bluuebunny/crossref_metadata_2025 huggingface dataset:
Supply chain integration improves performance: the Emperor's new suit?
Authors: Fabbe‐Costes Nathalie , Jahre Marianne
Published: January 2008

Purpose

In the literature authors state that there is a positive relation between supply chain integration (SCI) and performance. They claim that this relation is widely discussed and supported empirically. Other authors, however, suggest that integration might be more difficult in practice than in theory, that it should be differentiated and that it is more rhetoric than reality. As integration has been core of logistics and supply chain management since the 1980s, the purpose of this paper is to investigate these somewhat contradictory statements and analyse prior studies regarding definitions and measures of integration and performance as well as the reported empirical evidence on their relation.

Design/methodology/approach

Based on an extensive and systematic review of integration articles within four highly ranked academic journals in logistics, supply chain and operations management, this paper presents and discusses the results of prior empirical studies on relations between integration and performance.

Findings

The analysis of the relevant articles indicates that empirical evidence cannot permit to clearly conclude and that integration as well as performance is defined, operationalised and measured in different and often limited ways. This might be a problem and the paper concludes with a provoking question of whether SCI might be the Emperors' New Suit of business.

Originality/value

The paper's departure point is a controversial hypothesis: the contribution of SCI is not as obvious as logistics and supply chain researchers usually think. The rigorous selection and analysis of previous studies contributes with systematic knowledge within an important question.
Summer nights
Authors: Macdowall Wendy , Wellings Kaye , Stephenson Judith , Glasier Anna
Published: January 2008

Purpose

This paper aims to examine whether greater consideration should be given to the timing of sexual health interventions within the calendar year.

Design/methodology/approach

The paper uses a review of the literature.

Findings

The evidence points to seasonality in a number of areas of sexual health among young people, including: the timing of first intercourse and conceptions, both of which peak in the summer and over Christmas; abortions which peak approximately two months later in February and late summer and sexually transmitted infections, which peak over the summer and autumn. In the case of conceptions there is evidence that the seasonal pattern among young people is different from that of adults. Potential explanations fall into four main categories: biological; behavioural; social, and service‐related.

Research limitations/implications

Many of the studies included in this review are from the USA, and some are based on either small samples or specific risk groups, which raises questions of representativeness and generalisability. Further, it is notable how little research there has been regarding seasonal variations in other aspects of sexual behaviour, such as risk reduction practice and other potential explanatory factors such as health‐seeking behaviour and availability of services.

Practical implications

The findings consistently point to periods of heightened sexual activity among young people in the summer and over Christmas, and suggest that greater consideration should indeed be given to the timing of sexual health interventions within the calendar year.

Originality/value

To the best of the authors' knowledge, no other review of this kind has yet been found.
Hitting back: strategic responses to low‐cost rivals
Authors: Morehouse Jim , O'Meara Bob , Hagen Christian , Huseby Todd
Published: January 2008

Purpose of this paper

No company is safe from low‐cost rivals. Almost overnight, nimble low‐cost competitors can exploit their offshore advantage, partnerships, and inexpensive technologies to break down barriers and rewrite the rules of competition. This paper aims to show how to counterattack.

Design/methodology/approach

The paper shows that way to beat low‐cost competitors that have the potential to become serious competitors is to identify and deal with them early, before they get a foothold in a market.

Findings

The paper finds that the best way to identify and thwart a low‐cost rival is to adopt its mindset, anticipate its next competitive move and measure your costs against its costs. This best practice analysis requires four steps.

Practical implications

“What to do” to defeat low‐cost competitors involves two separate but related tasks: First, “stop the bleeding”, and second, reposition the company for success in the new market. The paper shows how to break down potential moves into short‐term tactics and long‐term strategies.

Originality/value

The paper shows how to win the battle with a low‐cost competitor by identifying the genuine threats, taking on the serious competition, adapting its tactics quickly and hitting back with a well‐placed blow.
Interview with growth consultant Chris Zook: a less risky path to business model innovation
Authors: Davidson Alistair , Leavy Brian
Published: January 2008

Purpose

Creating a fundamentally different business in the shadow of the old one – while its assembly lines continue to roll – is a daunting challenge. Bain consultant Chris Zook recently published the last book in a trilogy which addresses the question of how to make “fundamental change in your business model, while still running your business.”. This paper aims to explores his views on this subject.

Design/methodology/approach

For this interview, two Strategy & Leadership senior editor's – one a Silicon Valley consultant and former CEO and the other an academic – – asked Zook to take them on a guided tour of his reinvention process.

Findings

The paper finds that the underlying thesis in each of the three books is that companies need to master all phases of a strategic life cycle: from extracting the full potential from their core business, to expanding their business successfully, to redefining themselves For most companies and in more industries, the strategy cycle – from Focus, to Expand, to Redefine – has become shorter, and therefore companies frequently confront moments of redefinition of their core.

Practical implications

In this interview, Zook's how‐to advice for managers covers: the role of hidden assets, the “state of the core diagnostic” tool, the “shrink to grow” strategy, how to test “the waters,” and the FER (focus‐expand‐redefine) cycle.

Originality/value

Because the interview considers the whole trilogy the reader gets a unique view of how Zook's ideas fit together and build a cogent thesis.
Offences concerning directors and officers of a company
Authors: Scanlan G.
Published: January 2008

Purpose

The purpose of this paper is to consider the present and possible future nature of the legal regime regulating and seeking to control fraud and corruption on the part of directors and officers of companies in the UK.

Design/methodology/approach

This paper outlines aspects in the present and future fight against fraud and corruption on the part of directors and officers of companies, particularly with regard to public and listed companies in the UK.

Findings

The paper emphasises the need for the UK Government to secure adequate resources for the investigating and enforcement authorities to ensure that the law of fraud and corruption is effectively enforced, rather than pursue a policy of constant enactment of new legislation which is increasingly complex and ineffective.

Originality/value

The paper considers the creation of a new generic offence to supplement the new generic offences created under the Fraud Act 2006, based on the established principle of the fiduciary duty, a duty owed by all directors and officers to their companies. These offences could form the central core of a future legal regime regulating the conduct of directors and officers.
How long should a training program be? A field study of “rules‐of‐thumb”
Authors: Cole Nina
Published: January 2008

Purpose

This study aims to examine the question of how long a behavioral skills training program should be in order to result in measurable behavioral change.

Design/methodology/approach

An empirical field study was conducted to compare two different lengths of time for a managerial skills training program aimed at achieving behavioral change. The training time for the first training condition was based on “rules‐of‐thumb” found in the literature. The training time was increased in an “extended” training condition that covered the same material but permitted more time for lecture, role‐playing and discussion.

Findings

Results showed that, relative to a control group, participants in the “extended” training condition exhibited behavioral change, but those in the “rules‐of‐thumb” training condition did not. Self‐efficacy increased significantly for trainees in both training conditions.

Practical implications

More attention is required to the length of training programs as they are being designed, especially if behavioral change is a goal of the training. Using rules‐of‐thumb regarding training length may be insufficient for bringing about behavioral change. More importantly, the need for more effective management skills will not be met, and organizational performance outcomes may be jeopardized.

Originality/value

The results of this research have the potential to be broadly applicable to management training and may possibly generalize to training in other disciplines where the training is intended to effect behavioral change.
Alternative measures to value at risk
Authors: Thompson Colin J. , McCarthy Michael A.
Published: January 2008

Purpose

The purpose of this article is to introduce a new method of estimating risk as an alternative to value at risk (VaR), drawing on the risk assessment literature in environmental science.

Design/methodology/approach

A commonly used and accepted measure of market risk is VaR, defined as the difference between initial portfolio value and a probabilistic lower bound B on the portfolio value at time T. To take account of situations where the portfolio value may fall below B prior to time T, an an alternative to VaR is proposed based on first passage time distributions.

Findings

It is argued that the resulting expected minimum portfolio value over the time frame T provides a clear alternative measure of market risk. Analytical expressions are obtained and numerical comparisons given when the distribution of portfolio returns is lognormal.

Research limitations/implications

Analytical results are presented for lognormal distributions for returns. Results for other models can be easily obtained from simulation.

Practical implications

The new measure of risk recognizes that investors might be sensitive to risks of decline in the value of a portfolio at any time within a given time horizon, not just at the end of the anticipated period of investment. The expected minimum portfolio value measures the largest loss that is expected at some stage over that period.

Originality/value

A new measure of risk is presented that arises from literature on risk assessment in environmental science. It is complementary to VaR for assessing risk.
Energy‐efficient adaptive resource management strategy for large‐scale mobile ad hoc networks
Authors: Shi Shengfei , Li Jianzhong , Wang Chaokun , Wu Yuhui
Published: January 2008

Purpose

The purpose of this paper is to propose a novel resource management strategy, which needs no special frameworks and directory servers.

Design/methodology/approach

The key idea is to piggyback a little extra packet header on the normal routing message by resource providers randomly. The clients can obtain the resource information gradually and need no dedicated resource queries.

Findings

The results of simulation confirm the good performance of our algorithms in different situations in terms of query latency and power consumption.

Originality/value

A novel resource management strategy, which needs no special frameworks and directory servers. The approach can be used in many current routing protocols. The quality of service issue is also considered for resource discovery algorithm and broadcasting method.
Mouse strain‐specific coding polymorphism in the Slc4a2/Ae2 gene encodes Ae2c2 variants differing in isoform‐specific dominant negative activity
Authors: Kurschat Christine E. , Shmukler Boris E. , Jiang Lianwei , Hevi Sarah , Kim Edward H. , Stewart Andrew K. , Alper Seth L.
Published: January 2008

The Slc4a2/Ae2 gene encodes multiple polypeptides arising from alternate promoter usage. The Ae2c promoter gives rise to only one Ae2c transcript from the human Ae2 gene, but to two, alternatively spliced, Ae2c1 and Ae2c2 transcripts from the mouse and rat genes. Unlike in the rat, the mouse Ae2c2 transcript encodes a novel Ae2c2 polypeptide. Here we report that the Ae2c2 residue 9 can be either proline or serine in a mouse strain‐specific manner. Both Ae2c2 polypeptides express low function in Xenopus oocytes secondary to reduced or absent surface expression. Ae2c2S, but not Ae2c2P, exerts a dominant negative effect when coexpressed with Ae2a polypeptide, has a less prominent effect when coexpressed with Ae2b1 or Ae2c1 polypeptides, but has no effect on the function of coexpressed Ae2b2 polypeptide. Coexpression of Ae2c2P does not reduce activity of any Ae2 polypeptide variant. Ae2c2S and Ae2c2P also express low functional activity in HEK‐293 cells. Knowledge of strain‐specific coding polymorphisms with potential functional consequences such as that of Ae2c2 should aid in interpretation of strain‐specific phenotypes investigated in the mouse phenome project.
Bilateral representation in the deep cerebellar nuclei
Authors: Soteropoulos Demetris S. , Baker Stuart N.
Published: January 2008

The cerebellum is normally assumed to represent ipsilateral movements. We tested this by making microelectrode penetrations into the deep cerebellar nuclei (mainly nucleus interpositus) of monkeys trained to perform a reach and grasp task with either hand. Following weak single electrical stimuli, many sites produced clear bilateral facilitation of multiple forelimb muscles. The short onset latencies, which were similar for each side, suggested that at least some of the muscle responses were mediated by descending tracts originating in the brainstem, rather than via the cerebral cortex. Additionally, cerebellar neurones modulated their discharge with both ipsilateral and contralateral movements. This was so, even when we carefully excluded contralateral trials with evidence of electromyogram modulation on the ipsilateral side. We conclude that the deep cerebellar nuclei have a bilateral movement representation, and relatively direct, powerful access to limb muscles on both sides of the body. This places the cerebellum in an ideal position to coordinate bilateral movements.
Resource Letter Scy-3: Superconductivity
Authors: Butch N. P. , de Andrade M. C. , Maple M. B.
Published: January 2008

This Resource Letter provides a guide to the literature on superconductivity. Since the last Resource Letter on superconductivity, Scy-2, was published in 1970, there have been dramatic advances in our basic understanding of superconductivity, discovery of new superconducting materials, and improved technological exploitation of superconductors. We review basic phenomenology, followed by concise descriptions of several main classes of superconductors recognized today. Journal articles and books are cited for the following topics: Conventional superconductors, paramagnetic impurities in superconductors, magnetically ordered superconductors, heavy fermion superconductors, high Tc superconductors, organic superconductors, applications of superconductivity, and laboratory demonstrations of superconductivity. Owing to the large volume of available literature on superconductivity, the journal articles and books we discuss constitute good starting points for further exploration of particular topics.
Transition between short and long wavelength limits in quantum mechanical reflection from a linear potential
Authors: Kennedy S. M. , Paganin D. M. , Jesson D. E.
Published: January 2008

The phase changes experienced by a wave reflected from an interface are a familiar fixture in introductory physics courses. Examples include the ±π phase shift acquired upon reflection from a hard mirror (for example, in thin film interference patterns and Newton’s rings) and the −π∕2 phase shift studied in soft mirror reflections (for example, in mirage ray paths and the WKB connection formulas). We focus on the transition between these two limits, where the phase change upon reflection evolves continuously between the limiting cases of −π and −π∕2. We study a simple quantum system that exhibits this transition: a one-dimensional free electron reflected from a linear potential.
Measurement of mutual inductance from the frequency dependence of impedance of AC coupled circuits using a digital dual-phase lock-in amplifier
Authors: Schauber Michael J. , Newman Seth A. , Goodman Lindsey R. , Suzuki Itsuko S. , Suzuki Masatsugu
Published: January 2008

We present a simple method for determining the mutual inductance between two coils in a coupled AC circuit using a digital dual-phase lock-in amplifier. The frequency dependence of the real and imaginary parts is measured as the coupling is changed. The mutual inductance decreases as the distance d between the centers of coils is increased. We show that the coupling is proportional to d−n with n≈3. This coupling is similar to that of two magnetic dipoles.
Promoting instructional change in new faculty: An evaluation of the physics and astronomy new faculty workshop
Authors: Henderson Charles
Published: January 2008

An important finding of physics and astronomy education research (PAER) is that traditional, transmission-based instructional approaches are not effective in promoting meaningful student learning. Instead, PAER research suggests that physics and astronomy should be taught using more interactive instructional methods. These ways of teaching require significant changes in the way faculty think about teaching and learning and corresponding changes in their teaching behavior. Although the research base and corresponding pedagogies and strategies are well documented and widely available, widespread changes in physics and astronomy teaching at the college level has yet to occur. The Workshop for New Physics and Astronomy Faculty has been working to address this problem since 1996. This workshop, which is jointly administered by the American Association of Physics Teachers, the American Astronomical Society, and the American Physical Society, has attracted approximately 25% of all new physics and astronomy faculty each year to a four-day workshop designed to introduce new faculty to PAER-based instructional ideas and materials. This paper describes the impact of the Workshop as measured by surveys of Workshop participants and physics and astronomy department chairs. The results indicate that the Workshop is successful in meeting its goals and might be significantly contributing to the spread and acceptance of PAER-based instructional ideas and materials.
Coupled oscillations in suspended magnets
Authors: Moloney Michael J.
Published: January 2008

A pair of strong magnets suspended by a single thread between them can act as a pendulum and also exhibit torsion as the magnets align with the Earth’s magnetic field. This arrangement demonstrates visible coupled oscillations, alternating between pendulum motion and twisting about the line of the thread, often at large angles. The vertical component of the Earth’s magnetic field is the coupling agent between the pendulum and twisting motions. The pendulum and torsion motions become uncoupled if an external coil is used to cancel this field component. An analysis of this motion is in agreement with experimental observations.
Identification of Host Proteins Required for HIV Infection Through a Functional Genomic Screen
Authors: Brass Abraham L. , Dykxhoorn Derek M. , Benita Yair , Yan Nan , Engelman Alan , Xavier Ramnik J. , Lieberman Judy , Elledge Stephen J.
Published: January 2008

HIV-1 exploits multiple host proteins during infection. We performed a large-scale small interfering RNA screen to identify host factors required by HIV-1 and identified more than 250 HIV-dependency factors (HDFs). These proteins participate in a broad array of cellular functions and implicate new pathways in the viral life cycle. Further analysis revealed previously unknown roles for retrograde Golgi transport proteins (Rab6 and Vps53) in viral entry, a karyopherin (TNPO3) in viral integration, and the Mediator complex (Med28) in viral transcription. Transcriptional analysis revealed that HDF genes were enriched for high expression in immune cells, suggesting that viruses evolve in host cells that optimally perform the functions required for their life cycle. This effort illustrates the power with which RNA interference and forward genetics can be used to expose the dependencies of human pathogens such as HIV, and in so doing identify potential targets for therapy.
Lipase Expression in
Pseudomonas alcaligenes
Is Under the Control of a Two-Component Regulatory System
Authors: Krzeslak Joanna , Gerritse Gijs , van Merkerk Ronald , Cool Robbert H. , Quax Wim J.
Published: January 2008

Preliminary observations in a large-scale fermentation process suggested that the lipase expression of
Pseudomonas alcaligenes
can be switched on by the addition of certain medium components, such as soybean oil. In an attempt to elucidate the mechanism of induction of lipase expression, we have set up a search method for genes controlling lipase expression by use of a cosmid library containing fragments of
P. alcaligenes
genomic DNA. A screen for lipase hyperproduction resulted in the selection of multiple transformants, of which the best-producing strains comprised cosmids that shared an overlapping genomic fragment. Within this fragment, two previously unidentified genes were found and named
lipQ
and
lipR
. Their encoded proteins belong to the NtrBC family of regulators that regulate gene expression via binding to a specific upstream activator sequence (UAS). Such an NtrC-like UAS was identified in a previous study in the
P. alcaligenes
lipase promoter, strongly suggesting that LipR acts as a positive regulator of lipase expression. The regulating role could be confirmed by down-regulated lipase expression in a strain with an inactivated
lipR
gene and a threefold increase in lipase yield in a large-scale fermentation when expressing the
lipQR
operon from the multicopy plasmid pLAFR3. Finally, cell extracts of a LipR-overexpressing strain caused a retardation of the lipase promoter fragment in a band shift assay. Our results indicate that lipase expression in
Pseudomonas alcaligenes
is under the control of the LipQR two-component system.
Changes in Bacterial and Archaeal Community Structure and Functional Diversity along a Geochemically Variable Soil Profile
Authors: Hansel Colleen M. , Fendorf Scott , Jardine Phillip M. , Francis Christopher A.
Published: January 2008

Spatial heterogeneity in physical, chemical, and biological properties of soils allows for the proliferation of diverse microbial communities. Factors influencing the structuring of microbial communities, including availability of nutrients and water, pH, and soil texture, can vary considerably with soil depth and within soil aggregates. Here we investigated changes in the microbial and functional communities within soil aggregates obtained along a soil profile spanning the surface, vadose zone, and saturated soil environments. The composition and diversity of microbial communities and specific functional groups involved in key pathways in the geochemical cycling of nitrogen, Fe, and sulfur were characterized using a coupled approach involving cultivation-independent analysis of both 16S rRNA (bacterial and archaeal) and functional genes (
amoA
and
dsrAB
) as well as cultivation-based analysis of Fe(III)-reducing organisms. Here we found that the microbial communities and putative ammonia-oxidizing and Fe(III)-reducing communities varied greatly along the soil profile, likely reflecting differences in carbon availability, water content, and pH. In particular, the
Crenarchaeota
16S rRNA sequences are largely unique to each horizon, sharing a distribution and diversity similar to those of the putative (
amoA
-based) ammonia-oxidizing archaeal community. Anaerobic microenvironments within soil aggregates also appear to allow for both anaerobic- and aerobic-based metabolisms, further highlighting the complexity and spatial heterogeneity impacting microbial community structure and metabolic potential within soils.
Protein Engineering of Toluene Monooxygenases for Synthesis of Chiral Sulfoxides
Authors: Feingersch Roi , Shainsky Janna , Wood Thomas K. , Fishman Ayelet
Published: January 2008

Enantiopure sulfoxides are valuable asymmetric starting materials and are important chiral auxiliaries in organic synthesis. Toluene monooxygenases (TMOs) have been shown previously to catalyze regioselective hydroxylation of substituted benzenes and phenols. Here we show that TMOs are also capable of performing enantioselective oxidation reactions of aromatic sulfides. Mutagenesis of position V106 in the α-hydroxylase subunit of toluene
ortho
-monooxygenase (TOM) of
Burkholderia cepacia
G4 and the analogous position I100 in toluene 4-monooxygenase (T4MO) of
Pseudomonas mendocina
KR1 improved both rate and enantioselectivity. Variant TomA3 V106M of TOM oxidized methyl phenyl sulfide to the corresponding sulfoxide at a rate of 3.0 nmol/min/mg protein compared with 1.6 for the wild-type enzyme, and the enantiomeric excess (pro-
S
) increased from 51% for the wild type to 88% for this mutant. Similarly, T4MO variant TmoA I100G increased the wild-type oxidation rate by 1.7-fold, and the enantiomeric excess rose from 86% to 98% (pro-
S
). Both wild-type enzymes showed lower activity with methyl
para
-tolyl sulfide as a substrate, but the improvement in the activity and enantioselectivity of the mutants was more dramatic. For example, T4MO variant TmoA I100G oxidized methyl
para
-tolyl sulfide 11 times faster than the wild type did and changed the selectivity from 41% pro-
R
to 77% pro-
S
. A correlation between regioselectivity and enantioselectivity was shown for TMOs studied in this work. Using in silico homology modeling, it is shown that residue I100 in T4MO aids in steering the substrate into the active site at the end of the long entrance channel. It is further hypothesized that the main function of V106 in TOM is the proper positioning or docking of the substrate with respect to the diiron atoms. The results from this work suggest that when the substrate is not aligned correctly in the active site, the oxidation rate is decreased and enantioselectivity is impaired, resulting in products with both chiral configurations.
Bombyx mori
Midgut Membrane Protein P252, Which Binds to
Bacillus thuringiensis
Cry1A, Is a Chlorophyllide-Binding Protein, and the Resulting Complex Has Antimicrobial Activity
Authors: Pandian Ganesh N. , Ishikawa Toshiki , Togashi Makoto , Shitomi Yasuyuki , Haginoya Kohsuke , Yamamoto Shuhei , Nishiumi Tadayuki , Hori Hidetaka
Published: January 2008

The epithelial cell membrane 252-kDa protein (P252) isolated in our laboratory from
Bombyx mori
midgut was shown to bind strongly with Cry1Aa, Cry1Ab, and Cry1Ac toxins of
Bacillus thuringiensis
(15). In the current paper, P252 was shown to bind with chlorophyllide (Chlide) to form red fluorescent protein (RFP) complex, termed Bm252RFP, with absorbance and fluorescence emission peaks at 600 nm and 620 nm, respectively. P252 at a concentration of 1 μM is shown to bind with about 50 μM Chlide in a positively cooperative reaction to form Bm252RFP under aerobic conditions and in the presence of light at 37°C. Various parameters influencing this reaction have been optimized for efficient in vitro chemical synthesis of Bm252RFP. Circular dichroism spectra revealed that P252 is composed of a β-structure (39.8% ± 2.2%, based on 5 samples) with negligible contribution of α-helix structure. When bound to Chlide, the β-structure content in the complex is reduced to 21.6% ± 3.1% (
n
= 5). Since Chlide had no secondary structure, the observed reduction suggests significant conformational changes of P252 during the formation of Bm252RFP complex. Bm252RFP had antimicrobial activity against
Escherichia coli
,
Serratia marcescens
,
B. thuringiensis
, and
Saccharomyces cerevisiae
with 50% effective concentrations of 2.82, 2.94, 5.88 μM, and 21.6 μM, respectively. This is the first report ever to show clear, concrete binding characteristics of the midgut protein to form an RFP having significant antimicrobial activity.
A
Rhodococcus qsdA
-Encoded Enzyme Defines a Novel Class of Large-Spectrum Quorum-Quenching Lactonases
Authors: Uroz Stéphane , Oger Phil M. , Chapelle Emilie , Adeline Marie-Thérèse , Faure Denis , Dessaux Yves
Published: January 2008

A gene involved in
N
-acyl homoserine lactone (N-AHSL) degradation was identified by screening a genomic library of
Rhodococcus erythropolis
strain W2. This gene, named
qsdA
(for
q
uorum-sensing
s
ignal
d
egradation), encodes an N-AHSL lactonase unrelated to the two previously characterized N-AHSL-degrading enzymes, i.e., the lactonase AiiA and the amidohydrolase AiiD. QsdA is related to phosphotriesterases and constitutes the reference of a novel class of N-AHSL degradation enzymes. It confers the ability to inactivate N-AHSLs with an acyl chain ranging from C
6
to C
14
, with or without substitution at carbon 3. Screening of a collection of 15
Rhodococcus
strains and strains closely related to this genus clearly highlighted the relationship between the ability to degrade N-AHSLs and the presence of the
qsdA
gene in
Rhodococcus
. Bacteria harboring the
qsdA
gene interfere very efficiently with quorum-sensing-regulated functions, demonstrating that
qsdA
is a valuable tool for developing quorum-quenching procedures.
Molecular Detection of
Enterocytozoon bieneusi
and Identification of a Potentially Human-Pathogenic Genotype in Milk
Authors: Lee John Hwa
Published: January 2008

Milk specimens from 180 dairy cows were examined for the presence of
Enterocytozoon bieneusi
, using molecular assays. Fifteen specimens were found to be positive, of which 3 were identical to the human
E. bieneusi
types, which suggests that some
E. bieneusi
isolates from milk can infect humans. Overall, dairy cows' milk may play a significant role in the transmission of
E. bieneusi
infections to humans.
Intracellular Copper Accumulation Enhances the Growth ofKineococcus radiotoleransduring Chronic Irradiation
Authors: Bagwell C. E. , Milliken C. E. , Ghoshroy S. , Blom D. A.
Published: January 2008

The actinobacteriumKineococcus radiotoleransis highly resistant to ionizing radiation, desiccation, and oxidative stress, though the underlying biochemical mechanisms are unknown. The purpose of this study was to explore a possible linkage between the uptake of transition metals and extreme resistance to ionizing radiation and oxidative stress. The effects of six different divalent cationic metals on growth were examined in the absence of ionizing radiation. None of the metals tested were stimulatory, though cobalt was inhibitory to growth. In contrast, copper supplementation dramatically increased colony formation during chronic irradiation.K. radiotoleransexhibited specific uptake and intracellular accumulation of copper, compared to only a weak response to both iron and manganese supplementation. Copper accumulation sensitized cells to hydrogen peroxide. Acute-irradiation-induced DNA damage levels were similar in the copper-loaded culture and the age-synchronized no-copper control culture, though low-molecular-weight DNA was more persistent during postirradiation recovery in the Cu-loaded culture. Still, the estimated times for genome restoration differed by only 2 h between treatments. While we cannot discount the possibility that copper fulfills an unexpectedly important biochemical role in a low-radioactivity environment,K. radiotoleranshas a high capacity for intracellular copper sequestration and presumably efficiently coordinated oxidative stress defenses and detoxification systems, which confers cross-protection from the damaging effects of ionizing radiation.
Metagenomics: Read Length Matters
Authors: Wommack K. Eric , Bhavsar Jaysheel , Ravel Jacques
Published: January 2008

Obtaining an unbiased view of the phylogenetic composition and functional diversity within a microbial community is one central objective of metagenomic analysis. New technologies, such as 454 pyrosequencing, have dramatically reduced sequencing costs, to a level where metagenomic analysis may become a viable alternative to more-focused assessments of the phylogenetic (e.g., 16S rRNA genes) and functional diversity of microbial communities. To determine whether the short (∼100 to 200 bp) sequence reads obtained from pyrosequencing are appropriate for the phylogenetic and functional characterization of microbial communities, the results of BLAST and COG analyses were compared for long (∼750 bp) and randomly derived short reads from each of two microbial and one virioplankton metagenome libraries. Overall, BLASTX searches against the GenBank nr database found far fewer homologs within the short-sequence libraries. This was especially pronounced for a Chesapeake Bay virioplankton metagenome library. Increasing the short-read sampling depth or the length of derived short reads (up to 400 bp) did not completely resolve the discrepancy in BLASTX homolog detection. Only in cases where the long-read sequence had a close homolog (low BLAST E-score) did the derived short-read sequence also find a significant homolog. Thus, more-distant homologs of microbial and viral genes are not detected by short-read sequences. Among COG hits, derived short reads sampled at a depth of two short reads per long read missed up to 72% of the COG hits found using long reads. Noting the current limitation in computational approaches for the analysis of short sequences, the use of short-read-length libraries does not appear to be an appropriate tool for the metagenomic characterization of microbial communities.
Amyloid-Like Adhesins Produced by Floc-Forming and Filamentous Bacteria in Activated Sludge
Authors: Larsen Poul , Nielsen Jeppe Lund , Otzen Daniel , Nielsen Per Halkjær
Published: January 2008

Amyloid proteins (fimbriae or other microbial surface-associated structures) are expressed by many types of bacteria, not yet identified, in biofilms from various habitats, where they likely are of key importance to biofilm formation and biofilm properties. As these amyloids are potentially of great importance to the floc properties in activated sludge wastewater treatment plants (WWTP), the abundance of amyloid adhesins in activated sludge flocs from different WWTP and the identity of bacteria producing these were investigated. Amyloid adhesins were quantified using a combination of conformationally specific antibodies targeting amyloid fibrils, propidium iodide to target all fixed bacterial cells, confocal laser scanning microscopy, and digital image analysis. The biovolume fraction containing amyloid adhesins ranged from 10 to 40% in activated sludge from 10 different WWTP. The identity of bacteria producing amyloid adhesins was determined using fluorescence in situ hybridization with oligonucleotide probes in combination with antibodies or thioflavin T staining. Among the microcolony-forming bacteria, amyloids were primarily detected among
Alpha
- and
Betaproteobacteria
and
Actinobacteria
. A more detailed analysis revealed that many denitrifiers (from
Thauera, Azoarcus, Zoogloea
, and
Aquaspirillum
-related organisms) and
Actinobacteria
-related polyphosphate-accumulating organisms most likely produced amyloid adhesins, whereas nitrifiers did not. Many filamentous bacteria also expressed amyloid adhesins, including several
Alphaproteobacteria
(e.g.,
Meganema perideroedes
), some
Betaproteobacteria (e.g
.,
Aquaspirillum
-related filaments),
Gammaproteobacteria
(
Thiothrix
),
Bacteroidetes, Chloroflexi
(e.g., Eikelboom type 1851), and some foam-forming
Actinobacteria
(e.g.,
Gordonia amarae
). The results show that amyloid adhesins were an abundant component of activated sludge extracellular polymeric substances and seem to have unexpected, divers functions.
Role of the MexAB-OprM Efflux Pump of
Pseudomonas aeruginosa
in Tolerance to Tea Tree (
Melaleuca alternifolia
) Oil and Its Monoterpene Components Terpinen-4-ol, 1,8-Cineole, and α-Terpineol
Authors: Papadopoulos Chelsea J. , Carson Christine F. , Chang Barbara J. , Riley Thomas V.
Published: January 2008

Using a series of efflux mutants of
Pseudomonas aeruginosa
, the MexAB-OprM pump was identified as contributing to this organism's tolerance to the antimicrobial agent tea tree (
Melaleuca alternifolia
) oil and its monoterpene components terpinen-4-ol, 1,8-cineole, and α-terpineol. These data show that a multidrug efflux system of
P. aeruginosa
can extrude monoterpenes and related alcohols.
Quantification of the Detrimental Effect of a Single Primer-Template Mismatch by Real-Time PCR Using the 16S rRNA Gene as an Example
Authors: Bru D. , Martin-Laurent F. , Philippot L.
Published: January 2008

We investigated the effects of internal primer-template mismatches on the efficiency of PCR amplification using the 16S rRNA gene as the model template DNA. We observed that the presence of a single mismatch in the second half of the primer extension sequence can result in an underestimation of up to 1,000-fold of the gene copy number, depending on the primer and position of the mismatch.
Phylogenetic Characterization and Prevalence of “
Spirobacillus cienkowskii
,” a Red-Pigmented, Spiral-Shaped Bacterial Pathogen of Freshwater
Daphnia
Species
Authors: Rodrigues Jorge L. M. , Duffy Meghan A. , Tessier Alan J. , Ebert Dieter , Mouton Laurence , Schmidt Thomas M.
Published: January 2008

Microscopic examination of the hemolymph from diseased daphniids in 17 lakes in southwestern Michigan and five rock pools in southern Finland revealed the presence of tightly coiled bacteria that bore striking similarities to the drawings of a morphologically unique pathogen, “
Spirobacillus cienkowskii
,” first described by Elya Metchnikoff more than 100 years ago. The uncultivated microbe was identified as a deeply branching member of the
Deltaproteobacteria
through phylogenetic analyses of two conserved genes: the 16S rRNA-encoding gene (
rrs
) and the β-subunit of topoisomerase (
gyrB
). Fluorescence in situ hybridization confirmed that the rRNA gene sequence originated from bacteria with the tightly coiled morphology. Microscopy and PCR amplification with pathogen-specific primers confirmed infections by this bacterium in four species of
Daphnia
:
Daphnia dentifera, D. magna, D. pulicaria
, and
D. retrocurva
. Extensive field surveys reveal that this bacterium is widespread geographically and able to infect many different cladoceran species. In a survey of populations of
D. dentifera
in lakes in Michigan, we found the bacterium in 17 of 18 populations studied. In these populations, 0 to 12% of the individuals were infected, with an average of 3% during mid-summer and early autumn. Infections were less common in rock pool populations of
D. magna
in southern Finland, where the pathogen was found in 5 of 137 populations. The broad geographic distribution, wide host range, and high virulence of
S. cienkowskii
suggest it plays an important role in the ecology and evolution of daphniids.
Functional Analysis of the
Mycobacterium tuberculosis
FAD-Dependent Thymidylate Synthase, ThyX, Reveals New Amino Acid Residues Contributing to an Extended ThyX Motif
Authors: Ulmer Jonathan E. , Boum Yap , Thouvenel Christopher D. , Myllykallio Hannu , Sibley Carol Hopkins
Published: January 2008

A novel FAD-dependent thymidylate synthase, ThyX, is present in a variety of eubacteria and archaea, including the mycobacteria. A short motif found in all
thyX
genes, RHRX
7-8
S, has been identified. The three-dimensional structure of the
Mycobacterium tuberculosis
ThyX enzyme has been solved. Building upon this information, we used directed mutagenesis to produce 67 mutants of the
M. tuberculosis thyX
gene. Each enzyme was assayed to determine its ability to complement the defect in thymidine biosynthesis in a Δ
thyA
strain of
Escherichia coli
. Enzymes from selected strains were then tested in vitro for their ability to catalyze the oxidation of NADPH and the release of a proton from position 5 of the pyrimidine ring of dUMP. The results defined an extended motif of amino acids essential to enzyme activity in
M. tuberculosis
(Y44X
24
H69
X
25
R95HRX
7
S105
XRYX
90
R199 [with the underlined histidine acting as the catalytic residue and the underlined serine as the nucleophile]) and provided insight into the ThyX reaction mechanism. ThyX is found in a variety of bacterial pathogens but is absent in humans, which depend upon an unrelated thymidylate synthase, ThyA. Therefore, ThyX is a potential target for development of antibacterial drugs.
Borrelia burgdorferi
Uniquely Regulates Its Motility Genes and Has an Intricate Flagellar Hook-Basal Body Structure
Authors: Sal Melanie S. , Li Chunhao , Motalab M. A. , Shibata Satoshi , Aizawa Shin-Ichi , Charon Nyles W.
Published: January 2008

Borrelia burgdorferi
is a flat-wave, motile spirochete that causes Lyme disease. Motility is provided by periplasmic flagella (PFs) located between the cell cylinder and an outer membrane sheath. The structure of these PFs, which are composed of a basal body, a hook, and a filament, is similar to the structure of flagella of other bacteria. To determine if hook formation influences flagellin gene transcription in
B. burgdorferi
, we inactivated the hook structural gene
flgE
by targeted mutagenesis. In many bacteria, completion of the hook structure serves as a checkpoint for transcriptional control of flagellum synthesis and other chemotaxis and motility genes. Specifically, the hook allows secretion of the anti-sigma factor FlgM and concomitant late gene transcription promoted by σ
28
. However, the control of
B. burgdorferi
PF synthesis differs from the control of flagellum synthesis in other bacteria; the gene encoding σ
28
is not present in the genome of
B. burgdorferi
, nor are any σ
28
promoter recognition sequences associated with the motility genes. We found that
B. burgdorferi flgE
mutants lacked PFs, were rod shaped, and were nonmotile, which substantiates previous evidence that PFs are involved in both cell morphology and motility. Although most motility and chemotaxis gene products accumulated at wild-type levels in the absence of FlgE, mutant cells had markedly decreased levels of the flagellar filament proteins FlaA and FlaB. Further analyses showed that the reduction in the levels of flagellin proteins in the spirochetes lacking FlgE was mediated at the posttranscriptional level. Taken together, our results indicate that in
B. burgdorferi
, the completion of the hook does not serve as a checkpoint for transcriptional regulation of flagellum synthesis. In addition, we also present evidence that the hook protein in
B. burgdorferi
forms a high-molecular-weight complex and that formation of this complex occurs in the periplasmic space.
The Response Regulator CpxR Directly Regulates Expression of SeveralLegionella pneumophila icm/dotComponents as Well as New Translocated Substrates
Authors: Altman Efrat , Segal Gil
Published: January 2008

Legionella pneumophilahas been shown to utilize theicm/dottype IV secretion system for pathogenesis. This system was shown to be composed oficm/dotcomplex components and accessory proteins, as well as a large number of translocated substrates. Bioinformatic analysis of the regulatory regions of all the genes revealed that severalicm/dotgenes, as well as two genes encodingicm/dottranslocated substrates, contain the conserved CpxR regulatory element, a regulator that has been shown previously to control the expression of theicmRgene. An experimental analysis, which included a comparison of gene expression in aL. pneumophilawild-type strain and gene expression in acpxRdeletion mutant, construction of mutants with mutations in the CpxR conserved regulatory elements, controlled expression studies, and mobility shift assays, demonstrated the direct relationship between the CpxR regulator and the expression of the genes. Furthermore, genomic analysis identified nine additional genes that contain a putative CpxR regulatory element; five of these genes (twolegAgenes and threeceggenes) were suggested previously to be putativeicm/dottranslocated substrates. The threeceggenes identified, which were shown previously to contain a putative PmrA regulatory element, were found here to be regulated by both CpxR and PmrA. The other six genes (twolegAgenes and four new genes products were found to be regulated by CpxR. Moreover, using the CyaA translocation assay, these nine gene products were found to be translocated into host cells in an Icm/Dot-dependent manner. Our results establish that the CpxR regulator is a fundamental regulator of theicm/dottype IV secretion system inL. pneumophila.
Regulation of Type IV Secretion Apparatus Genes during
Ehrlichia chaffeensis
Intracellular Development by a Previously Unidentified Protein
Authors: Cheng Zhihui , Wang Xueqi , Rikihisa Yasuko
Published: January 2008

The type IV secretion (T4S) system is critical for the virulence of several pathogens. In the rickettsial pathogen
Ehrlichia chaffeensis
, the
virBD
genes are split into two operons, the
virB3
-
virB6
(preceded by
sodB
) and
virB8
-
virD4
operons. Between these two operons, there are duplications of
virB4
,
virB8
, and
virB9
. In this study we found that transcription of all five loci was downregulated prior to the release of
E. chaffeensis
from host THP-1 cells and was upregulated at the initiation of exponential growth. Electrophoretic mobility shift assays revealed an
E. chaffeensis
-encoded protein that specifically bound to the promoter regions upstream of the
virBD
loci. The protein was purified from the bacterial lysate by affinity chromatography using a biotinylated promoter region upstream of
sodB
. Mass spectrometry identified the protein as an
E. chaffeensis
12.3-kDa hypothetical protein, which was designated EcxR. Recombinant EcxR bound to the promoter regions upstream of five individual
virBD
loci. EcxR also activated transcription of all five
virBD
loci in
lacZ
reporter constructs. The expression of
ecxR
was positively autoregulated by EcxR. These results suggest that the five
virBD
loci are coordinately regulated by EcxR to allow developmental stage-specific expression of the T4S system in
E. chaffeensis.
A shift toward harmonics for high-frequency calling shown with phylogenetic study of frequency spectra in Eneopterinae crickets (Orthoptera, Grylloidea, Eneopteridae)
Authors: Robillard Tony , Grandcolas Philippe , Desutter-Grandcolas Laure
Published: January 2008

Dominant frequency is an important feature of cricket song, as it can be used for species recognition and mate choice. The dominant frequency usually ranges from 2 to 8 kHz and corresponds to the fundamental frequency of the song. In preliminary studies we documented high-frequency songs in the subfamily Eneopterinae. To analyse this phenomenon further, we investigate the spectral properties of these cricket songs. Based on the analysis of the frequency spectra in reference to phylogeny, we show that a shift of dominant frequency from the fundamental toward the second or the third harmonic of the song occurred in the Lebinthini tribe. In this clade the upper harmonics (second or third) become the most powerful frequencies of the song. From an evolutionary point of view, we document a case of convergence toward high-frequency calling between species of Eneoptera Burmeister, 1838, which emit alternatively low and high fundamental frequencies, and the Lebinthini, which emit high frequencies using upper harmonics. Functional hypotheses are discussed to explain how these high frequencies could be produced.