bluuebunny/crossref_metadata_2025 huggingface dataset:
Rehabilitation experiences after obstetric fistula repair: systematic review of qualitative studies
Authors: Lombard Ladeisha , de St. Jorre Jenna , Geddes Rosemary , El Ayadi Alison M. , Grant Liz
Published: January 2015

Objectives

To synthesise evidence on women's experiences surrounding rehabilitation and reintegration after obstetric fistula repair in sub‐Saharan Africa and explore recommendations from women and health service providers.

Method

Systematic literature review of qualitative studies surrounding rehabilitation experiences of women in sub‐Saharan Africa who have undergone obstetric fistula repair. Using a pre‐defined search strategy, seven databases, relevant source publications and grey literature were searched for primary qualitative studies. Data from ten studies were collected, and thematic analysis based on the framework approach was used to analyse the findings.

Results

The most important rehabilitating factor for women was fulfilment of social roles. Health service perspectives were more frequent than women's perspectives. Counselling and health education were the most common recommendations from both perspectives.

Conclusion

Little qualitative evidence is available on rehabilitation after obstetric fistula repair in sub‐Saharan Africa. Counselling services and community health education are priorities. Further research should emphasise women's perspectives to better inform interventions aimed at addressing the physical and social consequences of obstetric fistula.
Foreign Technology Acquisition and Changes in the Real Exchange Rate
Authors: Alvarez Roberto , López Ricardo A.
Published: January 2015

This paper uses plant‐level data from the manufacturing sector of Chile to investigate how changes in the real exchange rate affect the decision to purchase foreign technologies through licensing. Theoretically, a real depreciation has an ambiguous effect on foreign technology adoption. On the one hand, a real depreciation makes exports more competitive, and as exporters tend to adopt and use more advanced technologies, we should observe a higher propensity to import technologies among them. On the other hand, a real depreciation can also make imports of technology relatively more expensive. Thus, this question must be examined empirically. The empirical analysis shows that a real depreciation significantly increases the probability of using foreign technology licences for plants that export and for plants in the intermediate range of the size and productivity distribution.
Review on porcine endogenous retrovirus detection assays—impact on quality and safety of xenotransplants
Authors: Godehardt Antonia W. , Rodrigues Costa Michael , Tönjes Ralf R.
Published: January 2015

Xenotransplantation of porcine organs, tissues, and cells inherits a risk for xenozoonotic infections. Viable tissues and cells intended for transplantation have to be considered as potentially contaminated non‐sterile products. The demands on microbial testing, based on the regulatory requirements, are often challenging due to a restricted shelf life or the complexity of the product itself. In Europe, the regulatory framework for xenogeneic cell therapy is based on the advanced therapy medicinal products (ATMP) regulation (2007), the EMA CHMP Guideline on xenogeneic cell‐based medicinal products (2009), as well as the WHO and Council of Europe recommendations. In the USA, FDA guidance for industry (2003) regulates the use of xenotransplants. To comply with the regulations, validated test methods need to be established that reveal the microbial status of a transplant within its given shelf life, complemented by strictly defined action alert limits and supported by breeding in specific pathogen‐free (SPF) facilities. In this review, we focus on assays for the detection of the porcine endogenous retroviruses PERV‐A/‐B/‐C, which exhibit highly polymorphic proviral loci in pig genomes. PERVs are transmitted vertically and cannot be completely eliminated by breeding or gene knock out technology. PERVs entail a public health concern that will persist even if no evidence of PERV infection of xenotransplant recipients in vivo has been revealed yet. Nevertheless, infectious risks must be minimized by full assessment of pigs as donors by combining different molecular screening assays for sensitive and specific detection as well as a functional analysis of the infectivity of PERV including an adequate monitoring of recipients.
Mechanisms of renal sympathetic activation in renovascular hypertension
Authors: Campos Ruy R. , Oliveira‐Sales Elizabeth Barbosa , Nishi Erika E. , Paton Julian F. R. , Bergamaschi Cassia T.
Published: January 2015

New findings

What is the topic of this review?

This review addresses the underlying mechanisms involved in sympathoexcitation during renovascular hypertension, focusing on the importance of increased oxidative stress in the paraventricular nucleus and rostral ventrolateral medulla.

What advances does it highlight?

Whether renal or autonomic dysfunction is the major contributor to systemic hypertension following a renovascular insult is still a matter of debate. Here, we take an integrative approach by describing the crosstalk between the kidney and brain. We show how changes in the CNS, and in sympathetic premotor neurons in particular, are activated by ischaemic renal disease in an experimental model of renovascular hypertension.

This review addresses the underlying mechanisms involved in the sympathoexcitation in renovascular hypertension. We focus on the importance of increased oxidative stress in the paraventricular nucleus of hypothalamus (PVN) and rostral ventrolateral medulla (RVLM) for the autonomic dysfunction associated with renovascular hypertension in the two‐kidney, one‐clip (2K‐1C) model. We found in 2K‐1C rats, 6 weeks after clipping, a significant increase in the mRNA and protein expression of the angiotensin II type 1 receptor within the RVLM and PVN. In addition, mRNA from NADPH oxidase subunits (p47phox and gp91phox) was greater in the RVLM and PVN of 2K‐1C rats than in a sham‐operated group. However, CuZn superoxide dismutase gene expression in these regions was not changed, suggesting that excessive production of reactive oxygen species overwhelms any endogenous antioxidant system in the RVLM and PVN in renovascular hypertension. In fact, acute administration of tempol or vitamin C (either i.v. or directly into the PVN or RVLM) caused a significant decrease in blood pressure and renal sympathetic nerve activity in 2K‐1C rats, but not in control animals. Thus, we suggest that an increase in the activity of RVLM and PVN neurons triggered by angiotensin II and oxidative stress is a major mechanism involved in the maintenance of sympathoexcitation of the cardiovascular system in renovascular hypertension.
Human muscle fibre type‐specific regulation of AMPK and downstream targets by exercise
Authors: Kristensen Dorte E. , Albers Peter H. , Prats Clara , Baba Otto , Birk Jesper B. , Wojtaszewski Jørgen F. P.
Published: January 2015

Keypoints

AMP‐activated protein kinase (AMPK) is an important regulator of cellular energy status during exercise.

Most human studies investigating skeletal muscle protein signalling have been performed in whole muscle biopsy samples, yet recent studies suggest muscle fibre type‐specific AMPK expression with potential fibre type‐specific regulation of AMPK during exercise.

This study provides novel and comprehensive data on human muscle fibre type‐specific expression levels of AMPK subunits and downstream targets of AMPK.

We show a differentiated response to exercise of key metabolic signalling proteins in human type I and type II muscle fibres during interval exercise, not evident during continuous exercise. These differences between exercise types were not present in whole muscle biopsy samples.

Our findings highlight the importance of performing fibre type‐specific measurements and the increased activation of AMPK in interval vs. continuous exercise could be important for exercise type‐specific adaptations, i.e. metabolism, insulin sensitivity and mitochondrial density in human skeletal muscle.

AMP‐activated protein kinase (AMPK) is a regulator of energy homeostasis during exercise. Studies suggest muscle fibre type‐specific AMPK expression. However, fibre type‐specific regulation of AMPK and downstream targets during exercise has not been demonstrated. We hypothesized that AMPK subunits are expressed in a fibre type‐dependent manner and that fibre type‐specific activation of AMPK and downstream targets is dependent on exercise intensity. Pools of type I and II fibres were prepared from biopsies of vastus lateralis muscle from healthy men before and after two exercise trials: (1) continuous cycling (CON) for 30 min at 69 ± 1% peak rate of O2 consumption () or (2) interval cycling (INT) for 30 min with 6 × 1.5 min high‐intensity bouts peaking at 95 ± 2% . In type I vs. II fibres a higher β1 AMPK (+215%) and lower γ3 AMPK expression (−71%) was found. α1, α2, β2 and γ1 AMPK expression was similar between fibre types. In type I vs. II fibres phosphoregulation after CON was similar (AMPKThr172, ACCSer221, TBC1D1Ser231 and GS2+2a) or lower (TBC1D4Ser704). Following INT, phosphoregulation in type I vs. II fibres was lower (AMPKThr172, TBC1D1Ser231, TBC1D4Ser704 and ACCSer221) or higher (GS2+2a). Exercise‐induced glycogen degradation in type I vs. II fibres was similar (CON) or lower (INT). In conclusion, a differentiated response to exercise of metabolic signalling/effector proteins in human type I and II fibres was evident during interval exercise. This could be important for exercise type‐specific adaptations, i.e. insulin sensitivity and mitochondrial density, and highlights the potential for new discoveries when investigating fibre type‐specific signalling.
Rapid changes in NADH and flavin autofluorescence in rat cardiac trabeculae reveal large mitochondrial complex II reserve capacity
Authors: Wüst Rob C. I. , Helmes Michiel , Stienen Ger J. M.
Published: January 2015

Key points

A photometry‐based technique was developed to measure nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide (FAD) autofluorescence and contractile properties simultaneously in intact rat trabeculae at a high time resolution. This provides insight into the function of mitochondrial complex I and II.

Maximal complex I and complex II activities were determined in saponin‐permeabilized right ventricular tissue by respirometry.

In trabeculae, complex II function was considerably smaller than the maximal complex II activity, suggesting large complex II reserve capacity.

Up–down asymmetry in NADH and FAD kinetics suggests a complex interaction between mitochondrial and contractile function.

These data show that simultaneous measurement of contractile properties and NADH and FAD kinetics in cardiac trabeculae provides a mean to study the differences in complex I and II function in intact preparations in health and disease.

The functional properties of cardiac mitochondria in intact preparations have been mainly studied by measurements of nicotinamide adenine dinucleotide (NADH) autofluorescence, which reflects mitochondrial complex I function. To assess complex II function, we extended this method by measuring flavin adenine dinucleotide (FAD)‐related autofluorescence in electrically stimulated cardiac trabeculae isolated from the right ventricle from the rat at 27°C. NADH and FAD autofluorescence and tension responses were measured when stimulation frequency was increased from 0.5 Hz to 1, 2 or 3 Hz for 3 min, and thereafter decreased to 0.5 Hz. Maximal complex I and complex II activity in vitro were determined in saponin‐permeabilized right ventricular tissue by respirometry. NADH responses upon an increase in stimulation frequency showed a rapid decline, followed by a slow recovery towards the initial level. FAD responses followed a similar time course, but in the opposite direction. The amplitudes of early rapid changes in the NADH and FAD concentration correlated well with the change in tension time integral per second (R2 = 0.833 and 0.660 for NADH and FAD, respectively), but with different slopes for the up and down transient. Maximal velocity of the increase in FAD concentration (16 ± 4 μm s−1), measured upon an increase in stimulation frequency from 0.5 to 3 Hz was considerably smaller than that of the decrease in NADH (78 ± 13 μm s−1). The respiration measurements indicated that the maximal velocity of NADH utilization (143 ± 14 μm s−1) was 2 times smaller than that of FADH2 (291 ± 19 μm s−1). This indicates that in cardiac mitochondria considerable complex II activity reserve is present.
Actin cytoskeletal rearrangement and dysfunction due to activation of the receptor for advanced glycation end products is inhibited by thymosin beta 4
Authors: Kim Sokho , Kwon Jungkee
Published: January 2015

Key points

Thymosin beta 4 (Tβ4) attenuates the vascular cellular toxicity induced by advanced glycation end products (AGEs) in human umbilical vein endothelial cells (HUVECs).

Tβ4 reduces expression of both the receptor of AGEs (RAGE) and the filamentous actin (F‐actin) to globular actin (G‐actin) ratio.

RAGE expression was regulated by actin cytoskeleton involved in Tβ4.

Tβ4 attenuates the vascular cellular toxicity induced by AGEs via remodelling of the actin cytoskeleton.

AGEs attenuate vascular‐like tube formation of HUVECs, which is reversed by Tβ4 via remodelling of the actin cytoskeleton.

The receptor of advanced glycation end products (RAGE) is a cell‐surface receptor that is a key factor in the pathogenesis of diabetic complications, including vascular disorders. Dysfunction of the actin cytoskeleton contributes to disruption of cell membrane repair in response to various type of endothelial cell damage. However, mechanism underlying RAGE remodelling of the actin cytoskeleton, by which globular actin (G‐actin) forms to filamentous actin (F‐actin), remains unclear. In this study we examined the role of thymosin beta 4 (Tβ4) – which binds to actin, blocks actin polymerization, and maintains the dynamic equilibrium between G‐actin and F‐actin in human umbilical vein endothelial cells (HUVECs) – in the response to RAGE. Tβ4 increased cell viability and decreased levels of reactive oxygen species in HUVECs incubated with AGEs. Tβ4 reduced the expression of RAGE, consistent with a down‐regulation of the F‐actin to G‐actin ratio. The effect of remodelling of the actin cytoskeleton on RAGE expression was clarified by adding Phalloidin, which stabilizes F‐actin. Moreover, small interfering RNA was used to determine whether intrinsic Tβ4 regulates RAGE expression in the actin cytoskeleton. The absence of intrinsic Tβ4 in HUVECs evoked actin cytoskeleton disorder and increased RAGE expression. These findings suggest that regulation of the actin cytoskeleton by Tβ4 plays a pivotal role in the RAGE response to AGEs.
On the Buckling of a Two-Dimensional Micropolar Strip
Authors: Hasanyan Armanj D. , Waas Anthony M.
Published: January 2015

This study examines the buckling of a single strip of material, modeled as a two-dimensional (2D) micropolar solid. The effects of material microstructure are incorporated by modeling the material using micropolar theory. By setting the micropolar constants to zero, the equations of classical elasticity are obtained and these results are compared to the buckling analysis performed by previous authors on elastic materials. In the limiting case, when the thickness of the strip becomes small in comparison to the overall length, the micropolar beam equations are developed. Because buckling analysis requires the consideration of geometric nonlinearity, nonlinear micropolar equations are derived using a variational procedure, which also results in variationally consistent boundary conditions. Due to the complexity of micropolar theory, its application has been limited to linear analysis with a few exceptions.
The Joule Heating Effects on Natural Convection of Participating Magnetohydrodynamics Under Different Levels of Thermal Radiation in a Cavity
Authors: Zhang Jing-Kui , Li Ben-Wen , Chen Yuan-Yuan
Published: January 2015

A numerical study is conducted for the Joule heating effects on fluid flow and heat transfer of radiatively participating magnetohydrodynamics (MHD) under different levels of thermal radiation considering the Hall effects in a square cavity. In the cavity, the vertical walls are isothermal with constant but different temperatures, while the horizontal walls are adiabatic. The absorption, emission, and scattering of the fluid and the reflection, absorption, and emission of the walls are all taken into account. The governing equations for momentum and energy together with the boundary conditions are solved by the finite volume method (FVM), while the governing equation for radiative transfer is solved by the discrete ordinates method (DOM). Tabular and graphical results are presented in terms of streamlines, isotherms, Nusselt number, and the average temperature of the fluid. After detailed analysis, we found that the Joule heating has notable effects on fluid flow and heat transfer in the cavity and Joule heating cannot be neglected in certain range of parameters.
Fluid Stiction Modeling for Quickly Separating Plates Considering the Liquid Tensile Strength
Authors: Roemer Daniel B. , Johansen Per , Pedersen Henrik C. , Andersen Torben O.
Published: January 2015

Fluid stiction may significantly influence the dynamic behavior when attempting to quickly separate two plates in close contact. The liquid fluid film, filling the gap between the plates, experiences a pressure drop resulting from an increasing distance, and cavitation may appear if sufficient separation speed and low plate distance are present. In the case of small initial plate separation, fluid tension is known to develop and the stiction force may exceed the maximum stiction force calculated by assuming strictly positive pressures in the fluid film. In this paper, a model for simulating the time dependent fluid stiction phenomenon, including a fluid tensile strength and cavitation effects, is proposed. The model is based on Reynolds theory, and the pressure distribution in the liquid zone is solved analytically for each time step, leading to a computationally efficient model without the need for finite element/volume methods. The considered geometry is two long parallel plates submerged in liquid, as present in many valve applications. The model is compared to experimental measurements, and it is found that the model is able to predict the stiction effect with reasonable accuracy given that proper selections of liquid tensile strength and initial plate distance are made.
Full-Parameter Approach for the Intake Port Design of a Four-Valve Direct-Injection Gasoline Engine
Authors: Cui Lei , Wang Tianyou , Lu Zhen , Jia Ming , Sun Yanzhe
Published: January 2015

The design of the intake port plays a critical role in the development of modern internal combustion (IC) engines. The traditional method of the intake port design is a time-consuming process including a huge amount of tests and the production of core box. Compared with the traditional methods, parametric approach attracts increasing attentions by virtue of its high-efficiency, traceability, and flexibility. Based on a tangential port model created by a three-dimensional (3D) computer aided design (cad) software, a new tangential port can be quickly generated with different sets of structure parameters, then computational fluid dynamics (CFD) was employed to explore the influence of structure parameters on the intake port performance. The results show that the flow capacity and the large-scale vortex intensity change regularly with the variations of structure parameters. Finally, the parametric approach was employed to design the intake port of a production four-valve direct-injection (DI) gasoline engine, and the good applicability this approach is well illustrated.
Damage Detection of Steel Beam Using Frequency Response Function Measurement Data and Fractal Dimension
Authors: Lee Eun-Taik , Eun Hee-Chang
Published: January 2015

Fractal-dimension-based signal processing has been extensively applied to various fields for nondestructive testing. The dynamic response signal can be utilized as an analytical tool to evaluate the structural health state without baseline data. The fractal features of the dynamic responses with fractal dimensions (FDs) were investigated using the Higuchi, Katz, and Sevcik methods. The waveform FD proposed by these methods was extracted from the measured frequency response function (FRF) data in the frequency domain. Damage was observed within this region, which resulted in an abrupt change in the curvature of the FD. The effectiveness of the methods was investigated via the results of a steel beam test and a numerical experiment to detect damage.
On the Effects of Mistuning a Force-Excited System Containing a Quasi-Zero-Stiffness Vibration Isolator
Authors: Abolfathi Ali , Brennan M. J. , Waters T. P. , Tang B.
Published: January 2015

Nonlinear isolators with high-static-low-dynamic-stiffness have received considerable attention in the recent literature due to their performance benefits compared to linear vibration isolators. A quasi-zero-stiffness (QZS) isolator is a particular case of this type of isolator, which has a zero dynamic stiffness at the static equilibrium position. These types of isolators can be used to achieve very low frequency vibration isolation, but a drawback is that they have purely hardening stiffness behavior. If something occurs to destroy the symmetry of the system, for example, by an additional static load being applied to the isolator during operation, or by the incorrect mass being suspended on the isolator, then the isolator behavior will change dramatically. The question is whether this will be detrimental to the performance of the isolator and this is addressed in this paper. The analysis in this paper shows that although the asymmetry will degrade the performance of the isolator compared to the perfectly tuned case, it will still perform better than the corresponding linear isolator provided that the amplitude of excitation is not too large.
On the Transverse, Low Frequency Vibrations of a Traveling String With Boundary Damping
Authors: Gaiko Nick V. , van Horssen Wim T.
Published: January 2015

In this paper, we study the free transverse vibrations of an axially moving (gyroscopic) material represented by a perfectly flexible string. The problem can be used as a simple model to describe the low frequency oscillations of elastic structures such as conveyor belts. In order to suppress these oscillations, a spring–mass–dashpot system is attached at the nonfixed end of the string. In this paper, it is assumed that the damping in the dashpot is small and that the axial velocity of the string is small compared to the wave speed of the string. This paper has two main objectives. The first aim is to give explicit approximations of the solution on long timescales by using a multiple-timescales perturbation method. The other goal is to construct accurate approximations of the lower eigenvalues of the problem, which describe the oscillation and the damping properties of the problem. The eigenvalues follow from a so-called characteristic equation obtained by the direct application of the Laplace transform method to the initial-boundary value problem. Both approaches give a complete and accurate picture of the damping and the low frequency oscillatory behavior of the traveling string.
On effective dose for radiotherapy based on doses to nontarget organs and tissues
Authors: Uselmann Adam J. , Thomadsen Bruce R.
Published: January 2015

Purpose:

The National Council for Radiation Protection and Measurement (NCRP) published estimates for the collective population dose and the mean effective dose to the population of the United States from medical imaging procedures for 1980/1982 and for 2006. The earlier report ignored the effective dose from radiotherapy and the latter gave a cursory discussion of the topic but again did not include it in the population exposure for various reasons. This paper explains the methodology used to calculate the effective dose in due to radiotherapy procedures in the latter NCRP report and revises the values based on more detailed modeling.

Methods:

This study calculated the dose to nontarget organs from radiotherapy for reference populations using CT images and published peripheral dose data.

Results:

Using International Commission on Radiological Protection (ICRP) 60 weighting factors, the total effective dose to nontarget organs in radiotherapy patients is estimated as 298 ± 194 mSv per patient, while the U.S. population effective dose is 0.939 ± 0.610 mSv per person, with a collective dose of 283 000 ± 184 000 person Sv per year. Using ICRP 103 weighting factors, the effective dose is 281 ± 183 mSv per patient, 0.887 ± 0.577 mSv per person in the U.S., and 268 000 ± 174 000 person Sv per year. The uncertainty in the calculations is largely governed by variations in patient size, which was accounted for by considering a range of patient sizes and taking the average treatment site to nontarget organ distance.

Conclusions:

The methods used to estimate the effective doses from radiotherapy used in NCRP Report No. 160 have been explained and the values updated.
A moment of truth arrives for U.S. ocean science
Authors: Kintisch Eli
Published: January 2015

Report urges infrastructure cuts to boost research.
Credit card study blows holes in anonymity
Authors: Bohannon John
Published: January 2015

Attack suggests need for new data safeguards.
Risk of exposure
Authors: Enserink Martin
Published: January 2015

When new or dangerous infectious diseases strike, public health often trumps personal privacy.
Natural Hot Spots for Gain of Multiple Resistances: Arsenic and Antibiotic Resistances in Heterotrophic, Aerobic Bacteria from Marine Hydrothermal Vent Fields
Authors: Farias Pedro , Espírito Santo Christophe , Branco Rita , Francisco Romeu , Santos Susana , Hansen Lars , Sorensen Soren , Morais Paula V.
Published: January 2015

Microorganisms are responsible for multiple antibiotic resistances that have been associated with resistance/tolerance to heavy metals, with consequences to public health. Many genes conferring these resistances are located on mobile genetic elements, easily exchanged among phylogenetically distant bacteria. The objective of the present work was to isolate arsenic-, antimonite-, and antibiotic-resistant strains and to determine the existence of plasmids harboring antibiotic/arsenic/antimonite resistance traits in phenotypically resistant strains, in a nonanthropogenically impacted environment. The hydrothermal Lucky Strike field in the Azores archipelago (North Atlantic, between 11°N and 38°N), at the Mid-Atlantic Ridge, protected under the OSPAR Convention, was sampled as a metal-rich pristine environment. A total of 35 strains from 8 different species were isolated in the presence of arsenate, arsenite, and antimonite. ACR3 and
arsB
genes were amplified from the sediment's total DNA, and 4 isolates also carried ACR3 genes. Phenotypic multiple resistances were found in all strains, and 7 strains had recoverable plasmids. Purified plasmids were sequenced by Illumina and assembled by EDENA V3, and contig annotation was performed using the “Rapid Annotation using the Subsystems Technology” server. Determinants of resistance to copper, zinc, cadmium, cobalt, and chromium as well as to the antibiotics β-lactams and fluoroquinolones were found in the 3 sequenced plasmids. Genes coding for heavy metal resistance and antibiotic resistance in the same mobile element were found, suggesting the possibility of horizontal gene transfer and distribution of theses resistances in the bacterial population.
Sediment and Vegetation as Reservoirs of Vibrio vulnificus in the Tampa Bay Estuary and Gulf of Mexico
Authors: Chase Eva , Young Suzanne , Harwood Valerie J.
Published: January 2015

The opportunistic pathogen
Vibrio vulnificus
occurs naturally in estuarine habitats and is readily cultured from water and oysters under warm conditions but infrequently at ambient conditions of <15°C. The presence of
V. vulnificus
in other habitats, such as sediments and aquatic vegetation, has been explored much less frequently. This study investigated the ecology of
V. vulnificus
in water by culture and quantitative PCR (qPCR) and in sediment, oysters, and aquatic vegetation by culture.
V. vulnificus
samples were taken from five sites around Tampa Bay, FL. Levels determined by qPCR and culture were significantly correlated (
P
= 0.0006;
r
= 0.352); however,
V. vulnificus
was detected significantly more frequently by qPCR (85% of all samples) compared to culture (43%). Culturable
V. vulnificus
bacteria were recovered most frequently from oyster samples (70%), followed by vegetation and sediment (∼50%) and water (43%). Water temperature, which ranged from 18.5 to 33.4°C, was positively correlated with
V. vulnificus
concentrations in all matrices but sediments. Salinity, which ranged from 1 to 35 ppt, was negatively correlated with
V. vulnificus
levels in water and sediments but not in other matrices. Significant interaction effects between matrix and temperature support the hypothesis that temperature affects
V. vulnificus
concentrations differently in different matrices and that sediment habitats may serve as seasonal reservoirs for
V. vulnificus
.
V. vulnificus
levels in vegetation have not been previously measured and reveal an additional habitat for this autochthonous estuarine bacterium.
Gas Chromatography-Mass Spectrometry-Based Metabolite Profiling of Salmonella enterica Serovar Typhimurium Differentiates between Biofilm and Planktonic Phenotypes
Authors: Wong Hui San , Maker Garth L. , Trengove Robert D. , O'Handley Ryan M.
Published: January 2015

The aim of this study was to utilize gas chromatography coupled with mass spectrometry (GC-MS) to compare and identify patterns of biochemical change between
Salmonella
cells grown in planktonic and biofilm phases and
Salmonella
biofilms of different ages. Our results showed a clear separation between planktonic and biofilm modes of growth. The majority of metabolites contributing to variance between planktonic and biofilm supernatants were identified as amino acids, including alanine, glutamic acid, glycine, and ornithine. Metabolites contributing to variance in intracellular profiles were identified as succinic acid, putrescine, pyroglutamic acid, and
N
-acetylglutamic acid. Principal-component analysis revealed no significant differences between the various ages of intracellular profiles, which would otherwise allow differentiation of biofilm cells on the basis of age. A shifting pattern across the score plot was illustrated when analyzing extracellular metabolites sampled from different days of biofilm growth, and amino acids were again identified as the metabolites contributing most to variance. An understanding of biofilm-specific metabolic responses to perturbations, especially antibiotics, can lead to the identification of novel drug targets and potential therapies for combating biofilm-associated diseases. We concluded that under the conditions of this study, GC-MS can be successfully applied as a high-throughput technique for “bottom-up” metabolomic biofilm research.
Inducible Suppression of Global Translation by Overuse of Rare Codons
Authors: Kobayashi Hideki
Published: January 2015

Recently, artificial gene networks have been developed in synthetic biology to control gene expression and make organisms as controllable as robots. Here, I present an artificial posttranslational gene-silencing system based on the codon usage bias and low tRNA content corresponding to minor codons. I engineered the green fluorescent protein (GFP) gene to inhibit translation indirectly with the lowest-usage codons to monopolize various minor tRNAs (
lgfp
). The expression of
lgfp
interfered nonspecifically with the growth of
Escherichia coli
,
Saccharomyces cerevisiae
, human HeLa cervical cancer cells, MCF7 breast cancer cells, and HEK293 kidney cells, as well as phage and adenovirus expansion. Furthermore, insertion of
lgfp
downstream of a phage response promoter conferred phage resistance on
E. coli
. Such engineered gene silencers could act as components of biological networks capable of functioning with suitable promoters in
E. coli
,
S. cerevisiae
, and human cells to control gene expression. The results presented here show general suppressor artificial genes for live cells and viruses. This robust system provides a gene expression or cell growth control device for artificially synthesized gene networks.
Genome-Wide Transcriptional Responses to Carbon Starvation in Nongrowing Lactococcus lactis
Authors: Ercan Onur , Wels Michiel , Smid Eddy J. , Kleerebezem Michiel
Published: January 2015

This paper describes the transcriptional adaptations of nongrowing, retentostat cultures of
Lactococcus lactis
to starvation. Near-zero-growth cultures (μ = 0.0001 h
−1
) obtained by extended retentostat cultivation were exposed to starvation by termination of the medium supply for 24 h, followed by a recovery period of another 24 h by reinitiating the medium supply to the retentostat culture. During starvation, the viability of the culture was largely retained, and the expression of genes involved in transcription and translational machineries, cell division, and cell membrane energy metabolism was strongly repressed. Expression of these genes was largely recovered following the reinitiation of the medium supply. Starvation triggered the elevated expression of genes associated with synthesis of branched-chain amino acids, histidine, purine, and riboflavin. The expression of these biosynthesis genes was found to remain at an elevated level after reinitiation of the medium supply. In addition, starvation induced the complete gene set predicted to be involved in natural competence in
L. lactis
KF147, and the elevated expression of these genes was sustained during the subsequent recovery period, but our attempts to experimentally demonstrate natural transformation in these cells failed. Mining the starvation response gene set identified a conserved
cis
-acting element that resembles the lactococcal CodY motif in the upstream regions of genes associated with transcription and translational machineries, purine biosynthesis, and natural transformation in
L. lactis
, suggesting a role for CodY in the observed transcriptome adaptations to starvation in nongrowing cells.
Development of a Protocol for Predicting Bacterial Resistance to Microbicides
Authors: Knapp Laura , Amézquita Alejandro , McClure Peter , Stewart Sara , Maillard Jean-Yves
Published: January 2015

Regulations dealing with microbicides in Europe and the United States are evolving and now require data on the risk of the development of resistance in organisms targeted by microbicidal products. There is no standard protocol to assess the risk of the development of resistance to microbicidal formulations. This study aimed to validate the use of changes in microbicide and antibiotic susceptibility as initial markers for predicting microbicide resistance and cross-resistance to antibiotics. Three industrial isolates (
Pseudomonas aeruginosa
,
Burkholderia cepacia
, and
Klebsiella pneumoniae
) and two
Salmonella enterica
serovar Typhimurium strains (SL1344 and 14028S) were exposed to a shampoo, a mouthwash, eye makeup remover, and the microbicides contained within these formulations (chlorhexidine digluconate [CHG] and benzalkonium chloride [BZC]) under realistic, in-use conditions. Baseline and postexposure data were compared. No significant increases in the MIC or the minimum bactericidal concentration (MBC) were observed for any strain after exposure to the three formulations. Increases as high as 100-fold in the MICs and MBCs of CHG and BZC for SL1344 and 14028S were observed but were unstable. Changes in antibiotic susceptibility were not clinically significant. The use of MICs and MBCs combined with antibiotic susceptibility profiling and stability testing generated reproducible data that allowed for an initial prediction of the development of resistance to microbicides. These approaches measure characteristics that are directly relevant to the concern over resistance and cross-resistance development following the use of microbicides. These are low-cost, high-throughput techniques, allowing manufacturers to provide to regulatory bodies, promptly and efficiently, data supporting an early assessment of the risk of resistance development.
Molecular Gene Profiling of Clostridium botulinum Group III and Its Detection in Naturally Contaminated Samples Originating from Various European Countries
Authors: Woudstra Cedric , Le Maréchal Caroline , Souillard Rozenn , Bayon-Auboyer Marie-Hélène , Anniballi Fabrizio , Auricchio Bruna , De Medici Dario , Bano Luca , Koene Miriam , Sansonetti Marie-Hélène , Desoutter Denise , Hansbauer Eva-Maria , Dorner Martin B. , Dorner Brigitte G. , Fach Patrick
Published: January 2015

We report the development of real-time PCR assays for genotyping
Clostridium botulinum
group III targeting the newly defined
C. novyi sensu lato
group; the nontoxic nonhemagglutinin (NTNH)-encoding gene
ntnh
; the botulinum neurotoxin (BoNT)-encoding genes
bont/C
,
bont/C/D
,
bont/D
, and
bont/D/C
; and the flagellin (
fliC
) gene. The genetic diversity of
fliC
among
C. botulinum
group III strains resulted in the definition of five major subgroups named
fliC
-I to
fliC
-V. Investigation of
fliC
subtypes in 560 samples, with various European origins, showed that
fliC
-I was predominant and found exclusively in samples contaminated by
C. botulinum
type C/D,
fliC
-II was rarely detected, no sample was recorded as
fliC
-III or
fliC
-V, and only
C. botulinum
type D/C samples tested positive for
fliC
-IV. The lack of genetic diversity of the flagellin gene of
C. botulinum
type C/D would support a clonal spread of type C/D strains in different geographical areas.
fliC
-I to
fliC
-III are genetically related (87% to 92% sequence identity), whereas
fliC
-IV from
C. botulinum
type D/C is more genetically distant from the other
fliC
types (with only 50% sequence identity). These findings suggest
fliC
-I to
fliC
-III have evolved in a common environment and support a different genetic evolution for
fliC
-IV. A combination of the
C. novyi sensu lato
,
ntnh
,
bont
, and
fliC
PCR assays developed in this study allowed better characterization of
C. botulinum
group III and showed the group to be less genetically diverse than
C. botulinum
groups I and II, supporting a slow genetic evolution of the strains belonging to
C. botulinum
group III.
Temporal and Spatial Differences in Microbial Composition during the Manufacture of a Continental-Type Cheese
Authors: O'Sullivan Daniel J. , Cotter Paul D. , O'Sullivan Orla , Giblin Linda , McSweeney Paul L. H. , Sheehan Jeremiah J.
Published: January 2015

We sought to determine if the time, within a production day, that a cheese is manufactured has an influence on the microbial community present within that cheese. To facilitate this, 16S rRNA amplicon sequencing was used to elucidate the microbial community dynamics of brine-salted continental-type cheese in cheeses produced early and late in the production day. Differences in the microbial composition of the core and rind of the cheese were also investigated. Throughout ripening, it was apparent that cheeses produced late in the day had a more diverse microbial population than their early equivalents. Spatial variation between the cheese core and rind was also noted in that cheese rinds were initially found to have a more diverse microbial population but thereafter the opposite was the case. Interestingly, the genera
Thermus
,
Pseudoalteromonas
, and
Bifidobacterium
, not routinely associated with a continental-type cheese produced from pasteurized milk, were detected. The significance, if any, of the presence of these genera will require further attention. Ultimately, the use of high-throughput sequencing has facilitated a novel and detailed analysis of the temporal and spatial distribution of microbes in this complex cheese system and established that the period during a production cycle at which a cheese is manufactured can influence its microbial composition.
Female-Specific Specialization of a Posterior End Region of the Midgut Symbiotic Organ in Plautia splendens and Allied Stinkbugs
Authors: Hayashi Toshinari , Hosokawa Takahiro , Meng Xian-Ying , Koga Ryuichi , Fukatsu Takema
Published: January 2015

Many stinkbugs (Insecta: Hemiptera: Heteroptera) are associated with bacterial symbionts in a posterior region of the midgut. In these stinkbugs, adult females excrete symbiont-containing materials from the anus for transmission of the beneficial symbionts to their offspring. For ensuring the vertical symbiont transmission, a variety of female-specific elaborate traits at the cellular, morphological, developmental, and behavioral levels have been reported from diverse stinkbugs of the families Plataspidae, Urostylididae, Parastrachiidae, etc. Meanwhile, such elaborate female-specific traits for vertical symbiont transmission have been poorly characterized for the largest and economically important stinkbug family Pentatomidae. Here, we investigated the midgut symbiotic system of a pentatomid stinkbug,
Plautia splendens
. A specific gammaproteobacterial symbiont was consistently present extracellularly in the cavity of numerous crypts arranged in four rows on the midgut fourth section. The symbiont was smeared on the egg surface upon oviposition by adult females, orally acquired by newborn nymphs, and thereby transmitted vertically to the next generation and important for growth and survival of the host insects. We found that, specifically in adult females, several rows of crypts at the posterior end region of the symbiotic midgut were morphologically differentiated and conspicuously enlarged, often discharging the symbiotic bacteria from the crypt cavity to the main tract of the symbiotic midgut. The female-specific enlarged end crypts were also found in other pentatomid stinkbugs
Plautia stali
and
Carbula crassiventris
. These results suggest that the enlarged end crypts represent a female-specific specialized morphological trait for vertical symbiont transmission commonly found among stinkbugs of the family Pentatomidae.
Signaling Domains of Mucin Msb2 in Candida albicans
Authors: Swidergall Marc , van Wijlick Lasse , Ernst Joachim F.
Published: January 2015

Candida albicans
adapts to the human host by environmental sensing using the Msb2 signal mucin, which regulates fungal morphogenesis and resistance characteristics. Msb2 is anchored within the cytoplasmic membrane by a single transmembrane (TM) region dividing it into a large N-terminal exodomain, which is shed, and a small cytoplasmic domain. Analyses of strains carrying deleted Msb2 variants revealed an exodomain segment required for cleavage, shedding, and all functions of Msb2. Phosphorylation of the mitogen-activated protein kinase (MAP kinase) Cek1 was regulated by three distinct regions in Msb2: in unstressed cells, N-terminal sequences repressed phosphorylation, while its induction under cell wall stress required the cytoplasmic tail (C-tail) and sequences N-terminally flanking the TM region, downstream of the proposed cleavage site. Within the latter Msb2 region, overlapping but not identical sequences were also required for hyphal morphogenesis, basal resistance to antifungals, and, in unstressed cells, downregulation of the
PMT1
transcript, encoding protein
O
-mannosyltransferase-1. Deletion of two-thirds of the exodomain generated a truncated Msb2 variant with a striking ability to induce hyperfilamentous growth, which depended on the presence of the Msb2-interacting protein Sho1, the MAP kinase Cek1, and the Efg1 transcription factor. Under cell wall stress, the cytoplasmic tail relocalized partially to the nucleus and contributed to regulation of 117 genes, as revealed by transcriptomic analyses. Genes regulated by the C-tail contained binding sites for the Ace2 and Azf1 transcription factors and included the
ALS
cell wall genes. We concluded that Msb2 fulfills its numerous functions by employing functional domains that are distributed over its entire length.
Components of the Calcium-Calcineurin Signaling Pathway in Fungal Cells and Their Potential as Antifungal Targets
Authors: Liu Shuyuan , Hou Yinglong , Liu Weiguo , Lu Chunyan , Wang Weixin , Sun Shujuan
Published: January 2015

In recent years, the emergence of fungal resistance has become frequent, partly due to the widespread clinical use of fluconazole, which is minimally toxic and effective in the prevention and treatment of
Candida albicans
infections. The limited selection of antifungal drugs for clinical fungal infection therapy has prompted us to search for new antifungal drug targets. Calcium, which acts as the second messenger in both mammals and fungi, plays a direct role in controlling the expression patterns of its signaling systems and has important roles in cell survival. In addition, calcium and some of the components, mainly calcineurin, in the fungal calcium signaling pathway mediate fungal resistance to antifungal drugs. Therefore, an overview of the components of the fungal calcium-calcineurin signaling network and their potential roles as antifungal targets is urgently needed. The calcium-calcineurin signaling pathway consists of various channels, transporters, pumps, and other proteins or enzymes. Many transcriptional profiles have indicated that mutant strains that lack some of these components are sensitized to fluconazole or other antifungal drugs. In addition, many researchers have identified efficient compounds that exhibit antifungal activity by themselves or in combination with antifungal drugs by targeting some of the components in the fungal calcium-calcineurin signaling pathway. This targeting disrupts Ca
2+
homeostasis, which suggests that this pathway contains potential targets for the development of new antifungal drugs.
Evaluation of Ebola Virus Inactivation Procedures for Plasmodium falciparum Malaria Diagnostics
Authors: Lau Rachel , Wang Amanda , Chong-Kit Ann , Ralevski Filip , Boggild Andrea K.
Published: January 2015

Plasmodium falciparum
malaria is highly endemic in the three most affected countries in the current epidemic of Ebola virus disease (EVD) in West Africa. As EVD and malaria are clinically indistinguishable, both remain part of the differential diagnosis of ill travelers from returning from areas of EVD transmission. We compared the performances of a rapid diagnostic test (BinaxNOW) and real-time PCR with
P. falciparum-
positive specimens before and after heat and Triton X-100 inactivation, and we documented no loss of sensitivity.