleman David C. , Sullivan Derek J.
Published: November 2010

Because most fungi have evolved to be free-living in the environment and because the infections they cause are usually opportunistic in nature, it is often difficult to identify specific traits that contribute to fungal pathogenesis. In recent years, there has been a surge in the number of sequenced genomes of human fungal pathogens, and comparison of these sequences has proved to be an excellent resource for exploring commonalities and differences in how these species interact with their hosts. In order to survive in the human body, fungi must be able to adapt to new nutrient sources and environmental stresses. Therefore, genes involved in carbohydrate and amino acid metabolism and transport and genes encoding secondary metabolites tend to be overrepresented in pathogenic species (e.g.,
Aspergillus fumigatus
). However, it is clear that human commensal yeast species such as
Candida albicans
have also evolved a range of specific factors that facilitate direct interaction with host tissues. The evolution of virulence across the human pathogenic fungi has occurred largely through very similar mechanisms. One of the most important mechanisms is gene duplication and the expansion of gene families, particularly in subtelomeric regions. Unlike the case for prokaryotic pathogens, horizontal transfer of genes between species and other genera does not seem to have played a significant role in the evolution of fungal virulence. New sequencing technologies promise the prospect of even greater numbers of genome sequences, facilitating the sequencing of multiple genomes and transcriptomes within individual species, and will undoubtedly contribute to a deeper insight into fungal pathogenesis.
Aerobic Degradation of Mercaptosuccinate by the Gram-Negative BacteriumVariovorax paradoxusStrain B4
Authors: Carbajal-Rodríguez Irma , Stöveken Nadine , Satola Barbara , Wübbeler Jan Hendrik , Steinbüchel Alexander
Published: November 2010

The Gram-negative bacteriumVariovorax paradoxusstrain B4 was isolated from soil under mesophilic and aerobic conditions to elucidate the so far unknown catabolism of mercaptosuccinate (MS). During growth with MS this strain released significant amounts of sulfate into the medium. Tn5::mob-induced mutagenesis was successfully employed and yielded nine independent mutants incapable of using MS as a carbon source. In six of these mutants, Tn5::mobinsertions were mapped in a putative gene encoding a molybdenum (Mo) cofactor biosynthesis protein (moeA). In two further mutants the Tn5::mobinsertion was mapped in the gene coding for a putative molybdopterin (MPT) oxidoreductase. In contrast to the wild type, these eight mutants also showed no growth on taurine. In another mutant a gene putatively encoding a 3-hydroxyacyl-coenzyme A dehydrogenase (paaH2) was disrupted by transposon insertion. Upon subcellular fractionation of wild-type cells cultivated with MS as sole carbon and sulfur source, MPT oxidoreductase activity was detected in only the cytoplasmic fraction. Cells grown with succinate, taurine, or gluconate as a sole carbon source exhibited no activity or much lower activity. MPT oxidoreductase activity in the cytoplasmic fraction of the Tn5::mob-induced mutant Icr6 was 3-fold lower in comparison to the wild type. Therefore, a new pathway for MS catabolism inV. paradoxusstrain B4 is proposed: (i) MPT oxidoreductase catalyzes the conversion of MS first into sulfinosuccinate (a putative organo-sulfur compound composed of succinate and a sulfino group) and then into sulfosuccinate by successive transfer of oxygen atoms, (ii) sulfosuccinate is cleaved into oxaloacetate and sulfite, and (iii) sulfite is oxidized to sulfate.
argC
Orthologs from
Rhizobiales
Show Diverse Profiles of Transcriptional Efficiency and Functionality in
Sinorhizobium meliloti
Authors: Díaz Rafael , Vargas-Lagunas Carmen , Villalobos Miguel Angel , Peralta Humberto , Mora Yolanda , Encarnación Sergio , Girard Lourdes , Mora Jaime
Published: November 2010

Several factors can influence ortholog replacement between closely related species. We evaluated the transcriptional expression and metabolic performance of ortholog substitution complementing a
Sinorhizobium meliloti argC
mutant with
argC
from
Rhizobiales
(
Agrobacterium tumefaciens
,
Rhizobium etli
, and
Mesorhizobium loti
). The
argC
gene is necessary for the synthesis of arginine, an amino acid that is central to protein and cellular metabolism. Strains were obtained carrying plasmids with
argC
orthologs expressed under the
speB
and
argC
(
S. meliloti
) and
lac
(
Escherichia coli
) promoters. Complementation analysis was assessed by growth, transcriptional activity, enzymatic activity, mRNA levels, specific detection of ArgC proteomic protein, and translational efficiency. The
argC
orthologs performed differently in each complementation, reflecting the diverse factors influencing gene expression and the ability of the ortholog product to function in a foreign metabolic background. Optimal complementation was directly related to sequence similarity with
S. meliloti
, and was inversely related to species signature, with
M. loti argC
showing the poorest performance, followed by
R. etli
and
A. tumefaciens
. Different copy numbers of genes and amounts of mRNA and protein were produced, even with genes transcribed from the same promoter, indicating that coding sequences play a role in the transcription and translation processes. These results provide relevant information for further genomic analyses and suggest that orthologous gene substitutions between closely related species are not completely functionally equivalent.
Type I Signal Peptidase and Protein Secretion inStaphylococcus epidermidis
Authors: Powers Michael E. , Smith Peter A. , Roberts Tucker C. , Fowler Bruce J. , King Charles C. , Trauger Sunia A. , Siuzdak Gary , Romesberg Floyd E.
Published: November 2010

Bacterial protein secretion is a highly orchestrated process that is essential for infection and virulence. Despite extensive efforts to predict or experimentally detect proteins that are secreted, the characterization of the bacterial secretome has remained challenging. A central event in protein secretion is the type I signal peptidase (SPase)-mediated cleavage of the N-terminal signal peptide that targets a protein for secretion via the general secretory pathway, and the arylomycins are a class of natural products that inhibit SPase, suggesting that they may be useful chemical biology tools for characterizing the secretome. Here, using an arylomycin derivative, along with two-dimensional gel electrophoresis and liquid chromatography-tandem mass spectrometry (LC-MS/MS), we identify 11 proteins whose secretion from stationary-phaseStaphylococcusepidermidisis dependent on SPase activity, 9 of which are predicted to be translated with canonical N-terminal signal peptides. In addition, we find that the presence of extracellular domains of lipoteichoic acid synthase (LtaS) and the β-lactam response sensor BlaR1 in the medium is dependent on SPase activity, suggesting that they are cleaved at noncanonical sites within the protein. In all, the data define the proteins whose stationary-phase secretion depends on SPase and also suggest that the arylomycins should be valuable chemical biology tools for the study of protein secretion in a wide variety of different bacteria.
Translation Efficiency of Antiterminator Proteins Is a Determinant for the Difference in Glucose Repression of Two β-Glucoside Phosphotransferase System Gene Clusters inCorynebacterium glutamicumR
Authors: Tanaka Yuya , Teramoto Haruhiko , Inui Masayuki , Yukawa Hideaki
Published: November 2010

Corynebacterium glutamicumR has two β-glucoside phosphoenolpyruvate, carbohydrate phosphotransferase systems (PTS) encoded bybglFandbglF2located in the respective clusters,bglF-bglA-bglGandbglF2-bglA2-bglG2. Previously, we reported that whereas β-glucoside-dependent induction ofbglFis strongly repressed by glucose, glucose repression ofbglF2is very weak. Here, we reveal the mechanism behind the different effects of glucose on the twobglgenes. Deletion of the ribonucleic antiterminator sequence and transcriptional terminator located upstream of the translation initiation codon ofbglFmarkedly relieved the glucose repression of abglF-lacZfusion, indicating that glucose affects the antitermination mechanism that is responsible for the β-glucoside-dependent induction of thebglFcluster. The glucose repression ofbglFmRNA was also relieved by introducing a multicopy plasmid carrying thebglGgene encoding an antiterminator of thebglFcluster. Moreover, replacement of the GUG translation initiation codon ofbglGwith AUG was effective in relieving the glucose repression ofbglFandbglG. Inversely, expression ofbglF2andbglG2was subject to strict glucose repression in a mutant strain in which the AUG translation initiation codon ofbglG2encoding antiterminator of thebglF2cluster was replaced with GUG. These results suggest that the translation initiation efficiency of the antiterminator proteins, at least in part, determines whether the target genes are subject to glucose repression. We also found thatbglFexpression was induced by glucose in the BglG-overexpressing strains, which may be explained by the ability of BglF to transport glucose.
Complete Genome Sequence of Japanese
Erwinia
Strain Ejp617, a Bacterial Shoot Blight Pathogen of Pear
Authors: Park Duck Hwan , Thapa Shree Prasad , Choi Beom-Soon , Kim Won-Sik , Hur Jang Hyun , Cho Jun Mo , Lim Jong-Sung , Choi Ik-Young , Lim Chun Keun
Published: November 2010

The Japanese
Erwinia
strain Ejp617 is a plant pathogen that causes bacterial shoot blight of pear in Japan. Here, we report the complete genome sequence of strain Ejp617 isolated from Nashi pears in Japan to provide further valuable insight among related
Erwinia
species.
Complete Genome Sequence of Adherent Invasive
Escherichia
coli
UM146 Isolated from Ileal Crohn's Disease Biopsy Tissue
Authors: Krause Denis O. , Little Ainsley C. , Dowd Scot E. , Bernstein Charles N.
Published: November 2010

Escherichia
coli
UM146 was isolated from the ileum of a Crohn's disease patient. It adheres to and invades enterocytes and can replicate inside macrophages. Its complete genome sequence reveals that it is most closely related to the human urinary tract pathogen
E
.
coli
CFT073, but it has a host of genes that are novel and to which no function has been ascribed.
Genome Sequence of
Leuconostoc fallax
KCTC 3537
Authors: Nam Seong-Hyeuk , Choi Sang-Haeng , Kang Aram , Kim Dong-Wook , Kim Dae-Soo , Kim Ryong Nam , Kim Aeri , Park Hong-Seog
Published: November 2010

Leuconostoc fallax
is known to be present during the manufacturing process of kimchi, the best-known traditional Korean dish. Here, we present the draft genome sequence of the type strain
Leuconostoc fallax
KCTC 3537 (1,638,971 bp, with a G+C content of 37.5%), which consists of 30 large contigs (>100 bp in size).
Effectiveness of an external ankle brace in reducing parachuting-related ankle injuries
Authors: Luippold Rose S , Sulsky Sandra I , Amoroso Paul J
Published: November 2010

Outside-the-boot parachute ankle braces (PABs) worn during US Army paratrooper training have been shown to reduce the risk of severe ankle injuries. In spite of evidence to the contrary, anecdotal reports continue to suggest increases in risk of other types of injury, and the cost of obtaining and periodically replacing the PAB has been used to justify its discontinued use. The authors identified inpatient and outpatient treatment for injuries during US Army paratrooper training. Those undergoing training during two periods when PAB use was mandated had 40% lower risks of ankle injury (brace I, RR=0.60 (95% CI 0.47 to 0.75); brace II, RR=0.62 (95% CI 0.49 to 0.78)), with no difference in risks of other types of injury. There were no differences in risk of ankle injury during periods when brace use was not mandated. The PAB is safe, effective and cost effective.