bluuebunny/crossref_metadata_2025 huggingface dataset:
Altered States
Authors: Icaza Eduardo E. , Mashour George A.
Published: September 2013

The psychedelic experience has been reported since antiquity, but there is relatively little known about the underlying neural mechanisms. A recent neuroimaging study on psilocybin revealed a pattern of decreased cerebral blood flow and functional disconnections that is surprisingly similar to that caused by various anesthetics. In this article, the authors review historical examples of psychedelic experiences induced by general anesthetics and then contrast the mechanisms by which these two drug classes generate altered states of consciousness.
Histone Deacetylase Complex1 Expression Level Titrates Plant Growth and Abscisic Acid Sensitivity in Arabidopsis
Authors: Perrella Giorgio , Lopez-Vernaza Manuel A. , Carr Craig , Sani Emanuela , Gosselé Veronique , Verduyn Christoph , Kellermeier Fabian , Hannah Matthew A. , Amtmann Anna
Published: September 2013

Histone deacetylation regulates gene expression during plant stress responses and is therefore an interesting target for epigenetic manipulation of stress sensitivity in plants. Unfortunately, overexpression of the core enzymes (histone deacetylases [HDACs]) has either been ineffective or has caused pleiotropic morphological abnormalities. In yeast and mammals, HDACs operate within multiprotein complexes. Searching for putative components of plant HDAC complexes, we identified a gene with partial homology to a functionally uncharacterized member of the yeast complex, which we called Histone Deacetylation Complex1 (HDC1). HDC1 is encoded by a single-copy gene in the genomes of model plants and crops and therefore presents an attractive target for biotechnology. Here, we present a functional characterization of HDC1 in Arabidopsis thaliana. We show that HDC1 is a ubiquitously expressed nuclear protein that interacts with at least two deacetylases (HDA6 and HDA19), promotes histone deacetylation, and attenuates derepression of genes under water stress. The fast-growing HDC1-overexpressing plants outperformed wild-type plants not only on well-watered soil but also when water supply was reduced. Our findings identify HDC1 as a rate-limiting component of the histone deacetylation machinery and as an attractive tool for increasing germination rate and biomass production of plants.
Nonallergic comorbidities of atopic eczema: an overview of systematic reviews
Authors: Deckert S. , Kopkow C. , Schmitt J.
Published: September 2013

The aims of this overview are to synthesize the current evidence of published systematic reviews (SRs) on nonallergic comorbidities of atopic eczema (AE). EMBASE and MEDLINE were searched for SRs published from inception to November 2012. SRs were selected independently based on predefined inclusion criteria. Methodological quality of SRs included was assessed by two independent reviewers using the Revised Assessment of Multiple Systematic Reviews (R‐AMSTAR) checklist. Nine SRs met all inclusion criteria. Six reviews addressing the association between AE and cancer suggest a decreased risk of glioma, meningioma, and acute lymphoblastic leukemia in patients with current or previous AE. One SR reported a consistent positive association of AE with attention‐deficit hyperactivity disorder (ADHD). Diabetes mellitus type 1 and multiple sclerosis (MS) were not significantly related to AE in reviews based on cross‐sectional and case–control studies. Patients with AE appear to be at decreased risk of brain tumors. The relationship of AE with Th1‐ and Th17‐mediated (auto‐)inflammatory conditions such as diabetes mellitus type 1 and MS should be clarified in prospective observational studies. Children with AE are at increased risk of ADHD. SRs on the risk of depression and Th17‐mediated disorders such as inflammatory bowel disease of patients with AE are missing.
Multiple sclerosis and risk of Parkinson's disease: a Danish nationwide cohort study
Authors: Nielsen N. M. , Pasternak B. , Stenager E. , Koch‐Henriksen N. , Frisch M.
Published: September 2013

Background and purpose

Case reports have observed a co‐occurrence of multiple sclerosis (MS) and Parkinson's disease (PD) and it has been hypothesized that MS lesions could affect dopaminergic pathways causing parkinsonism. Our aim was to examine the association between MS and PD in a historically prospective cohort study using Danish nationwide register data.

Methods

Multiple sclerosis patients identified in the Multiple Sclerosis Registry were followed for PD from 1977 to 2011 in the National Patient Register. As measures of relative risk, ratios of observed to expected incidence rates of first hospitalization for PD amongst persons with MS were used, i.e. standardized incidence ratios (SIRs) with 95% confidence intervals (CIs).

Results

Amongst 15 557 MS patients 26 cases of PD were observed versus 26.51 expected, reflecting no overall increased risk of PD (SIR 0.98, 95% CI 0.67–1.44). Similar estimates were seen for female (SIR 0.99, 95% CI 0.58–1.67) and male MS patients (SIR 0.97, 95% CI 0.55–1.72). Likewise, no increased risk of PD amongst MS patients was observed in a robustness analysis backdating the date of diagnosis of PD by 5 years to account for the time lag between disease onset and first hospital contact with PD (SIR 0.57, 95% CI 0.32–1.00).

Conclusion

Our data do not suggest an increased risk of PD amongst patients with MS.
Increased breast cancer risk for patients with multiple sclerosis: a nationwide population‐based cohort study
Authors: Sun L.‐M. , Lin C.‐L. , Chung C.‐J. , Liang J.‐A. , Sung F.‐C. , Kao C.‐H.
Published: September 2013

Background and purpose

Studies have suggested that multiple sclerosis (MS) might be linked to an overall reduced cancer rate, but a positive relationship is also found for several types of cancer. This study determines whether MS is associated with cancer risk in Taiwan.

Methods

Data from the National Health Insurance System of Taiwan were used to assess this issue. The MS cohort included 1292 patients, and each patient was randomly frequency‐matched with four participants without MS, based on their age, sex and index year (control cohort). Cox proportional hazards regression analysis was conducted to estimate the influence of MS on cancer risk.

Results

A significantly higher risk of developing overall cancer was found amongst the MS cohort compared with the control cohort [adjusted hazard ratio (HR) 1.85, 95% confidence interval (CI) 1.26–2.74], as well as breast cancer (adjusted HR 2.23, 95% CI 1.11–4.46).

Conclusions

The nationwide population‐based cohort study revealed that Taiwanese patients with MS have a higher risk of developing overall cancer types and breast cancer in particular.
Characterization of Bacillus Licheniformis Strain Ta62bi as Potential Selective Plugging Agent for Enchanced Oil Recovery
Authors: Daud Fareh Nunizawati , Johari Mohd Nazrin , Bahar Arifah , Idris Ahmad Kamal , Yahya Adibah
Published: September 2013

Bacterial plugging agents for microbial enhanced oil recovery were peviously studied using non-hydrocarbon substrate. They lacked the ability to survive and form stable plug at high concentration of hydrocarbon compounds. As an alternative, hydrocarbon was used as substrate to determine the bacterial potential as plugging agent. In this study, Bacillus licheniformis Ta62bi was used to study the potential of the bacteria as plugging agent in polycyclic aromatic hydrocarbon (PAH)-rich condition. Three responses (growth, exopolysaccharides (EPS) and PAH consumption) were analyzed. The survivability pattern was observed at 72 hours. From the analysis, pyrene was the best PAH compared to naphthalene. It was based on increment of 214% (415 CFU/mL) in growth and 30% (0.759 g/L) in EPS production. However, the consumption of soluble PAH (0.002 to 0.015 mg/L) was low. The assimilation of hydrocarbon by potential bacterial plugging agent is the only means of survival. Otherwise, it would degrade to a great extent the oil components that  would lead to the reduction of the oil quality. Next, a two-level factorial design was conducted to analyze the effects of different concentration of pyrene (0.1 to 10 g/L) and temperatures (27°C to 50°C) to the responses. The results showed that both factors significantly affect the responses (P < 0.05). Both factors inhibited growth of bacterium Ta62bi. As the PAH concentration was  increased, the EPS production and PAH consumption was also found to increase at 27˚C.  At 50°C, there was an increase  in the EPS production but not in the PAH consumption. Therefore, EPS might be implied to having an important role in the tolerance of the TA62bi strain towards hydrocarbon. The findings will be further used  in future research as a model to predict and control  enhanced oil recovery plugging mechanism.
Multiscale Element–Free Galerkin Method with Penalty for 2D Burgers’ Equation
Authors: Liew Siaw Ching , Yeak Su Hoe
Published: September 2013

In this paper, a new numerical method which is based on the coupling between multiscale method and meshless method with penalty is developed for 2D Burgers’ equation. The advantage of meshless method over the finite element method (FEM) is that remeshing process is not required. This is because the meshless method approximation is constructed entirely in terms of a set of nodes. Since the moving least squares (MLS) shape function does not satisfy the Kronecker delta property, so penalty method is adopted to enforce the essential boundary conditions in this paper. In order to obtain the fine scale approximation, the local enrichment basis is applied. The local enrichment basis may adopt the polynomial basis functions or any other analytical basis functions. Here, the polynomial basis functions are chosen as local enrichment basis. This multiscale meshless method with penalty will provide a more accurate result especially in the critical region which requires higher accuracy. It is believed that this proposed method is an attractive approach for solving more general problems which involve large deformation.
Persepsi Pelajar Terhadap Penggunaan Animasi dalam Pembelajaran Bahasa Arab
Authors: Che Hat Norhayati , Sha'ari Shaferul Hafes , Abdul Hamid Mohd Fauzi
Published: September 2013

Implementasi animasi sebagai bahan bantu mengajar (BBM) dalam pembelajaran bahasa Arab merupakan satu inovasi dalam mewujudkan suasana yang mampu mempengaruhi minat pelajar. Artikel ini membincangkan persepsi pelajar terhadap penggunaan animasi sebagai bahan bantu mengajar (BBM) dalam pembelajaran bahasa Arab. Satu set soal selidik kuantitatif dibentuk bagi mendapatkan data. Data dianalisis secara deskriptif bagi mencari taburan kekerapan, peratusan dan min. Hasil kajian mendapati bahawa pelajar mempunyai persepsi yang tinggi dan memberi respon positif terhadap penggunaan animasi dalam pembelajaran bahasa Arab dengan nilai purata 4.34. Kesimpulannya, animasi sesuai dipraktikkan sebagai bahan bantu mengajar bahasa Arab dan mampu menarik minat pelajar untuk menguasainya.
A Test for Normality in the Presence of Outliers
Authors: Ah Hin Pooi , Ching Soo Huei
Published: September 2013

The Jarque-Bera test is a test based on the coefficients of skewness (S) and kurtosis (K) for testing whether the given random sample is from a normal population. When the random sample of size n contains m outliers, we use the remaining n-m observations to compute two statistics S* and K* which mimic the statistics S and K. The statistics S* and  K* are next  transformed to z1 and z2 which are uncorrelated and having standard normal distributions when the original population is normal. We show that the acceptance region given by a circle in the (z1, z2) plane is suitable for testing the normality assumption.
Self-Explaining Agents
Authors: Fähndrich Johannes , Ahrndt Sebastian , Albayrak Sahin
Published: September 2013

This work advocate self-explanation as one foundation of self-* properties. Arguing that for system component to become more self-explanatory the underlining foundation is an awareness of themselves and their environment. In the research area of adaptive software, self-* properties have shifted into focus caused by the tendency to push ever more design decisions to the applications runtime. Thus fostering new paradigms for system development like intelligent and learning agents. This work surveys the state-of-the-art methods of self-explanation in software systems and distills a definition of self-explanation. Additionally, we introduce a measure to compare explanations and propose an approach for the first steps towards extending descriptions to become more explanatory. The conclusion shows that explanation is a special kind of description. The kind of description that provides additional information about a subject of interest and is understandable for the audience of the explanation. Further the explanation is dependent on the context it is used in, which brings about that one explanation can transport different information in different contexts. The proposed measure reflects those requirements.
Mathematical Communication Skills of Junior Secondary School Students in Coastal Area
Authors: Jl Kadir, , Parman Mayjen S.
Published: September 2013

Mathematical communication skills of junior secondary school students in coastal area are still considered low due to the lack of contextual problem technique in the teaching of mathematics. The various potencies of the coastal area have been damaged without any concern. It is interesting to investigate the contextual problem in mathematics teaching because it can be identified, required, and related to everyday life. The objective of this study is to enhance mathematical communication skills of junior secondary school students in the coastal area. Using coastal-based contextual teaching and learning (CCTL) can enhance: (1) students’ mathematical communication skills better than conventional teaching and learning (CVTL); and (2) the students’ learning activity, fluency of argument in problem solving process, advanced question skills, and knowledge of coastal area potencies and problems.
Student’s Competency in Solving and Creating Mathematical Problem in Pre-Service Training Program
Authors: S. Sugiman
Published: September 2013

Student as a mathematics teacher candidate must have competence in solving and creating mathematical problems. This paper describes how the two competencies are mastered by students. On the one competence, problem solving ability is reviewed by using four aspects: (1) conceptual and procedural understanding, (2) strategy knowledge, (3) mathematical communication ability and (4) accuracy. On the other competence, student’s creativity in developing mathematical problem is evaluated based on: (1) fluency, (2) flexibility and (3) novelty. Research subjects are students who take Integral Calculus course in the academic year of 2012. Data are collected through documentation, observation and interview and then analyzed quantitatively and qualitatively. Students show their abilities and some difficulties in both solving and creating mathematical problem.
Model Perkongsian Pengetahuan dalam Organisasi Sektor Swasta di Malaysia dan Hubungannya dengan Inovasi dan Prestasi Organisasi
Authors: Md. Noor Noorazah , Salim Juhana
Published: September 2013

Perkongsian pengetahuan merupakan kesediaan pekerja untuk menyumbang dan  kemampuan beliau untuk mengumpul pengetahuan daripada pekerja lain dalam organisasi. Kajian lepas mendapati perkongsian pengetahuan yang berjaya akan menggalak inovasi pekerja dan meningkatkan prestasi organisasi. Namun, terdapat pelbagai halangan dalam perkongsian pengetahuan seperti faktor manusia dan teknologi. Matlamat kajian ini adalah untuk membina dan mengesahkan model perkongsian pengetahuan sektor swasta (MPS) yang menggabung dua pendekatan utama iaitu pendekatan teknikal dan bukan teknikal. Kajian ini bertujuan untuk memeriksa pengaruh individu, organisasi dan teknologi terhadap amalan perkongsian pengetahuan di kalangan pekerja serta hubungannya dengan inovasi dan prestasi organisasi. Tiga teori yang menyokong pembinaan model MPS bagi memeriksa tiga faktor pengaruh adalah Social Capital Theory, Institutional Theory dan Adaptive Structuration Theory. Kajian ini menggunakan kaedah kuantitatif dengan teknik soal selidik dan kaedah kualitatif dengan teknik temu bual. Data dianalisis menggunakan SPSS bagi analisis deskriptif dan demografi, manakala model disahkan mengguna Structural Equation Modelling. Kajian mendapati pengaruh individu; ‘berkongsi visi dan matlamat’ dan ‘kepercayaan antara pekerja’, pengaruh organisasi; ‘tugas saling bergantungan’ dan ‘sokongan pengurusan atasan’ dan pengaruh teknologi; ‘kesetiaan’ menggunakan sistem pengurusan pengetahuan mempengaruhi amalan perkongsian pengetahuan. Seterusnya, amalan perkongsian pengetahuan mempunyai hubungan yang signifikan dengan inovasi dan inovasi mempunyai hubungan yang signifikan ke atas prestasi organisasi.
Tahap Kemahiran Generik Pelajar dalam Pembelajaran Kesusasteraan Melayu
Authors: Mahamod Zamri , Roni Noor Syazwani
Published: September 2013

Kajian ini dijalankan untuk mengenal pasti tahap kemahiran generik murid ketika mempelajari Kesusasteraan Melayu (KM). Antara elemen kemahiran generik yang ingin dikenal pasti ialah kemahiran berkomunikasi, kemahiran Teknologi maklumat dan komunikasi (TMK), kemahiran kepimpinan, kemahiran kerja berpasukan, dan pemikiran kritis serta kemahiran menyelesaikan masalah. Kajian ini juga ingin melihat perbezaan kemahiran generik berdasarkan jantina. Seramai 295 orang murid tingkatan empat yang mengambil mata pelajaran KM sebagai subjek elektif di daerah Tumpat, Kelantan dijadikan responden kajian. Soal selidik digunakan sebagai alat kajian untuk mengutip data. Data dianalisis menggunakan SPSS versi 18 sebagai alat untuk pemerihalan data deskriptif dan inferensi. Dapatan kajian menunjukkan tahap kemahiran generik murid berada di tahap yang sederhana. Selain itu, terdapat perbezaan yang signifikan antara kemahiran generik dengan jantina murid t (295) =2.236, p<0.05. Implikasi kajian ialah guru perlu menerapkan kemahiran generik ke dalam diri murid supaya mereka dapat mempersiapkan diri untuk bersaing untuk mendapatkan pekerjaan kelak.
Review of Percent Time Spent Following (PTSF) as Performance Measure for Two-lane Highways
Authors: Ibrahim Muttaka Na'iya , Puan Othman Che , Mustaffar Mushairry
Published: September 2013

The Highway Capacity Manual (HCM) uses Percent Time Spent Following (PTSF) as key service measure for assessing the level of service of two-lane highways. However, the indicator is difficult to measure directly in the field. For this reason, its estimation to date has been based on analytical procedures using equations derived from simulations and field observations at representative location based on surrogate measure; as the percent of vehicles traveling with headway less than 3 seconds (3 s). Findings from empirical studies confirmed that the HCM analytical procedures used in estimating PTSF yield results that are inconsistent with the 3 s surrogate measure and mostly overestimate the indicator. This paper presents a review on the estimation of PTSF on two-lane highways and suggests probable approach to substantiate the application of the current practice. Further, the authors of this paper argued that the use of 3 s as surrogate for estimating PTSF based on field observation at a specific point may not represent the actual time spent following over a long segment of two-lane highway since PTSF is space related measure. Hence, the authors suggest the use of test vehicle approach over the highway segment to be evaluated to identify the variables that are required for the development of a representative PTSF measurement model. It is expected that this review and suggestion offered will contribute in advancing performance analysis of two-lane highways.
Relationship between Occupational Stress and Turnover Intention among Employees in a Furniture Manufacturing Company in Selangor
Authors: Lee Fong Yoong , Mahfar Mastura
Published: September 2013

This study aims to investigate the relationship between occupational stress and turnover intention among employees in a furniture manufacturing company in Selangor state. A total of 95 respondents were randomly chosen by the researchers at a furniture manufacturing company in Selangor. The descriptive statistical analysis was used to analyse the demographic data of respondents, level of occupational stress, and level of turnover intention among employees in the selected furniture manufacturing company. Menawhile, Pearson (r) correlation was used to examine the relationship between occupational stress and turnover intention among the employees. Result revealed that majority of the respondents experienced moderate level of occupational stress whereas more than half of the respondents were found to have moderate level of turnover intention. Result showed that occupational stress was significantly positively correlated with turnover intention. Further analysis also indicated that the dimensions of occupational stress such as organisational structure, social support, work overload, role conflict, and working environment were significantly correlated with turnover intention. In conclusion, there was a statistically significant positive relationship between occupational stress and turnover intention among the employees.
Enhanced Pool Boiling With Ethanol at Subatmospheric Pressures for Electronics Cooling
Authors: Kalani Ankit , Kandlikar Satish G.
Published: September 2013

The growing trend in miniaturization of electronics has generated a need for efficient thermal management of these devices. Boiling has the ability to dissipate a high heat flux while maintaining a small temperature difference. A vapor chamber with pool boiling offers an effective way to provide cooling and to maintain temperature uniformity. The objective of the current work is to investigate pool boiling performance of ethanol on enhanced microchannel surfaces. Ethanol is an attractive working fluid due to its better heat transfer performance and higher heat of vaporization compared to refrigerants, and lower normal boiling point compared to water. The saturation temperature of ethanol can be further reduced to temperatures suitable for electronics cooling by lowering the pressure. Experiments were performed at four different absolute pressures, 101.3 kPa, 66.7 kPa, 33.3 kPa, and 16.7 kPa using different microchannel surface configurations. Heat dissipation in excess of 900 kW/m2 was obtained while maintaining the wall surface below 85 °C at 33 kPa. Flammability, toxicity, and temperature overshoot issues need to be addressed before practical implementation of ethanol-based cooling systems can occur.
Why Nonuniform Density Suppresses the Precessing Vortex Core
Authors: Oberleithner Kilian , Terhaar Steffen , Rukes Lothar , Oliver Paschereit Christian
Published: September 2013

Linear stability analysis is applied to a swirl-stabilized combustor flow with the aim to understand how the flame shape and associated density field affects the manifestation of self-excited flow instabilities. In isothermal swirling jets, self-excited flow oscillations typically manifest in a precessing vortex core and synchronized growth of large-scale spiral-shaped vortical structures. Recent theoretical studies relate these dynamics to a hydrodynamic global instability. These global modes also emerge in reacting flows, thereby crucially affecting the mixing characteristics and the flame dynamics. It is, however, observed that these self-excited flow oscillations are often suppressed in the reacting flow, while they are clearly present at isothermal conditions. This study provides strong evidence that the suppression of the precessing vortex core is caused by density inhomogeneities created by the flame. This mechanism is revealed by considering two reacting flow configurations: The first configuration represents a perfectly premixed steam-diluted detached flame featuring a strong precessing vortex core. The second represents a perfectly premixed dry flame anchoring near the combustor inlet, which does not exhibit self-excited oscillations. Experiments are conducted in a generic combustor test rig and the flow dynamics are captured using PIV and LDA. The corresponding density fields are approximated from the seeding density using a quantitative light sheet technique. The experimental results are compared to the global instability properties derived from hydrodynamic linear stability theory. Excellent agreement between the theoretically derived global mode frequency and measured precession frequency provide sufficient evidence to conclude that the self-excited oscillations are, indeed, driven by a global hydrodynamic instability. The effect of the density field on the global instability is studied explicitly by performing the analysis with and without density stratification. It turns out that the significant change in instability is caused by the radial density gradients in the inner recirculation zone and not by the change of the mean velocity field. The present work provides a theoretical framework to analyze the global hydrodynamic instability of realistic combustion configurations. It allows for relating the flame position and the resulting density field to the emergence of a precessing vortex core.
Development of the low-cost multi-channel analyzer system for γ-ray spectroscopy with a PC sound card
Authors: Sugihara Kenkoh , Nakamura Satoshi N. , Chiga Nobuyuki , Fujii Yuu , Tamura Hirokazu
Published: September 2013

A low-cost multi-channel analyzer (MCA) system was developed using a custom-build interface circuit and a PC sound card. The performance of the system was studied using γ-ray spectroscopy measurements with a NaI(Tl) scintillation detector. Our system successfully measured the energy of γ-rays at a rate of 1000 counts per second (cps).
Generalization of Torricelli's parabola to problems with a moving source
Authors: Heppler G. R. , D'Eleuterio G. M. T.
Published: September 2013

Analytical forms for the envelopes of trajectories for particles radially ejected from a moving source in uniform gravity are derived. These results generalize Torricelli's (safety) parabola for ballistic problems. As a motivating scenario we consider the spherical case shot, later named the shrapnel shell. Several cases that illustrate interesting features of the problem are presented along with an example inspired by the spherical case shot.
Re-creating Gauss's method for non-electrical absolute measurements of magnetic fields and moments
Authors: Van Baak D. A.
Published: September 2013

In 1832, Gauss made the first absolute measurements of magnetic fields and of magnetic moments in experiments that are straightforward and instructive to replicate. We show, using rare-earth permanent magnets and a variation of Gauss's technique, that the horizontal component of the ambient geomagnetic field, as well as the size of the magnetic moments of such magnets, can be found. The method shows the connection between the SI and cgs emu unit systems for these quantities and permits an absolute realization of the Ampere with considerable precision.
A graphical description of optical parametric generation of squeezed states of light
Authors: Bauchrowitz Jöran , Westphal Tobias , Schnabel Roman
Published: September 2013

The standard process for the production of strongly squeezed states of light is degenerate optical parametric amplification (OPA) below threshold in nonlinear dielectric media such as LiNbO3 or periodically poled potassium titanyl phosphate (KTP). Here, we present a graphical description of squeezed-light generation via OPA, visualizing the interaction between the nonlinear dielectric polarization of the medium and the electromagnetic quantum field. We explicitly focus on the transfer from the field's ground state to a squeezed vacuum state and from a coherent state to a bright squeezed state by the medium's second-order nonlinearity, respectively. Our pictures illustrate the phase-dependent amplification and deamplification of quantum uncertainties and give the phase relations between all propagating electromagnetic fields as well as the internally induced dielectric polarizations. The graphical description can also be used to describe the generation of nonclassical states of light via higher-order effects of the nonlinear dielectric polarization such as four-wave mixing and the optical Kerr effect.
Early and Late Trisporoids Differentially Regulate β-Carotene Production and Gene Transcript Levels in the Mucoralean Fungi Blakeslea trispora and Mucor mucedo
Authors: Sahadevan Yamuna , Richter-Fecken Mareike , Kaerger Kerstin , Voigt Kerstin , Boland Wilhelm
Published: September 2013

The multistep cleavage of carotenoids in
Mucorales
during the sexual phase results in a cocktail of trisporic acid (C
18
) sex pheromones. We hypothesized that the C
18
trisporoid intermediates have a specific regulatory function for sex pheromone production and carotenogenesis that varies with genus/species and vegetative and sexual phases of their life cycles. Real-time quantitative PCR kinetics determined for
Blakeslea trispora
displayed a very high transcript turnover in the gene for carotenoid cleavage dioxygenase,
tsp3
, during the sexual phase. An
in vivo
enzyme assay and chromatographic analysis led to the identification of β-apo-12′-carotenal as the first apocarotenoid involved in trisporic acid biosynthesis in
B. trispora
. Supplementation of C
18
trisporoids, namely D'orenone, methyl trisporate C, and trisporin C, increased
tsp3
transcripts in the plus compared to minus partners. Interestingly, the
tsp1
gene, which is involved in trisporic acid biosynthesis, was downregulated compared to
tsp3
irrespective of asexual or sexual phase. Only the minus partners of both
B. trispora
and
Mucor mucedo
had enhanced β-carotene production after treatment with C
20
apocarotenoids, 15 different trisporoids, and their analogues. We conclude that the apocarotenoids and trisporoids influence gene transcription and metabolite production, depending upon the fungal strain, corresponding genus, and developmental phase, representing a “chemical dialect” during sexual communication.
Survival of Bactericidal Antibiotic Treatment by a Persister Subpopulation of Listeria monocytogenes
Authors: Knudsen Gitte M. , Ng Yin , Gram Lone
Published: September 2013

Listeria monocytogenes
can cause the serious infection listeriosis, which despite antibiotic treatment has a high mortality. Understanding the response of
L. monocytogenes
to antibiotic exposure is therefore important to ensure treatment success. Some bacteria survive antibiotic treatment by formation of persisters, which are a dormant antibiotic-tolerant subpopulation. The purpose of this study was to determine whether
L. monocytogenes
can form persisters and how bacterial physiology affects the number of persisters in the population. A stationary-phase culture of
L. monocytogenes
was adjusted to 10
8
CFU ml
−1
, and 10
3
to 10
4
CFU ml
−1
survived 72-h treatment with 100 μg of norfloxacin ml
−1
, indicating a persister subpopulation. This survival was not caused by antibiotic resistance as regrown persisters were as sensitive to norfloxacin as the parental strain. Higher numbers of persisters (10
5
to 10
6
) were surviving when older stationary phase or surface-associated cells were treated with 100 μg of norfloxacin ml
−1
. The number of persisters was similar when a Δ
sigB
mutant and the wild type were treated with norfloxacin, but the killing rate was higher in the Δ
sigB
mutant. Dormant norfloxacin persisters could be activated by the addition of fermentable carbohydrates and subsequently killed by gentamicin; however, a stable surviving subpopulation of 10
3
CFU ml
−1
remained. Nitrofurantoin that has a growth-independent mode of action was effective against both growing and dormant cells, suggesting that eradication of persisters is possible. Our study adds
L. monocytogenes
to the list of bacterial species capable of surviving bactericidal antibiotics in a dormant stage, and this persister phenomenon should be borne in mind when developing treatment regimens.
Aerobic Biofilms Grown from Athabasca Watershed Sediments Are Inhibited by Increasing Concentrations of Bituminous Compounds
Authors: Yergeau Etienne , Lawrence John R. , Sanschagrin Sylvie , Roy Julie L. , Swerhone George D. W. , Korber Darren R. , Greer Charles W.
Published: September 2013

Sediments from the Athabasca River and its tributaries naturally contain bitumen at various concentrations, but the impacts of this variation on the ecology of the river are unknown. Here, we used controlled rotating biofilm reactors in which we recirculated diluted sediments containing various concentrations of bituminous compounds taken from the Athabasca River and three tributaries. Biofilms exposed to sediments having low and high concentrations of bituminous compounds were compared. The latter were 29% thinner, had a different extracellular polysaccharide composition, 67% less bacterial biomass per μm
2
, 68% less cyanobacterial biomass per μm
2
, 64% less algal biomass per μm
2
, 13% fewer protozoa per cm
2
, were 21% less productive, and had a 33% reduced content in chlorophyll
a
per mm
2
and a 20% reduction in the expression of photosynthetic genes, but they had a 23% increase in the expression of aromatic hydrocarbon degradation genes. Within the
Bacteria
, differences in community composition were also observed, with relatively more
Alphaproteobacteria
and
Betaproteobacteria
and less
Cyanobacteria
,
Bacteroidetes
, and
Firmicutes
in biofilms exposed to high concentrations of bituminous compounds. Altogether, our results suggest that biofilms that develop in the presence of higher concentrations of bituminous compounds are less productive and have lower biomass, linked to a decrease in the activities and abundance of photosynthetic organisms likely due to inhibitory effects. However, within this general inhibition, some specific microbial taxa and functional genes are stimulated because they are less sensitive to the inhibitory effects of bituminous compounds or can degrade and utilize some bitumen-associated compounds.
Fungal Communities Associated with the Biodegradation of Polyester Polyurethane Buried under Compost at Different Temperatures
Authors: Zafar Urooj , Houlden Ashley , Robson Geoffrey D.
Published: September 2013

Plastics play an essential role in the modern world due to their low cost and durability. However, accumulation of plastic waste in the environment causes wide-scale pollution with long-lasting effects, making plastic waste management expensive and problematic. Polyurethanes (PUs) are heteropolymers that made up ca. 7% of the total plastic production in Europe in 2011. Polyester PUs in particular have been extensively reported as susceptible to microbial biodegradation in the environment, particularly by fungi. In this study, we investigated the impact of composting on PUs, as composting is a microbially rich process that is increasingly being used for the processing of green waste and food waste as an economically viable alternative to landfill disposal. PU coupons were incubated for 12 weeks in fresh compost at 25°C, 45°C, and 50°C to emulate the thermophilic and maturation stages of the composting process. Incubation at all temperatures caused significant physical deterioration of the polyester PU coupons and was associated with extensive fungal colonization. Terminal restriction fragment length polymorphism (TRFLP) analysis and pyrosequencing of the fungal communities on the PU surface and in the surrounding compost revealed that the population on the surface of PU was different from the surrounding compost community, suggesting enrichment and selection. The most dominant fungi identified from the surfaces of PU coupons by pyrosequencing was
Fusarium solani
at 25°C, while at both 45°C and 50°C,
Candida ethanolica
was the dominant species. The results of this preliminary study suggest that the composting process has the potential to biodegrade PU waste if optimized further in the future.
Assessment of Persistence of Bartonella henselae in Ctenocephalides felis
Authors: Bouhsira Emilie , Franc Michel , Boulouis Henri-Jean , Jacquiet Philippe , Raymond-Letron Isabelle , Liénard Emmanuel
Published: September 2013

Bartonella henselae(Rhizobiales:Bartonellaceae) is a Gram-negative fastidious bacterium of veterinary and zoonotic importance. The cat fleaCtenocephalides felis(Siphonaptera: Pulicidae) is the main recognized vector ofB. henselae, and transmission among cats and humans occurs mainly through infected flea feces. The present study documents the use of a quantitative molecular approach to follow the daily kinetics ofB. henselaewithin the cat flea and its excreted feces after exposure to infected blood for 48 h in an artificial membrane system.B. henselaeDNA was detected in both fleas and feces for the entire life span of the fleas (i.e., 12 days) starting from 24 h after initiation of the blood meal.
Preadaptation to Cold Stress in Salmonella enterica Serovar Typhimurium Increases Survival during Subsequent Acid Stress Exposure
Authors: Shah Jigna , Desai Prerak T. , Chen Dong , Stevens John R. , Weimer Bart C.
Published: September 2013

Salmonella
is an important cause of bacterial food-borne gastroenteritis.
Salmonella
encounters multiple abiotic stresses during pathogen elimination methods used in food processing, and these stresses may influence its subsequent survivability within the host or in the environment. Upon ingestion,
Salmonella
is exposed to gastrointestinal acidity, a first line of the host innate defense system. This study tested the hypothesis that abiotic stresses encountered during food processing alter the metabolic mechanisms in
Salmonella
that enable survival and persistence during subsequent exposure to the host gastrointestinal acidic environment. Out of the four different abiotic stresses tested,
viz
., cold, peroxide, osmotic, and acid, preadaptation of the log-phase culture to cold stress (5°C for 5 h) significantly enhanced survival during subsequent acid stress (pH 4.0 for 90 min). The gene expression profile of
Salmonella
preadapted to cold stress revealed induction of multiple genes associated with amino acid metabolism, oxidative stress, and DNA repair, while only a few of the genes in the above-mentioned stress response and repair pathways were induced upon exposure to acid stress alone. Preadaptation to cold stress decreased the NAD
+
/NADH ratio and hydroxyl (OH·) radical formation compared with those achieved with the exposure to acid stress alone, indicating alteration of aerobic respiration and the oxidative state of the bacteria. The results from this study suggest that preadaptation to cold stress rescues
Salmonella
from the deleterious effect of subsequent acid stress exposure by induction of genes involved in stress response and repair pathways, by modification of aerobic respiration, and by redox modulation.
Prevalence of Diarrhea-Associated Virulence Genes and Genetic Diversity in Escherichia coli Isolates from Fecal Material of Various Animal Hosts
Authors: Chandran Abhirosh , Mazumder Asit
Published: September 2013

In order to assess the health risk associated with a given source of fecal contamination using bacterial source tracking (BST), it is important to know the occurrence of potential pathogens as a function of host.
Escherichia coli
isolates (
n
= 593) from the feces of diverse animals were screened for various virulence genes:
stx
1
and
stx
2
(Shiga toxin-producing
E. coli
[STEC]),
eae
and EAF (enteropathogenic
E. coli
[EPEC]), STh, STp, and LT (enterotoxigenic
E. coli
[ETEC]), and
ipaH
(enteroinvasive
E. coli
[EIEC]). Eleven hosts were positive for only the
eae
(10.11%) gene, representing atypical EPEC, while two hosts were positive for both
eae
and EAF (1.3%), representing typical EPEC.
stx
1
,
stx
2
, or both
stx
1
and
stx
2
were present in 1 (0.1%,) 10 (5.56%), and 2 (1.51%) hosts, respectively, and confirmed as non-O157 by using a
E. coli
O157
rfb
(
rfb
O157
) TaqMan assay. STh and STp were carried by 2 hosts (2.33%) and 1 host (0.33%), respectively, while none of the hosts were positive for LT and
ipaH
. The repetitive element palindromic PCR (rep-PCR) fingerprint analysis identified 221 unique fingerprints with a Shannon diversity index of 2.67. Multivariate analysis of variance revealed that majority of the isolates clustered according to the year of sampling. The higher prevalence of atypical EPEC and non-O157 STEC observed in different animal hosts indicates that they can be a reservoir of these pathogens with the potential to contaminate surface water and impact human health. Therefore, we suggest that
E. coli
from these sources must be included while constructing known source fingerprint libraries for tracking purposes. However, the observed genetic diversity and temporal variation need to be considered since these factors can influence the accuracy of BST results.
Using Transcriptomics To Improve Butanol Tolerance of Synechocystis sp. Strain PCC 6803
Authors: Anfelt Josefine , Hallström Björn , Nielsen Jens , Uhlén Mathias , Hudson Elton P.
Published: September 2013

Cyanobacteria are emerging as promising hosts for production of advanced biofuels such as
n
-butanol and alkanes. However, cyanobacteria suffer from the same product inhibition problems as those that plague other microbial biofuel hosts. High concentrations of butanol severely reduce growth, and even small amounts can negatively affect metabolic processes. An understanding of how cyanobacteria are affected by their biofuel product can enable identification of engineering strategies for improving their tolerance. Here we used transcriptome sequencing (RNA-Seq) to assess the transcriptome response of
Synechocystis
sp. strain PCC 6803 to two concentrations of exogenous
n
-butanol. Approximately 80 transcripts were differentially expressed at 40 mg/liter butanol, and 280 transcripts were different at 1 g/liter butanol. Our results suggest a compromised cell membrane, impaired photosynthetic electron transport, and reduced biosynthesis. Accumulation of intracellular reactive oxygen species (ROS) scaled with butanol concentration. Using the physiology and transcriptomics data, we selected several genes for overexpression in an attempt to improve butanol tolerance. We found that overexpression of several proteins, notably, the small heat shock protein HspA, improved tolerance to butanol. Transcriptomics-guided engineering created more solvent-tolerant cyanobacteria strains that could be the foundation for a more productive biofuel host.
Characterization of Three Ammonium Transporters of the Glomeromycotan Fungus Geosiphon pyriformis
Authors: Ellerbeck Matthias , Schüßler Arthur , Brucker David , Dafinger Claudia , Loos Friedemann , Brachmann Andreas
Published: September 2013

Members of the
Glomeromycota
form the arbuscular mycorrhiza (AM) symbiosis. They supply plants with inorganic nutrients, including nitrogen, from the soil. To gain insight into transporters potentially facilitating nitrogen transport processes, ammonium transporters (AMTs) of
Geosiphon pyriformis
, a glomeromycotan fungus forming a symbiosis with cyanobacteria, were studied. Three AMT genes were identified, and all three were expressed in the symbiotic stage. The localization and functional characterization of the proteins in a heterologous yeast system revealed distinct characteristics for each of them. AMT1 of
G. pyriformis
(GpAMT1) and GpAMT2 were both plasma membrane localized, but only GpAMT1 transported ammonium. Neither protein transported the ammonium analogue methylammonium. Unexpectedly, GpAMT3 was localized in the vacuolar membrane, and it has as-yet-unknown transport characteristics. An unusual cysteine residue in the AMT signature of GpAMT2 and GpAMT3 was identified, and the corresponding residue was demonstrated to play an important role in ammonium transport. Surprisingly, each of the three AMTs of
G. pyriformis
had very distinct features. The localization of an AMT in the yeast vacuolar membrane is novel, as is the described amino acid residue that clearly influences ammonium transport. The AMT characteristics might reflect adaptations to the lifestyle of glomeromycotan fungi.
Bidirectional-Genetics Platform, a Dual-Purpose Mutagenesis Strategy for Filamentous Fungi
Authors: Park Jaejin , Lee Yong-Hwan
Published: September 2013

Rapidly increasing fungal genome sequences call for efficient ways of generating mutants to translate quickly gene sequences into their functions. A reverse genetic strategy via targeted gene replacement (TGR) has been inefficient for many filamentous fungi due to dominant production of undesirable ectopic transformants. Although large-scale random insertional mutagenesis via transformation (i.e., forward genetics) facilitates high-throughput uncovering of novel genes of interest, generating a huge number of transformants, which is necessary to ensure the likelihood of mutagenizing most genes, is time-consuming. We propose a new strategy, entitled theBidirectional-Genetics (BiG) platform, which combines both forward and reverse genetic strategies by recycling ectopic transformants derived from TGR as a source for random insertional mutants. The BiG platform was evaluated using the rice blast fungusMagnaporthe oryzaeas a model. Over 10% of >1,000M. oryzaeectopic transformants, generated during disruption of specific genes, displayed abnormality in vegetative growth, pigmentation, and/or asexual reproduction. In this pool of putative mutants, we isolated insertional mutants with mutations in three genes involved in histidine biosynthesis (MoHIS5), vegetative growth (MoVPS74), or conidiophore formation (MoFRQ) (where “Mo” indicates “M. oryzae”), supporting the utility of this platform for systematic gene function studies.
Interaction Maps of the Saccharomyces cerevisiae ESCRT-III Protein Snf7
Authors: Sciskala Barbara , Kölling Ralf
Published: September 2013

The
Saccharomyces cerevisiae
ESCRT-III protein Snf7 is part of an intricate interaction network at the endosomal membrane. Interaction maps of Snf7 were established by measuring the degree of binding of individual binding partners to putative binding motifs along the Snf7 sequence by glutathione
S
-transferase (GST) pulldown. For each interaction partner, distinct binding profiles were obtained. The following observations were made. The ESCRT-III subunits Vps20 and Vps24 showed a complementary binding pattern, suggesting a model for the series of events in the ESCRT-III functional cycle. Vps4 bound to individual Snf7 motifs but not to full-length Snf7. This suggests that Vps4 does not bind to the closed conformation of Snf7. We also demonstrate for the first time that the ALIX/Bro1 homologue Rim20 binds to the α6 helix of Snf7. Analysis of a Snf7 α6 deletion mutant showed that the α6 helix is crucial for binding of Bro1 and Rim20
in vivo
and is indispensable for the multivesicular body (MVB)-sorting and Rim-signaling functions of Snf7. The Snf7Δα6 protein still appeared to be incorporated into ESCRT-III complexes at the endosomal membrane, but disassembly of the complex seemed to be defective. In summary, our study argues against the view that the ESCRT cycle is governed by single one-to-one interactions between individual components and emphasizes the network character of the ESCRT interactions.