bluuebunny/crossref_metadata_2025 huggingface dataset:
Rice Hull Smoke Extract Inactivates Salmonella Typhimurium in Laboratory Media and Protects Infected Mice against Mortality
Authors: Kim Sung Phil , Kang Mi Young , Park Jun Cheol , Nam Seok Hyun , Friedman Mendel
Published: December 2011

Abstract:  A previously characterized rice hull smoke extract (RHSE) was tested for bactericidal activity against Salmonella Typhimurium using the disc‐diffusion method. The minimum inhibitory concentration (MIC) value of RHSE was 0.822% (v/v). The in vivo antibacterial activity of RHSE (1.0%, v/v) was also examined in a Salmonella‐infected Balb/c mouse model. Mice infected with a sublethal dose of the pathogens were administered intraperitoneally a 1.0% solution of RHSE at four 12‐h intervals during the 48‐h experimental period. The results showed that RHSE inhibited bacterial growth by 59.4%, 51.4%, 39.6%, and 28.3% compared to 78.7%, 64.6%, 59.2%, and 43.2% inhibition with the medicinal antibiotic vancomycin (20 mg/mL). By contrast, 4 consecutive administrations at 12‐h intervals elicited the most effective antibacterial effect of 75.0% and 85.5% growth reduction of the bacteria by RHSE and vancomycin, respectively. The combination of RHSE and vancomycin acted synergistically against the pathogen. The inclusion of RHSE (1.0% v/w) as part of a standard mouse diet fed for 2 wk decreased mortality of 10 mice infected with lethal doses of the Salmonella. Photomicrographs of histological changes in liver tissues show that RHSE also protected the liver against Salmonella‐induced pathological necrosis lesions. These beneficial results suggest that the RHSE has the potential to complement wood‐derived smokes as antimicrobial flavor formulations for application to human foods and animal feeds.

Practical Application:  The new antimicrobial and anti‐inflammatory rice hull derived liquid smoke has the potential to complement widely used wood‐derived liquid smokes as an antimicrobial flavor and health‐promoting formulation for application to foods.
Optimization and Validation of an Extraction Method for the Analysis of Polycyclic Aromatic Hydrocarbons in Chocolate Candies
Authors: Kumari Rupender , Chaturvedi Prashant , Ansari Nasreen G. , Murthy Ramesh C. , Patel Devendra K.
Published: December 2011

Abstract:  Chocolate is a key ingredient in many foods such as milk shakes, candies, bars, cookies, and cereals. Chocolate candies are often consumed by mankind of all age groups. The presence of polycyclic aromatic hydrocarbons (PAHs) in chocolate candies may result in health risk to people. A rapid, precise, and economic extraction method was optimized and validated for the simultaneous determination of polycyclic aromatic hydrocarbons in chocolate candy by high‐performance liquid chromatography (HPLC) and gas chromatography‐mass spectrometry (GS‐MS) as a confirmatory technique. The method was optimized by using different solvents for liquid–liquid extraction, varying volume of de‐emulsifying agent, and quantity of silica gel used for purification. The HPLC separation of 16 PAHs was carried out by C‐18 column with mobile phase composed of acetonitrile : water (70 : 30) in isocratic mode with runtime of 20 min. Limit of detection, limit of quantification (LOQ), and correlation coefficients were found in the range of 0.3 to 4ng g−1, 0.9 to 12ng g−1, and 0.9109 to 0.9952, respectively. The exploration of 25 local chocolate candy samples for the presence of PAHs showed the mean content of benzo[a]pyrene as 1.62 ng g−1, which representing the need to evaluate effective measures to prevent more severe PAHs contamination in chocolate candies in future.

Practical Application:  Chocolate is one of the most favorite food items among people, especially children. Chocolate candies are often consumed by mankind of all age groups. Chocolate candies are often consumed by children in large quantities. The presence PAHs in chocolate candies may result in health risk to people. In the present study, a precise and cost effective rapid method was employed for the determination of PAHs, which can be employed for daily routine analysis of PAHs in chocolate products.
In vitro and in vivo characterization of silk fibroin/gelatin composite scaffolds for liver tissue engineering
Authors: YANG Zhao , XU Li Sha , YIN Fang , SHI Yong Quan , HAN Ying , ZHANG Lin , JIN Hai Feng , NIE Yong Zhan , WANG Jing Bo , HAO Xing , FAN Dai Ming , ZHOU Xin Min
Published: December 2011

OBJECTIVE:  To investigate the cytotoxicity of silk fibroin/gelatin (SF/G) composite scaffolds in vitro as well as their biocompatibility and degradation in vivo.

METHODS:  The proliferation and relative growth rate of human hepatic QZG cells grown on different blends of two‐dimensional (2‐D) SF/G scaffolds were assessed using the 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide (MTT) assay. Flow cytometry was used to evaluate apoptotic rate of QZG cells on different blends of 2‐D SF/G scaffolds. The effect of silk protein materials on cell growth was observed by scanning electron microscopy. Three‐dimensional (3‐D) SF/G scaffolds of three different ratios (diameter 10 mm, thickness 1 mm) were implanted into subcutaneous pockets on male Sprague–Dawley (SD) rats. On the 7th, 14th and 30th day post‐implantation, the rats were sacrificed. The scaffold area including the surrounding tissues was retrieved. Hematoxylin and eosin staining was performed for observation under a light microscope.

RESULTS:  Significant cell attachment and proliferation on the SF/G scaffolds were observed. As the increased gelatin concentration, SF/G scaffolds became more amenable to cell adhesion. After the subcutaneous implantation of the SF/G scaffolds in SD rats, immunological rejection tests showed only slight inflammation, measured by the presence of inflamed cells on day 7 and 14. By day 30, each scaffold had been completely infiltrated and organized by fibroblasts and inflamed cells. The greater the gelatin concentration in the scaffold, the faster the degradation rate.

CONCLUSION:  Composite SF/G scaffolds are a promising candidate matrix for implantable bio‐artificial livers.
Using an Established Telehealth Model to Train Urban Primary Care Providers on Hypertension Management
Authors: Masi Christopher , Hamlish Tamara , Davis Andrew , Bordenave Kristine , Brown Stephen , Perea Brenda , Aduana Glen , Wolfe Marcus , Bakris George , Johnson Daniel
Published: December 2011

J Clin Hypertens (Greenwich).

The objective of this study was to determine whether a videoconference‐based telehealth network can increase hypertension management knowledge and self‐assessed competency among primary care providers (PCPs) working in urban Federally Qualified Health Centers (FQHCs). We created a telehealth network among 6 urban FQHCs and our institution to support a 12‐session educational program designed to teach state‐of‐the‐art hypertension management. Each 1‐hour session included a brief lecture by a university‐based hypertension specialist, case presentations by PCPs, and interactive discussions among the specialist and PCPs. Twelve PCPs (9 intervention and 3 controls) were surveyed at baseline and immediately following the curriculum. The mean number of correct answers on the 26‐item hypertension knowledge questionnaire increased in the intervention group (13.11 [standard deviation (SD)]=3.06) to 17.44 [SD=1.59], P<.01) but not among controls (14.33 [SD=3.21] to 13.00 [SD=3.46], P=.06). Similarly, the mean score on a 7‐item hypertension management self‐assessed competency scale increased in the intervention group (4.68 [SD=0.94] to 5.41 [SD=0.89], P<.01) but not among controls (5.28 [SD=0.43] to 5.62 [SD=0.67], P=.64). This model holds promise for enhancing hypertension care provided by urban FQHC providers.
Markers of Inflammation, Metabolic Risk Factors, and Incident Heart Failure in American Indians: The Strong Heart Study
Authors: Barac Ana , Wang Hong , Shara Nawar M. , de Simone Giovanni , Carter Elizabeth A. , Umans Jason G. , Best Lyle G. , Yeh Jeunliang , Dixon Damon B. , Devereux Richard B. , Howard Barbara V. , Panza Julio A.
Published: December 2011

Inflammation may play a role in increased risk of heart failure (HF) that is associated with obesity, metabolic syndrome (MS), and diabetes. This study investigated associations between inflammatory markers, MS, and incident HF in a population with a high prevalence of diabetes, obesity, and MS. The cohort consisted of 3098 American Indians without prevalent cardiovascular disease who had C‐reactive protein (CRP) and fibrinogen measured at the Strong Heart Study phase II examination. Independent associations between inflammatory markers, MS, and HF were analyzed by Cox hazard models. During a mean follow‐up of 11 years, 218 participants developed HF. After the adjustment for cardiovascular risk factors, fibrinogen, (hazard ratio [HR], 1.36; 95% confidence interval [CI], 1.15–1.59) but not CRP (HR, 1.25; 95% CI, 0.97–1.32) remained a significant HF predictor. In individuals without diabetes, concomitant presence of MS and elevated CRP or fibrinogen increased HF risk (for MS and CRP: HR, 2.02; 95% CI, 0.95–4.31; for CRP and fibrinogen: HR, 1.75; 95% CI, 0.83–3.72). In a population with a high prevalence of obesity, MS, and diabetes, elevated CRP and fibrinogen increased HF risk. These associations are attenuated by the adjustments for conventional risk factors suggesting that inflammation acts in concert with metabolic and clinical risk factors in increasing HF risk.
The When and How of Evaluative Readiness: A Social Cognitive Neuroscience Perspective
Authors: Ferguson Melissa J. , Wojnowicz Michael T.
Published: December 2011

In this article we consider the phenomenon of evaluative readiness, whereby the activation in memory of a goal leads to an unintentional increase in positivity toward stimuli that can facilitate the goal. We review four lines of work that together address the question of when goals lead to this kind of automatic shift in people’s attitudes. We then consider how contemporary models of cognition might explain this effect. We review whether dual systems models and single interacting system models can explain the phenomenon of evaluative readiness. Based on recent work in cognitive psychology and computational neuroscience, we then argue for the potential explanatory value of turning to a multiple interacting systems framework for explaining the phenomenon of evaluative readiness.
A Critical Look at Critical Community Psychology
Authors: Montero Maritza
Published: December 2011

This paper presents some questions directed to: (1) problematise researchers, practitioners and students, about ideas and practices in Community Psychology (CP), that are becoming naturalized as the perfect o the best models and processes; (2) allowing traditional practices to be sheltered under the name of critical, transforming, participatory and liberating CP. Critical questions about two types of issues are asked: Those related to horizon, limits, and theoretical scope of CP, and those related to the canonization of PC methods and techniques. The distinction between what is radical and what is critical is argued. Reflexive discussion in order to find how a theoretical or methodological conception introduces forms of oppression, or exclusion, as well as deconstruction of ways to ignore values and principles, even in the name of a transforming, liberating, participatory CP, is concluded.
Towards a Cultural–Clinical Psychology
Authors: Ryder Andrew G. , Ban Lauren M. , Chentsova‐Dutton Yulia E.
Published: December 2011

For decades, clinical psychologists have catalogued cultural group differences in symptom presentation, assessment, and treatment outcomes. We know that ‘culture matters’ in mental health – but do we know how it matters, or why? Answers may be found in an integration of cultural and clinical psychology. Cultural psychology demands a move beyond description to explanation of group variation. For its part, clinical psychology insists on the importance of individual people, while also extending the range of human variation. Cultural–clinical psychology integrates these approaches, opening up new lines of inquiry. The central assumption of this interdisciplinary field is that culture, mind, and brain constitute one another as a multi‐level dynamic system in which no level is primary, and that psychopathology is an emergent property of that system. We illustrate cultural–clinical psychology research using our work on depression in Chinese populations and conclude with a call for greater collaboration among researchers in this field.
Transitional Societies in Eastern Europe: Moving Beyond the Washington Consensus Paradigm in Transitology
Authors: Kokushkin Maksim
Published: December 2011

Post‐communist transitions are generally thought to be a part of the past. However, most students of those transitions now acknowledge that the processes of transition in the countries in Central and Eastern Europe and the Former Soviet Union are far from over. Instead of reaching a point where all countries converge towards normal capitalism, the experiences of the countries from the region are extremely diverse. This article surveys the literature on post‐communist transitions and argues that transitologists have experienced a shift from viewing transitions as mostly similar and converging to viewing transitions as uniquely complex and diverging. To advance this argument, the article: (i) systematizes the literature along methodological lines; (ii) uses a policy paradigm (namely, the Washington Consensus) as a metaphor to illustrate the tensions in the literature; and (iii) connects the shift away from one‐size‐fits‐all policies with the evolution in the literature from being formally prescriptive and abstract to being context‐sensitive and emphasizing complexity.
Oil revenues and macroeconomic volatility in Norway
Authors: Boye François
Published: December 2011

It is conventional wisdom that Norway is the role model for oil‐producing countries; its sensible policies and transparency in the management of its oil revenues have resulted in macroeconomic stability, which most oil producing countries from Africa and Latin America, hobbled by cycles of boom and bust or a Dutch disease, have always been denied.

This paper does not take this conventional wisdom for granted given that the Norwegian government's fiscal policy has remained aligned with the cycles of the international oil market. To test whether the Norwegian economy is stable, this paper considers whether the famous 2001 stabilisation policy reform, meant to spread the spending of oil revenues over time, has ushered in a period of lower volatility in Norway. Its results are negative: (i) volatility in Norway's macroeconomic variables has increased after 2001; (ii) that the behaviour of either the Central Bank or the macroeconomy has changed after 2001 is not robust to modelling techniques; and (iii) had it been fully implemented, the 2001 stabilisation policy package would have had destabilising effects. In other words, Norway's volatility is not as insignificant as expected.
What explains risk premiums in crude oil futures?*
Authors: Melolinna Marko
Published: December 2011

This paper studies the existence of risk premiums in crude oil futures prices with simple regression and Bayesian vector autoregressive models. It also studies the importance of three main risk premiums models in explaining and forecasting the risk premiums in practice. While the existence of the premiums and the validity of the models can be established at certain time points, it turns out that the choice of sample period has a considerable effect on the results. Hence, the risk premiums are highly time‐varying. The study also establishes a model, based on speculative positions in the futures markets, which has some predictive power for future oil spot prices.
Short wavelength light filtering by the natural human lens and IOLs – implications for entrainment of circadian rhythm
Authors: Brøndsted Adam Elias , Lundeman Jesper Holm , Kessel Line
Published: December 2011

Purpose:  Photoentrainment of circadian rhythm begins with the stimulation of melanopsin containing retinal ganglion cells that respond directly to blue light. With age, the human lens becomes a strong colour filter attenuating transmission of short wavelengths. The purpose of the study was to examine the effect the ageing human lens may have for the photoentrainment of circadian rhythm and to compare with intraocular implant lenses (IOLs) designed to block UV radiation, violet or blue light.

Methods:  The potential for photoentrainment of circadian rhythm was computed for 29 human donor lenses (18–76 years) and five IOLs (one UV, two violet and two blue light blocking) based on the transmission properties of the lenses and the spectral characteristics of melanopsin activation and two of it′s physiological outcomes; melanopsin‐driven pupillary light reponse and light‐induced melatonin suppression.

Results:  The potential for melanopsin stimulation and melatonin suppression was reduced by 0.6–0.7 percentage point per year of life because of yellowing of the natural lens. The computed effects were small for the IOLs and did not exceed that of a 22.2‐year‐old natural lens for the blue‐blocking IOLs.

Conclusion:  The results show that photoentrainment of circadian rhythm may be significantly impaired in older subjects because of the colour filtering characteristics of the human lens, whereas the effects were small for all three types of IOLs studied. Consequently, the ageing process of the natural lens is expected to influence the photoentrainment of circadian rhythm, whereas IOLs are not expected to be detrimental to circadian rhythm.
Do personality traits matter when choosing a group therapy for early psychosis?
Authors: Beauchamp Marie‐Chantal , Lecomte Tania , Lecomte Conrad , Leclerc Claude , Corbière Marc
Published: December 2011

Objectives. This study aimed at determining the predictive value of personality traits, based on the Five Factor Model (FFM) of personality, on therapeutic outcomes according to specific group treatments for first episode psychosis: cognitive‐behavioural therapy (CBT) or skills training for symptom management (SM).

Methods. Individuals experiencing early psychosis were recruited to participate in a randomized‐ controlled trial (RCT). Participants were randomized to one of two group treatments or to a wait‐list control group. Measures included a personality inventory (NEO‐FFI) and outcome measures of symptomatology (BPRS‐E) and coping strategies (CCS). Pearson correlation analyses were conducted on 78 individuals and linear regression analyses on 66.

Results. Links were found between personality traits, symptoms, and coping outcome measures, according to specific group treatments. Personality traits were particularly linked to therapeutic changes in active coping strategies, with Conscientiousness accounting for 14% of the variance in the CBT group, Extraversion accounting for 41% of the variance in the SM group, and Openness to experience accounting for 22% of the variance in the control group.

Conclusions. Individual differences in personality traits for people experiencing early psychosis should be considered when offering psychosocial treatments, since it appears that those with specific traits might benefit more than others in specific group interventions, particularly for interventions that do not solely aim at improving symptoms.
Survival of Host-Associated Bacteroidales Cells and Their Relationship with Enterococcus spp., Campylobacter jejuni, Salmonella enterica Serovar Typhimurium, and Adenovirus in Freshwater Microcosms as Measured by Propidium Monoazide-Quantitative PCR
Authors: Bae Sungwoo , Wuertz Stefan
Published: December 2011

The ideal host-associated genetic fecal marker would be capable of predicting the presence of specific pathogens of concern. Flowthrough freshwater microcosms containing mixed feces and inocula of the pathogens
Campylobacter jejuni
,
Salmonella enterica
serovar Typhimurium, and adenovirus were placed at ambient temperature in the presence and absence of diurnal sunlight. The total
Enterococcus
DNA increased during the early periods (23 h) under sunlight exposure, even though cultivable
Enterococcus
and DNA in intact cells, as measured by propidium monoazide (PMA), decreased with first-order kinetics during the entire period. We found a significant difference in the decay of host-associated
Bacteroidales
cells between sunlight exposure and dark conditions (
P
value < 0.05), whereas the persistence of host-associated
Bacteroidales
DNA was comparable. The 2-log reduction times of adenovirus were 72 h for sunlight exposure and 99 h for dark conditions with similar decay rate constants (
P
value = 0.13). The persistences of fecal
Bacteroidales
cells and
Campylobacter
cells exposed to sunlight were similar, and host-associated
Bacteroidales
DNA and waterborne pathogen DNA were degraded at comparable rates (
P
values > 0.05). Overall, the ratio of quantitative PCR (qPCR) cycle threshold (

C
T

) values with and without PMA treatment was indicative of the time elapsed since inoculation of the microcosm with (i) fecal material from different animal sources based on host-associated
Bacteroidales
and (ii) pure cultures of bacterial pathogens. The use of both PMA-qPCR and qPCR may yield more realistic information about recent sources of fecal contamination and result in improved prediction of waterborne pathogens and assessment of health risk.
Green Fluorescent Protein-Labeled Monitoring Tool To Quantify Conjugative Plasmid Transfer between Gram-Positive and Gram-Negative Bacteria
Authors: Arends Karsten , Schiwon Katarzyna , Sakinc Türkan , Hübner Johannes , Grohmann Elisabeth
Published: December 2011

On the basis of pIP501, a green fluorescent protein (GFP)-tagged monitoring tool was constructed for quantifying plasmid mobilization among Gram-positive bacteria and between Gram-positive
Enterococcus faecalis
and Gram-negative
Escherichia coli
. Furthermore, retromobilization of the GFP-tagged monitoring tool was shown from
E. faecalis
OG1X into the clinical isolate
E. faecalis
T9.
Transcriptome Dynamics of Pseudomonas putida KT2440 under Water Stress
Authors: Gülez Gamze , Dechesne Arnaud , Workman Christopher T. , Smets Barth F.
Published: December 2011

Water deprivation can be a major stressor to microbial life in surface and subsurface soil. In unsaturated soils, the matric potential (Ψm) is often the main component of the water potential, which measures the thermodynamic availability of water. A low matric potential usually translates into water forming thin liquid films in the soil pores. Little is known of how bacteria respond to such conditions, where, in addition to facing water deprivation that might impair their metabolism, they have to adapt their dispersal strategy as swimming motility may be compromised. Using the pressurized porous surface model (PPSM), which allows creation of thin liquid films by controlling Ψm, we examined the transcriptome dynamics ofPseudomonas putidaKT2440. We identified the differentially expressed genes in cells exposed to a mild matric stress (−0.4 MPa) for 4, 24, or 72 h. The major response was detected at 4 h before gradually disappearing. Upregulation of alginate genes was notable in this early response. Flagellar genes were not downregulated, and the microarray data even suggested increasing expression as the stress prolonged. Moreover, we tested the effect of polyethylene glycol 8000 (PEG 8000), a nonpermeating solute often used to simulate Ψm, on the gene expression profile and detected a different profile than that observed by directly imposing Ψm. This study is the first transcriptome profiling of KT2440 under directly controlled Ψmand also the first to show the difference in gene expression profiles between a PEG 8000-simulated and a directly controlled Ψm.
Surveillance Study of Hepatitis A Virus RNA on Fig and Date Samples
Authors: Boxman Ingeborg L. A. , te Loeke Nathalie A. J. M. , Klunder Kyara , Hägele Geke , Jansen Claudia C. C.
Published: December 2011

A total of 91 fig and 185 date samples were analyzed by reverse transcription (RT) real-time PCR for the presence of hepatitis A virus (HAV) RNA. Two batches of dates tested positive, and the HAV RNA detected was genotyped as IA. These findings warrant further development of methods applicable to food which is consumed untreated and is exported from countries in which HAV is endemic.
Bifidobacterium longum subsp. infantis ATCC 15697 α-Fucosidases Are Active on Fucosylated Human Milk Oligosaccharides
Authors: Sela David A. , Garrido Daniel , Lerno Larry , Wu Shuai , Tan Kemin , Eom Hyun-Ju , Joachimiak Andrzej , Lebrilla Carlito B. , Mills David A.
Published: December 2011

Bifidobacterium longum
subsp.
infantis
ATCC 15697 utilizes several small-mass neutral human milk oligosaccharides (HMOs), several of which are fucosylated. Whereas previous studies focused on endpoint consumption, a temporal glycan consumption profile revealed a time-dependent effect. Specifically, among preferred HMOs, tetraose was favored early in fermentation, with other oligosaccharides consumed slightly later. In order to utilize fucosylated oligosaccharides, ATCC 15697 possesses several fucosidases, implicating GH29 and GH95 α-
l
-fucosidases in a gene cluster dedicated to HMO metabolism. Evaluation of the biochemical kinetics demonstrated that ATCC 15697 expresses three fucosidases with a high turnover rate. Moreover, several ATCC 15697 fucosidases are active on the linkages inherent to the HMO molecule. Finally, the HMO cluster GH29 α-
l
-fucosidase possesses a crystal structure that is similar to previously characterized fucosidases.
Improvement of the Redox Balance Increasesl-Valine Production by Corynebacterium glutamicum under Oxygen Deprivation Conditions
Authors: Hasegawa Satoshi , Uematsu Kimio , Natsuma Yumi , Suda Masako , Hiraga Kazumi , Jojima Toru , Inui Masayuki , Yukawa Hideaki
Published: December 2011

Production ofl-valine under oxygen deprivation conditions byCorynebacterium glutamicumlacking the lactate dehydrogenase geneldhAand overexpressing thel-valine biosynthesis genesilvBNCDEwas repressed. This was attributed to imbalanced cofactor production and consumption in the overalll-valine synthesis pathway: two moles of NADH was generated and two moles of NADPH was consumed per mole ofl-valine produced from one mole of glucose. In order to solve this cofactor imbalance, the coenzyme requirement forl-valine synthesis was converted from NADPH to NADH via modification of acetohydroxy acid isomeroreductase encoded byilvCand introduction ofLysinibacillus sphaericusleucine dehydrogenase in place of endogenous transaminase B, encoded byilvE. The intracellular NADH/NAD+ratio significantly decreased, and glucose consumption andl-valine production drastically improved. Moreover,l-valine yield increased and succinate formation decreased concomitantly with the decreased intracellular redox state. These observations suggest that the intracellular NADH/NAD+ratio, i.e., reoxidation of NADH, is the primary rate-limiting factor forl-valine production under oxygen deprivation conditions. Thel-valine productivity and yield were even better and by-products derived from pyruvate further decreased as a result of a feedback resistance-inducing mutation in the acetohydroxy acid synthase encoded byilvBN. The resultant strain produced 1,470 mMl-valine after 24 h with a yield of 0.63 mol mol of glucose−1, and thel-valine productivity reached 1,940 mM after 48 h.
Hydrazine Synthase, a Unique Phylomarker with Which To Study the Presence and Biodiversity of Anammox Bacteria
Authors: Harhangi Harry R. , Le Roy Mathilde , van Alen Theo , Hu Bao-lan , Groen Joost , Kartal Boran , Tringe Susannah G. , Quan Zhe-Xue , Jetten Mike S. M. , Op den Camp Huub J. M.
Published: December 2011

Anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the biogeochemical cycling of nitrogen. They derive their energy for growth from the conversion of ammonium and nitrite into dinitrogen gas in the complete absence of oxygen. Several methods have been used to detect the presence and activity of anammox bacteria in the environment, including 16S rRNA gene-based approaches. The use of the 16S rRNA gene to study biodiversity has the disadvantage that it is not directly related to the physiology of the target organism and that current primers do not completely capture the anammox diversity. Here we report the development of PCR primer sets targeting a subunit of the hydrazine synthase (
hzsA
), which represents a unique phylogenetic marker for anammox bacteria. The tested primers were able to retrieve
hzsA
gene sequences from anammox enrichment cultures, full-scale anammox wastewater treatment systems, and a variety of freshwater and marine environmental samples, covering all known anammox genera.
False-Negative Rate and Recovery Efficiency Performance of a Validated Sponge Wipe Sampling Method
Authors: Krauter Paula A. , Piepel Greg F. , Boucher Raymond , Tezak Matt , Amidan Brett G. , Einfeld Wayne
Published: December 2011

Recovery of spores from environmental surfaces varies due to sampling and analysis methods, spore size and characteristics, surface materials, and environmental conditions. Tests were performed to evaluate a new, validated sponge wipe method using
Bacillus atrophaeus
spores. Testing evaluated the effects of spore concentration and surface material on recovery efficiency (RE), false-negative rate (FNR), limit of detection (LOD), and their uncertainties. Ceramic tile and stainless steel had the highest mean RE values (48.9 and 48.1%, respectively). Faux leather, vinyl tile, and painted wood had mean RE values of 30.3, 25.6, and 25.5, respectively, while plastic had the lowest mean RE (9.8%). Results show roughly linear dependences of RE and FNR on surface roughness, with smoother surfaces resulting in higher mean REs and lower FNRs. REs were not influenced by the low spore concentrations tested (3.10 × 10
−3
to 1.86 CFU/cm
2
). Stainless steel had the lowest mean FNR (0.123), and plastic had the highest mean FNR (0.479). The LOD
90
(≥1 CFU detected 90% of the time) varied with surface material, from 0.015 CFU/cm
2
on stainless steel up to 0.039 on plastic. It may be possible to improve sampling results by considering surface roughness in selecting sampling locations and interpreting spore recovery data. Further, FNR values (calculated as a function of concentration and surface material) can be used presampling to calculate the numbers of samples for statistical sampling plans with desired performance and postsampling to calculate the confidence in characterization and clearance decisions.
Distribution of Microbial Biomass and Potential for Anaerobic Respiration in Hanford Site 300 Area Subsurface Sediment
Authors: Lin Xueju , Kennedy David , Peacock Aaron , McKinley James , Resch Charles T. , Fredrickson James , Konopka Allan
Published: December 2011

Subsurface sediments were recovered from a 52-m-deep borehole cored in the 300 Area of the Hanford Site in southeastern Washington State to assess the potential for biogeochemical transformation of radionuclide contaminants. Microbial analyses were made on 17 sediment samples traversing multiple geological units: the oxic coarse-grained Hanford formation (9 to 17.4 m), the oxic fine-grained upper Ringold formation (17.7 to 18.1 m), and the reduced Ringold formation (18.3 to 52 m). Microbial biomass (measured as phospholipid fatty acids) ranged from 7 to 974 pmols per g in discrete samples, with the highest numbers found in the Hanford formation. On average, strata below 17.4 m had 13-fold less biomass than those from shallower strata. The
nosZ
gene that encodes nitrous oxide reductase (measured by quantitative real-time PCR) had an abundance of 5 to 17 relative to that of total 16S rRNA genes below 18.3 m and <5 above 18.1 m. Most
nosZ
sequences were affiliated with
Ochrobactrum anthropi
(97 sequence similarity) or had a nearest neighbor of
Achromobacter xylosoxidans
(90 similarity). Passive multilevel sampling of groundwater geochemistry demonstrated a redox gradient in the 1.5-m region between the Hanford-Ringold formation contact and the Ringold oxic-anoxic interface. Within this zone, copies of the
dsrA
gene and
Geobacteraceae
had the highest relative abundance. The majority of
dsrA
genes detected near the interface were related to
Desulfotomaculum
spp. These analyses indicate that the region just below the contact between the Hanford and Ringold formations is a zone of active biogeochemical redox cycling.
Protein Kinase A Contributes to the Negative Control of Snf1 Protein Kinase in Saccharomyces cerevisiae
Authors: Barrett LaKisha , Orlova Marianna , Maziarz Marcin , Kuchin Sergei
Published: December 2011

Snf1 protein kinase regulates responses to glucose limitation and other stresses. Snf1 activation requires phosphorylation of its T-loop threonine by partially redundant upstream kinases (Sak1, Tos3, and Elm1). Under favorable conditions, Snf1 is turned off by Reg1-Glc7 protein phosphatase. The
reg1
mutation causes increased Snf1 activation and slow growth. To identify new components of the Snf1 pathway, we searched for mutations that, like
snf1
, suppress
reg1
for the slow-growth phenotype. In addition to mutations in genes encoding known pathway components (
SNF1
,
SNF4
, and
SAK1
), we recovered “fast” mutations, designated
fst1
and
fst2
. Unusual morphology of the mutants in the Σ1278b strains employed here helped us identify
fst1
and
fst2
as mutations in the RasGAP genes
IRA1
and
IRA2
. Cells lacking Ira1, Ira2, or Bcy1, the negative regulatory subunit of cyclic AMP (cAMP)-dependent protein kinase A (PKA), exhibited reduced Snf1 pathway activation. Conversely, Snf1 activation was elevated in cells lacking the Gpr1 sugar receptor, which contributes to PKA signaling. We show that the Snf1-activating kinase Sak1 is phosphorylated
in vivo
on a conserved serine (Ser1074) within an ideal PKA motif. However, this phosphorylation alone appears to play only a modest role in regulation, and Sak1 is not the only relevant target of the PKA pathway. Collectively, our results suggest that PKA, which integrates multiple regulatory inputs, could contribute to Snf1 regulation under various conditions via a complex mechanism. Our results also support the view that, like its mammalian counterpart, AMP-activated protein kinase (AMPK), yeast Snf1 participates in metabolic checkpoint control that coordinates growth with nutrient availability.
SWP5, a Spore Wall Protein, Interacts with Polar Tube Proteins in the Parasitic Microsporidian Nosema bombycis
Authors: Li Zhi , Pan Guoqing , Li Tian , Huang Wei , Chen Jie , Geng Lina , Yang Donglin , Wang Linling , Zhou Zeyang
Published: December 2011

Microsporidia are a group of eukaryotic intracellular parasites that infect almost all vertebrates and invertebrates. The microsporidian invasion process involves the extrusion of a unique polar tube into host cells. Both the spore wall and the polar tube play an important role in microsporidian pathogenesis. So far, five spore wall proteins (SWP1, SWP2, Enp1, Enp2, and EcCDA) from
Encephalitozoon intestinalis
and
Encephalitozoon cuniculi
and five spore wall proteins (SWP32, SWP30, SWP26, SWP25, and NbSWP5) from the silkworm pathogen
Nosema bombycis
have been identified. Here we report the identification and characterization of a spore wall protein (SWP5) with a molecular mass of 20.3 kDa in
N. bombycis
. This protein has low sequence similarity to other eukaryotic proteins. Immunolocalization analysis showed SWP5 localized to the exospore and the region of the polar tube in mature spores. Immunoprecipitation, mass spectrometry, and immunofluorescence analyses revealed that SWP5 interacts with the polar tube proteins PTP2 and PTP3. Anti-SWP5 serum pretreatment of mature spores significantly decreased their polar tube extrusion rate. Taken together, our results show that SWP5 is a spore wall protein localized to the spore wall and that it interacts with the polar tube, may play an important role in supporting the structural integrity of the spore wall, and potentially modulates the course of infection of
N. bombycis
.
The Polo-Like Kinase PLKA in Aspergillus nidulans Is Not Essential but Plays Important Roles during Vegetative Growth and Development
Authors: Mogilevsky Klarita , Glory Amandeep , Bachewich Catherine
Published: December 2011

The Polo-like kinases (Plks) are conserved, multifunctional cell cycle regulators that are induced in many forms of cancer and play additional roles in metazoan development. We previously identified
plkA
in
Aspergillus nidulans
, the only Plk investigated in filamentous fungi to date, and partially characterized its function through overexpression. Here, we report the
plkA
null phenotype. Surprisingly,
plkA
was not essential, unlike Plks in other organisms that contain a single homologue. A subset of cells lacking PLKA contained defects in spindle formation and chromosome organization, supporting some conservation in cell cycle function. However, septa were present, suggesting that PLKA, unlike other Plks, is not a central regulator of septation. Colonies lacking PLKA were compact with multibranched hyphae, implying a role for this factor in aspects of hyphal morphogenesis. These defects were suppressed by high temperature or low concentrations of benomyl, suggesting that PLKA may function during vegetative growth by influencing microtubule dynamics. However, the colonies also showed reduced conidiation and precocious formation of sexual Hülle cells in a benomyl- and temperature-insensitive manner. This result suggests that PLKA may influence reproduction through distinct mechanisms and represents the first example of a link between Plk function and development in fungi. Finally, filamentous fungal Plks have distinct features, and phylogenetic analyses reveal that they may group more closely with metazoan PLK4. In contrast, yeast Plks are more similar to metazoan proteins PLK1 to PLK3. Thus,
A. nidulans
PLKA shows some conservation in cell cycle function but may also play novel roles during hyphal morphogenesis and development.
A Machine Learning Approach To Identify Hydrogenosomal Proteins in Trichomonas vaginalis
Authors: Burstein David , Gould Sven B. , Zimorski Verena , Kloesges Thorsten , Kiosse Fuat , Major Peter , Martin William F. , Pupko Tal , Dagan Tal
Published: December 2011

The protozoan parasite
Trichomonas vaginalis
is the causative agent of trichomoniasis, the most widespread nonviral sexually transmitted disease in humans. It possesses hydrogenosomes—anaerobic mitochondria that generate H
2
, CO
2
, and acetate from pyruvate while converting ADP to ATP via substrate-level phosphorylation.
T. vaginalis
hydrogenosomes lack a genome and translation machinery; hence, they import all their proteins from the cytosol. To date, however, only 30 imported proteins have been shown to localize to the organelle. A total of 226 nuclear-encoded proteins inferred from the genome sequence harbor a characteristic short N-terminal presequence, reminiscent of mitochondrial targeting peptides, which is thought to mediate hydrogenosomal targeting. Recent studies suggest, however, that the presequences might be less important than previously thought. We sought to identify new hydrogenosomal proteins within the 59,672 annotated open reading frames (ORFs) of
T. vaginalis
, independent of the N-terminal targeting signal, using a machine learning approach. Our training set included 57 gene and protein features determined for all 30 known hydrogenosomal proteins and 576 nonhydrogenosomal proteins. Several classifiers were trained on this set to yield an import score for all proteins encoded by
T. vaginalis
ORFs, predicting the likelihood of hydrogenosomal localization. The machine learning results were tested through immunofluorescence assay and immunodetection in isolated cell fractions of 14 protein predictions using hemagglutinin constructs expressed under the homologous SCSα promoter in transiently transformed
T. vaginalis
cells. Localization of 6 of the 10 top predicted hydrogenosome-localized proteins was confirmed, and two of these were found to lack an obvious N-terminal targeting signal.
Adaptation of Cryptococcus neoformans to Mammalian Hosts: Integrated Regulation of Metabolism and Virulence
Authors: Kronstad Jim , Saikia Sanjay , Nielson Erik David , Kretschmer Matthias , Jung Wonhee , Hu Guanggan , Geddes Jennifer M. H. , Griffiths Emma J. , Choi Jaehyuk , Cadieux Brigitte , Caza Mélissa , Attarian Rodgoun
Published: December 2011

The basidiomycete fungus
Cryptococcus neoformans
infects humans via inhalation of desiccated yeast cells or spores from the environment. In the absence of effective immune containment, the initial pulmonary infection often spreads to the central nervous system to result in meningoencephalitis. The fungus must therefore make the transition from the environment to different mammalian niches that include the intracellular locale of phagocytic cells and extracellular sites in the lung, bloodstream, and central nervous system. Recent studies provide insights into mechanisms of adaptation during this transition that include the expression of antiphagocytic functions, the remodeling of central carbon metabolism, the expression of specific nutrient acquisition systems, and the response to hypoxia. Specific transcription factors regulate these functions as well as the expression of one or more of the major known virulence factors of
C. neoformans
. Therefore, virulence factor expression is to a large extent embedded in the regulation of a variety of functions needed for growth in mammalian hosts. In this regard, the complex integration of these processes is reminiscent of the master regulators of virulence in bacterial pathogens.
Lag Phase Is a Distinct Growth Phase That Prepares Bacteria for Exponential Growth and Involves Transient Metal Accumulation
Authors: Rolfe Matthew D. , Rice Christopher J. , Lucchini Sacha , Pin Carmen , Thompson Arthur , Cameron Andrew D. S. , Alston Mark , Stringer Michael F. , Betts Roy P. , Baranyi József , Peck Michael W. , Hinton Jay C. D.
Published: December 2011

Lag phase represents the earliest and most poorly understood stage of the bacterial growth cycle. We developed a reproducible experimental system and conducted functional genomic and physiological analyses of a 2-h lag phase in
Salmonella enterica
serovar Typhimurium. Adaptation began within 4 min of inoculation into fresh LB medium with the transient expression of genes involved in phosphate uptake. The main lag-phase transcriptional program initiated at 20 min with the upregulation of 945 genes encoding processes such as transcription, translation, iron-sulfur protein assembly, nucleotide metabolism, LPS biosynthesis, and aerobic respiration. ChIP-chip revealed that RNA polymerase was not “poised” upstream of the bacterial genes that are rapidly induced at the beginning of lag phase, suggesting a mechanism that involves
de novo
partitioning of RNA polymerase to transcribe 522 bacterial genes within 4 min of leaving stationary phase. We used inductively coupled plasma mass spectrometry (ICP-MS) to discover that iron, calcium, and manganese are accumulated by
S
. Typhimurium during lag phase, while levels of cobalt, nickel, and sodium showed distinct growth-phase-specific patterns. The high concentration of iron during lag phase was associated with transient sensitivity to oxidative stress. The study of lag phase promises to identify the physiological and regulatory processes responsible for adaptation to new environments.
The Sulfur Oxygenase Reductase from the Mesophilic Bacterium Halothiobacillus neapolitanus Is a Highly Active Thermozyme
Authors: Veith Andreas , Botelho Hugo M. , Kindinger Florian , Gomes Cláudio M. , Kletzin Arnulf
Published: December 2011

A biochemical, biophysical, and phylogenetic study of the sulfur oxygenase reductase (SOR) from the mesophilic gammaproteobacterium
Halothiobacillus neapolitanus
(
Hn
SOR) was performed in order to determine the structural and biochemical properties of the enzyme. SOR proteins from 14 predominantly chemolithoautotrophic bacterial and archaeal species are currently available in public databases. Sequence alignment and phylogenetic analysis showed that they form a coherent protein family. The
Hn
SOR purified from
Escherichia coli
after heterologous gene expression had a temperature range of activity of 10 to 99°C with an optimum at 80°C (42 U/mg protein). Sulfite, thiosulfate, and hydrogen sulfide were formed at various stoichiometries in a range between pH 5.4 and 11 (optimum pH 8.4). Circular dichroism (CD) spectroscopy and dynamic light scattering showed that the
Hn
SOR adopts secondary and quaternary structures similar to those of the 24-subunit enzyme from the hyperthermophile
Acidianus ambivalens
(
Aa
SOR). The melting point of the
Hn
SOR was ≈20°C lower than that of the
Aa
SOR, when analyzed with CD-monitored thermal unfolding. Homology modeling showed that the secondary structure elements of single subunits are conserved. Subtle changes in the pores of the outer shell and increased flexibility might contribute to activity at low temperature. We concluded that the thermostability was the result of a rigid protein core together with the stabilizing effect of the 24-subunit hollow sphere.
Twenty-year review of quantitative transmission electron microscopy for the diagnosis of primary ciliary dyskinesia
Authors: Shoemark A , Dixon M , Corrin B , Dewar A
Published: December 2011

Background

The examination of ciliary ultrastructure in a nasal sample remains a definitive diagnostic test for primary ciliary dyskinesia (PCD).

Methods

The quantitative assessment of ciliary ultrastructure in the diagnosis of PCD over a 20-year period was reviewed.

Results

During this period, 1182 patients were referred for ciliary ultrastructural analysis, 242 (20%) of whom were confirmed as having the disease. The two main causes of PCD identified were a lack of outer dynein arms (43%) and a lack of both inner and outer dynein arms (24%). Other causes included transposition, radial spoke and inner dynein arm defects. No specific ultrastructural defects were detected in 33 patients (3%) diagnosed as having PCD on the basis of their clinical features and screening tests that included a low nasal nitric oxide concentration or slow saccharine clearance and abnormal ciliary beat frequency or pattern.

Conclusions

Electron microscopy analysis can confirm but does not always exclude a diagnosis of PCD.
Expression of p53, p21 and cyclin D1 in penile cancer: p53 predicts poor prognosis
Authors: Gunia Sven , Kakies Christoph , Erbersdobler Andreas , Hakenberg Oliver W , Koch Stefan , May Matthias
Published: December 2011

Aims

To evaluate the role of p53, p21 and cyclin D1 expression in patients with penile cancer (PC).

Methods

Paraffin-embedded tissues from PC specimens from six pathology departments were subjected to a central histopathological review performed by one pathologist. The tissue microarray technique was used for immunostaining which was evaluated by two independent pathologists and correlated with cancer-specific survival (CSS). κ-statistics were used to assess interobserver variability. Uni- and multivariable Cox proportional hazards analysis was applied to assess the independent effects of several prognostic factors on CSS over a median of 32 months (IQR 6–66 months).

Results

Specimens and clinical data from 110 men treated surgically for primary PC were collected. p53 staining was positive in 30 and negative in 62 specimens. κ-statistics showed substantial interobserver reproducibility of p53 staining evaluation (κ=0.73; p<0.001). The 5-year CSS rate for the entire study cohort was 74%. Five-year CSS was 84% in p53-negative and 51% in p53-positive PC patients (p=0.003). Multivariable analysis showed p53 (HR=3.20; p=0.041) and pT-stage (HR=4.29; p<0.001) as independent significant prognostic factors for CSS. Cyclin D1 and p21 expression were not correlated with survival. However, incorporating p21 into a multivariable Cox model did contribute to improved model quality for predicting CSS.

Conclusions

In patients with PC, the expression of p53 in the primary tumour specimen can be reproducibly assessed and is negatively associated with cancer specific survival.