bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical predictors of autoimmune and severe atopic disease in pediatric heart transplant recipients
Authors: Mouledoux Jessica H. , Albers Erin L. , Lu Zengqi , Saville Benjamin R. , Moore Daniel J. , Dodd Debra A.
Published: December 2013

Autoimmune and allergic diseases cause morbidity and diminished quality of life in pediatric organ transplant recipients. We hypothesize that younger age at transplantation and immunosuppression regimen play a role in the development of immune‐mediated disease following heart transplant. A single institution retrospective review identified all patients undergoing heart transplant at ≤18 yr of age from 1987 to 2010 who survived ≥1 yr. Using medical record and database review, patients were evaluated for development of autoimmune or severe allergic disease. Of 129 patients who met criteria, seven patients (5.4%) with autoimmune or severe atopic disease were identified. Immune‐mediated diseases included inflammatory bowel disease (n = 3), eosinophilic esophagitis/colitis (n = 4), and chronic bullous disease of childhood (n = 1). Patients <1 yr of age at transplant were at greater risk of developing autoimmune disease than patients 1–18 yr at transplant (OR = 9.3, 95% CI 1.1–79.2, p = 0.02). All affected patients underwent thymectomy at <1 yr of age (7/71 vs. 0/58, p = 0.02). In our experience, heart transplantation in infancy is associated with the development of immune‐mediated gastrointestinal and dermatologic diseases. Further study is needed to determine risk factors for the development of immune‐mediated disease to identify best practices to decrease incidence.
Ureteral complications after renal transplant in children: Timing of presentation, and their open and endoscopic management
Authors: Castagnetti Marco , Angelini Lorenzo , Ghirardo Giulia , Zucchetta Pietro , Gamba PierGiorgio , Zanon GiovanniFranco , Murer Luisa , Rigamonti Waifro
Published: December 2013

We retrospectively reviewed the records of 24 consecutive patients undergoing treatment for ureteral complications after RTx in the period 2001–2012 to determine the timing of presentation of the complications, and their open or endoscopic management. Three patients (12%) had a necrosis of the transplanted ureter soon after RTx. All required open urinary diversion in a native ureter. Ten cases (42%) developed ureteral obstruction. Time of presentation was variable mainly in relation to the underlying cause. Endoscopic treatment was successful in two cases with urinary stones and open surgery in two with mid‐ureteral obstruction. Six patients had VUJ stenosis, three underwent open reimplantation, whereas temporary double‐J stent placement was successfully performed in the remainder. Eleven patients (46%) had VUR. It seldom presented in the first year after RTx. Endoscopic treatment was attempted in all and was successful in all the six cases without vs. only one of the five with lower urinary tract pathology (p = 0.01). Endoscopic treatment is an option in patients with VUR in the absence of lower urinary tract pathology. It is an option also for the treatment of stones and can be attempted in case of VUJ stenosis. Ureteral necrosis always requires open treatment.
Is single‐port laparoscopy feasible after liver transplant?
Authors: Zani Augusto , Paul Anu , Dhawan Anil , Desai Ashish
Published: December 2013

The role of laparoscopy following liver transplant in children is debated. Herein, we report the first two cases of SIPES post‐liver transplant. In both patients, SIPES access was carried out using Olympus TriPort. Patient 1 was an 11 yr old born with biliary atresia, who had four previous major laparotomies: Kasai portoenterostomy, followed by liver transplant and two laparotomies for lymph node biopsies for PTLD. The child was referred for suspected PTLD relapse due to enlarged nodes on CT scan. At SIPES, following adequate adhesiolysis, the lymph node biopsy was achieved successfully. Patient 2 was a five yr old with bilateral intra‐abdominal testes who had undergone liver transplant aged two yr. He underwent a left one‐stage orchidopexy and right first‐stage Fowler–Stephen procedure at five yr of life, followed by a second stage Fowler–Stephen surgery on the right side, nine months later. All procedures were successfully performed by SIPES, and both patients were discharged home on first post‐operative day. We conclude that SIPES could be safely carried out in patients who have had liver transplant. In case of diffuse intraperitoneal adhesions, SIPES is beneficial to create space by blunt and sharp dissection and decreases post‐operative stay.
Evidence of imbalanced adaptation between muscle and tendon in adolescent athletes
Authors: Mersmann F. , Bohm S. , Schroll A. , Boeth H. , Duda G. , Arampatzis A.
Published: December 2013

Adolescence may be regarded as a critical phase of tissue plasticity in young growing athletes, as the adaptation process of muscle‐tendon unit is affected by both environmental mechanical stimuli and maturation. The present study investigated potential imbalances of knee extensor muscle strength and patellar tendon properties in adolescent compared with middle‐aged athletes featuring long‐term musculotendinous adaptations. Nineteen adolescent elite volleyball athletes [(A), 15.9 ± 0.6 years] and 18 middle‐aged competitively active former elite volleyball athletes [(MA), 46.9 ± 0.6 years] participated in magnetic resonance imaging and ultrasound‐dynamometry sessions to determine quadriceps femoris muscle strength, vastus lateralis morphology and patellar tendon mechanical and morphological properties. There was no significant age effect on the physiological cross‐sectional area of the vastus lateralis and maximum knee extension moment (P > 0.05) during voluntary isometric contractions. However, the patellar tendon cross‐sectional area was significantly smaller (A: 107.4 ± 27.5 mm2; MA: 121.7 ± 39.8 mm2) and the tendon stress during the maximal contractions was significantly higher in adolescent compared with the middle‐aged athletes (A: 50.0 ± 10.1 MPa; MA: 40.0 ± 9.5 MPa). These findings provide evidence of an imbalanced development of muscle strength and tendon mechanical and morphological properties in adolescent athletes, which may have implications for the risk of tendon overuse injuries.
Parenting Mediates the Effects of Income and Cumulative Risk on the Development of Effortful Control
Authors: Lengua Liliana J. , Kiff Cara , Moran Lyndsey , Zalewski Maureen , Thompson Stephanie , Cortes Rebecca , Ruberry Erika
Published: December 2013

This study tested the hypothesis that the effects of income and cumulative risk on the development of effortful control during preschool would be mediated by parenting. The study utilized a community sample of 306 children (36–40 months) representing the full range of family income, with 29 percent at or near poverty and 28 percent lower income. Two dimensions of effortful control (executive control and delay ability) were assessed at four time points, each separated by nine months, and growth trajectories were examined. Maternal warmth, negativity, limit setting, scaffolding, and responsiveness were observed. Above the effects of child cognitive ability, income, and cumulative risk, scaffolding predicted higher initial levels of executive control that remained higher across the study, and limit setting predicted greater gains in executive control. Parenting did not predict changes in delay ability. Significant indirect effects indicated that scaffolding mediated the effects of income and cumulative risk on growth in executive control. The findings suggest that parenting behaviors can promote effortful control in young children and could be targets of prevention programs in low‐income families.
HLA‐B*27:05:25 – a further HLA‐B*27:05 allele with a synonymous nucleotide substitution
Authors: Street J. , Bengtsson M. , Johnson J. , Harvey C. , Darke C.
Published: December 2013

HLA‐B*27:05:25 differs from B*27:05:02 by a single synonymous nucleotide substitution (192C>T) at codon 40 in exon 2.
Subsidy‐induced Dumping
Authors: Hansen Jørgen D. , Nielsen Jørgen U.‐M.
Published: December 2013

More than two‐thirds of all anti‐subsidy investigations in the EU are paired with an anti‐dumping investigation against the same non‐EU producers. The outcome may be a two‐component duty where one duty addresses the ‘unfairness’ of the subsidy and the other the dumping behaviour. The philosophy behind this practice is that, at least to some extent, the observed dumping has been induced by the subsidy, and as the GATT Treaty, Article VI commits the claimant not to impose double remedies for the same ‘misbehaviour’, it is necessary to make an assessment of the hypothetical dumping without the subsidy. The EU quantification of the hypothetical dumping margin assumes that an export subsidy translates fully to the dumping margin, while a domestic subsidy leaves the dumping margin unchanged. Using an oligopoly model, we show in this paper that in case of an export subsidy, the EU anti‐dumping duty is lower than the predicted hypothetical dumping margin from the oligopoly model. For a domestic subsidy, the results are ambiguous, and the difference between the size of the duty following the EU procedure and the model predictions is relatively small.
Cutaneous pythiosis in two dogs from Wisconsin, USA
Authors: Oldenhoff William , Grooters Amy , Pinkerton Marie E. , Knorr Jennifer , Trepanier Lauren
Published: December 2013

Background

Pythium insidiosum is an oomycete that causes cutaneous lesions or infiltrative gastrointestinal disease in dogs, cats, humans, horses and other mammals, primarily in tropical and subtropical climates.

Hypothesis/Objectives

We report the clinicopathological findings associated with cutaneous pythiosis in two dogs from a Northern temperate climate zone.

Animals

A 3‐year‐old intact male Chesapeake Bay retriever was presented with an ulcerated soft‐tissue swelling over the left eye. A 4‐year‐old spayed female German shepherd dog was presented with a soft‐tissue swelling overlying the right hock. Both dogs lived in northern latitudes (between 43 and 45°N) and neither had travelled outside of Wisconsin or Michigan's upper peninsula, USA.

Methods

Histopathological examination and culture of affected tissues on specialized media, serology for anti‐P. insidiosum antibodies, P. insidiosum‐specific PCR and ribosomal RNA gene sequencing were carried out.

Results

Histopathological examination revealed pyogranulomatous and eosinophilic inflammation associated with wide, poorly septate hyphae.

Conclusions and clinical importance

Even clinicians who practice in temperate climates should consider pythiosis as a differential diagnosis for young to middle‐aged adult dogs presented with ulcerated cutaneous nodules or infiltrative gastrointestinal disease.
Use of Quantitative Real-Time PCR for Direct Detection of Serratia marcescens in Marine and Other Aquatic Environments
Authors: Joyner Jessica , Wanless David , Sinigalliano Christopher D. , Lipp Erin K.
Published: December 2013

Serratia marcescens
is the etiological agent of acroporid serratiosis, a distinct form of white pox disease in the threatened coral
Acropora palmata
. The pathogen is commonly found in untreated human waste in the Florida Keys, which may contaminate both nearshore and offshore waters. Currently there is no direct method for detection of this bacterium in the aquatic or reef environment, and culture-based techniques may underestimate its abundance in marine waters. A quantitative real-time PCR assay was developed to detect
S. marcescens
directly from environmental samples, including marine water, coral mucus, sponge tissue, and wastewater. The assay targeted the
luxS
gene and was able to distinguish
S. marcescens
from other
Serratia
species with a reliable quantitative limit of detection of 10 cell equivalents (CE) per reaction. The method could routinely discern the presence of
S. marcescens
for as few as 3 CE per reaction, but it could not be reliably quantified at this level. The assay detected environmental
S. marcescens
in complex sewage influent samples at up to 761 CE ml
−1
and in septic system-impacted residential canals in the Florida Keys at up to 4.1 CE ml
−1
. This detection assay provided rapid quantitative abilities and good sensitivity and specificity, which should offer an important tool for monitoring this ubiquitous pathogen that can potentially impact both human health and coral health.
Highly Sensitive Quantitative PCR for the Detection and Differentiation of Pseudogymnoascus destructans and Other Pseudogymnoascus Species
Authors: Shuey Megan M. , Drees Kevin P. , Lindner Daniel L. , Keim Paul , Foster Jeffrey T.
Published: December 2013

White-nose syndrome is a fungal disease that has decimated bat populations across eastern North America. Identification of the etiologic agent,
Pseudogymnoascus destructans
(formerly
Geomyces destructans
), in environmental samples is essential to proposed management plans. A major challenge is the presence of closely related species, which are ubiquitous in many soils and cave sediments and often present in high abundance. We present a dual-probe real-time quantitative PCR assay capable of detecting and differentiating
P. destructans
from closely related fungi in environmental samples from North America. The assay, based on a single nucleotide polymorphism (SNP) specific to
P. destructans
, is capable of rapid low-level detection from various sampling media, including sediment, fecal samples, wing biopsy specimens, and skin swabs. This method is a highly sensitive, high-throughput method for identifying
P. destructans
, other
Pseudogymnoascus
spp., and
Geomyces
spp. in the environment, providing a fundamental component of research and risk assessment for addressing this disease, as well as other ecological and mycological work on related fungi.
Prevalence of Virulence Genes Associated with Pathogenic Escherichia coli Strains Isolated from Domestically Harvested Rainwater during Low- and High-Rainfall Periods
Authors: Dobrowsky P. H. , van Deventer A. , De Kwaadsteniet M. , Ndlovu T. , Khan S. , Cloete T. E. , Khan W.
Published: December 2013

The possible health risks associated with the consumption of harvested rainwater remains one of the major obstacles hampering its large-scale implementation in water limited countries such as South Africa. Rainwater tank samples collected on eight occasions during the low- and high-rainfall periods (March to August 2012) in Kleinmond, South Africa, were monitored for the presence of virulence genes associated with
Escherichia coli
. The identity of presumptive
E. coli
isolates in rainwater samples collected from 10 domestic rainwater harvesting (DRWH) tanks throughout the sampling period was confirmed through universal 16S rRNA PCR with subsequent sequencing and phylogenetic analysis. Species-specific primers were also used to routinely screen for the virulent genes,
aggR
,
stx
,
eae
, and
ipaH
found in enteroaggregative
E. coli
(EAEC), enterohemorrhagic
E. coli
(EHEC), enteropathogenic
E. coli
(EPEC), and enteroinvasive
E. coli
, respectively, in the rainwater samples. Of the 92
E. coli
strains isolated from the rainwater using culture based techniques, 6% were presumptively positively identified as
E. coli
O157:H7 using 16S rRNA. Furthermore, virulent pathogenic
E. coli
genes were detected in 3% (EPEC and EHEC) and 16% (EAEC) of the 80 rainwater samples collected during the sampling period from the 10 DRWH tanks. This study thus contributes valuable information to the limited data available regarding the ongoing prevalence of virulent pathotypes of
E. coli
in harvested rainwater during a longitudinal study in a high-population-density, periurban setting.
Culture Volume and Vessel Affect Long-Term Survival, Mutation Frequency, and Oxidative Stress of Escherichia coli
Authors: Kram Karin E. , Finkel Steven E.
Published: December 2013

Bacteria such as
Escherichia coli
are frequently studied during exponential- and stationary-phase growth. However, many strains can survive in long-term stationary phase (LTSP), without the addition of nutrients, from days to several years. During LTSP, cells experience a variety of stressors, including reactive oxidative species, nutrient depletion, and metabolic toxin buildup, that lead to physiological responses and changes in genetic stability. In this study, we monitored survival during LTSP, as well as reporters of genetic and physiological change, to determine how the physical environment affects
E. coli
during long-term batch culture. We demonstrate differences in yield during LTSP in cells incubated in LB medium in test tubes versus Erlenmeyer flasks, as well as growth in different volumes of medium. We determined that these differences are only partially due to differences in oxygen levels by incubating the cells in different volumes of media under anaerobic conditions. Since we hypothesized that differences in long-term survival are the result of changes in physiological outputs during the late log and early stationary phases, we monitored alkalization, mutation frequency, oxidative stress response, and glycation. Although initial cell yields are essentially equivalent under each condition tested, physiological responses vary greatly in response to culture environment. Incubation in lower-volume cultures leads to higher
oxyR
expression but lower mutation frequency and glycation levels, whereas incubation in high-volume cultures has the opposite effect. We show here that even under commonly used experimental conditions that are frequently treated as equivalent, the stresses experienced by cells can differ greatly, suggesting that culture vessel and incubation conditions should be carefully considered in the planning or analysis of experiments.
Production of Lycopene in the Non-Carotenoid-Producing Yeast Yarrowia lipolytica
Authors: Matthäus Falk , Ketelhot Markus , Gatter Michael , Barth Gerold
Published: December 2013

The codon-optimized genes
crtB
and
crtI
of
Pantoea ananatis
were expressed in
Yarrowia lipolytica
under the control of the
TEF1
promoter of
Y. lipolytica
. Additionally, the rate-limiting genes for isoprenoid biosynthesis in
Y. lipolytica
,
GGS1
and
HMG1
, were overexpressed to increase the production of lycopene. All of the genes were also expressed in a
Y. lipolytica
strain with
POX1
to
POX6
and
GUT2
deleted, which led to an increase in the size of lipid bodies and a further increase in lycopene production. Lycopene is located mainly within lipid bodies, and increased lipid body formation leads to an increase in the lycopene storage capacity of
Y. lipolytica
. Growth-limiting conditions increase the specific lycopene content. Finally, a yield of 16 mg g
−1
(dry cell weight) was reached in fed-batch cultures, which is the highest value reported so far for a eukaryotic host.
The Sialidases of Clostridium perfringens Type D Strain CN3718 Differ in Their Properties and Sensitivities to Inhibitors
Authors: Li Jihong , McClane Bruce A.
Published: December 2013

Clostridium perfringens
causes histotoxic infections and diseases originating in animal or human intestines. A prolific toxin producer, this bacterium also produces numerous enzymes, including sialidases, that may facilitate infection.
C. perfringens
type D strain CN3718 carries genes encoding three sialidases, including two large secreted sialidases (named NanI and NanJ) and one small sialidase (named NanH) that has an intracellular location in log-phase cultures but is present in supernatants of death phase cultures. Using isogenic mutants of CN3718 that are capable of expressing only NanJ, NanI, or NanH, the current study characterized the properties and activities of each sialidase. The optimal temperature determined for NanJ or NanH enzymatic activity was 37°C or 43°C, respectively, while NanI activity increased until temperature reached 48°C. NanI activity was also the most resistant against higher temperatures. All three sialidases showed optimal activities at pH 5.5. Compared to NanJ or NanH, NanI contributed most to the sialidase activity in CN3718 culture supernatants, regardless of the substrate sialic acid linkage; NanI also released the most sialic acid from Caco-2 cells. Only NanI activity was enhanced by trypsin pretreatment and then only for substrates with an α-2,3- or α-2,6-sialic acid linkage. NanJ and NanI activities were more sensitive than NanH activity to two sialidase inhibitors (N-acetyl-2,3-dehydro-2-deoxyneuraminic acid and siastatin B). The activities of the three sialidases were affected differently by several metal ions. These results indicated that each
C. perfringens
sialidase has distinct properties, which may allow these enzymes to play different roles depending upon environmental conditions.
Infection Dynamics of the Tick-Borne Pathogen “Candidatus Neoehrlichia mikurensis” and Coinfections with Borrelia afzelii in Bank Voles in Southern Sweden
Authors: Andersson Martin , Scherman Kristin , Råberg Lars
Published: December 2013

The tick-borne bacterium “
Candidatus
Neoehrlichia mikurensis” has recently been recognized as a human pathogen. Together with
Borrelia afzelii
, it is one of the most common pathogens found in the tick
Ixodes ricinus
. Here, we compared the epidemiologies of “
Ca
. Neoehrlichia mikurensis” and
B. afzelii
by longitudinal sampling from May to September in one of their most abundant vertebrate hosts, the bank vole (
Myodes glareolus
), using real-time PCR for detection and quantification. The prevalences of “
Ca
. Neoehrlichia mikurensis” and
B. afzelii
were determined to be 19% (50/261) and 22% (56/261), respectively. The prevalence of “
Ca
. Neoehrlichia mikurensis” increased significantly during the sampling season. The clearance rate of “
Ca
. Neoehrlichia mikurensis” was significantly higher than that of
B. afzelii
. We found a high frequency of double infections; 46% of all samples infected with “
Ca
. Neoehrlichia mikurensis” also had a coinfection with
B. afzelii
. The frequency of coinfections was significantly higher than expected from the prevalence of each pathogen. The high level of coinfections can be caused by interactions between the pathogens or might reflect variation in general susceptibility among voles.
Nanoscale Structural and Mechanical Analysis of Bacillus anthracis Spores Inactivated with Rapid Dry Heating
Authors: Xing Yun , Li Alex , Felker Daniel L. , Burggraf Larry W.
Published: December 2013

Effective killing of
Bacillus anthracis
spores is of paramount importance to antibioterrorism, food safety, environmental protection, and the medical device industry. Thus, a deeper understanding of the mechanisms of spore resistance and inactivation is highly desired for developing new strategies or improving the known methods for spore destruction. Previous studies have shown that spore inactivation mechanisms differ considerably depending upon the killing agents, such as heat (wet heat, dry heat), UV, ionizing radiation, and chemicals. It is believed that wet heat kills spores by inactivating critical enzymes, while dry heat kills spores by damaging their DNA. Many studies have focused on the biochemical aspects of spore inactivation by dry heat; few have investigated structural damages and changes in spore mechanical properties. In this study, we have inactivated
Bacillus anthracis
spores with rapid dry heating and performed nanoscale topographical and mechanical analysis of inactivated spores using atomic force microscopy (AFM). Our results revealed significant changes in spore morphology and nanomechanical properties after heat inactivation. In addition, we also found that these changes were different under different heating conditions that produced similar inactivation probabilities (high temperature for short exposure time versus low temperature for long exposure time). We attributed the differences to the differential thermal and mechanical stresses in the spore. The buildup of internal thermal and mechanical stresses may become prominent only in ultrafast, high-temperature heat inactivation when the experimental timescale is too short for heat-generated vapor to efficiently escape from the spore. Our results thus provide direct, visual evidences of the importance of thermal stresses and heat and mass transfer to spore inactivation by very rapid dry heating.
Zebrafish as a Natural Host Model for Vibrio cholerae Colonization and Transmission
Authors: Runft Donna L. , Mitchell Kristie C. , Abuaita Basel H. , Allen Jonathan P. , Bajer Sarah , Ginsburg Kevin , Neely Melody N. , Withey Jeffrey H.
Published: December 2013

The human diarrheal disease cholera is caused by the aquatic bacterium
Vibrio cholerae
.
V. cholerae
in the environment is associated with several varieties of aquatic life, including insect egg masses, shellfish, and vertebrate fish. Here we describe a novel animal model for
V. cholerae
, the zebrafish. Pandemic
V. cholerae
strains specifically colonize the zebrafish intestinal tract after exposure in water with no manipulation of the animal required. Colonization occurs in close contact with the intestinal epithelium and mimics colonization observed in mammals. Zebrafish that are colonized by
V. cholerae
transmit the bacteria to naive fish, which then become colonized. Striking differences in colonization between
V. cholerae
classical and El Tor biotypes were apparent. The zebrafish natural habitat in Asia heavily overlaps areas where cholera is endemic, suggesting that zebrafish and
V. cholerae
evolved in close contact with each other. Thus, the zebrafish provides a natural host model for the study of
V. cholerae
colonization, transmission, and environmental survival.
NrdH Redoxin Enhances Resistance to Multiple Oxidative Stresses by Acting as a Peroxidase Cofactor in Corynebacterium glutamicum
Authors: Si Mei-Ru , Zhang Lei , Yang Zhi-Fang , Xu Yi-Xiang , Liu Ying-Bao , Jiang Cheng-Ying , Wang Yao , Shen Xi-Hui , Liu Shuang-Jiang
Published: December 2013

NrdH redoxins are small protein disulfide oxidoreductases behaving like thioredoxins but sharing a high amino acid sequence similarity to glutaredoxins. Although NrdH redoxins are supposed to be another candidate in the antioxidant system, their physiological roles in oxidative stress remain unclear. In this study, we confirmed that the
Corynebacterium glutamicum
NrdH redoxin catalytically reduces the disulfides in the class Ib ribonucleotide reductases (RNR), insulin and 5,5′-dithiobis-(2-nitrobenzoic acid) (DTNB), by exclusively receiving electrons from thioredoxin reductase. Overexpression of NrdH increased the resistance of
C. glutamicum
to multiple oxidative stresses by reducing ROS accumulation. Accordingly, elevated expression of the
nrdH
gene was observed when the
C. glutamicum
wild-type strain was exposed to oxidative stress conditions. It was discovered that the NrdH-mediated resistance to oxidative stresses was largely dependent on the presence of the thiol peroxidase Prx, as the increased resistance to oxidative stresses mediated by overexpression of NrdH was largely abrogated in the
prx
mutant. Furthermore, we showed that NrdH facilitated the hydroperoxide reduction activity of Prx by directly targeting and serving as its electron donor. Thus, we present evidence that the NrdH redoxin can protect against the damaging effects of reactive oxygen species (ROS) induced by various exogenous oxidative stresses by acting as a peroxidase cofactor.
Soil Microbial Community Responses to a Decade of Warming as Revealed by Comparative Metagenomics
Authors: Luo Chengwei , Rodriguez-R Luis M. , Johnston Eric R. , Wu Liyou , Cheng Lei , Xue Kai , Tu Qichao , Deng Ye , He Zhili , Shi Jason Zhou , Yuan Mengting Maggie , Sherry Rebecca A. , Li Dejun , Luo Yiqi , Schuur Edward A. G. , Chain Patrick , Tiedje James M. , Zhou Jizhong , Konstantinidis Konstantinos T.
Published: December 2013

Soil microbial communities are extremely complex, being composed of thousands of low-abundance species (<0.1% of total). How such complex communities respond to natural or human-induced fluctuations, including major perturbations such as global climate change, remains poorly understood, severely limiting our predictive ability for soil ecosystem functioning and resilience. In this study, we compared 12 whole-community shotgun metagenomic data sets from a grassland soil in the Midwestern United States, half representing soil that had undergone infrared warming by 2°C for 10 years, which simulated the effects of climate change, and the other half representing the adjacent soil that received no warming and thus, served as controls. Our analyses revealed that the heated communities showed significant shifts in composition and predicted metabolism, and these shifts were community wide as opposed to being attributable to a few taxa. Key metabolic pathways related to carbon turnover, such as cellulose degradation (∼13%) and CO
2
production (∼10%), and to nitrogen cycling, including denitrification (∼12%), were enriched under warming, which was consistent with independent physicochemical measurements. These community shifts were interlinked, in part, with higher primary productivity of the aboveground plant communities stimulated by warming, revealing that most of the additional, plant-derived soil carbon was likely respired by microbial activity. Warming also enriched for a higher abundance of sporulation genes and genomes with higher G+C content. Collectively, our results indicate that microbial communities of temperate grassland soils play important roles in mediating feedback responses to climate change and advance the understanding of the molecular mechanisms of community adaptation to environmental perturbations.
Evaluation of Non-Saccharomyces Yeasts for the Reduction of Alcohol Content in Wine
Authors: Contreras A. , Hidalgo C. , Henschke P. A. , Chambers P. J. , Curtin C. , Varela C.
Published: December 2013

Over recent decades, the average ethanol concentration of wine has increased, largely due to consumer preference for wine styles associated with increased grape maturity; sugar content increases with grape maturity, and this translates into increased alcohol content in wine. However, high ethanol content impacts wine sensory properties, reducing the perceived complexity of flavors and aromas. In addition, for health and economic reasons, the wine sector is actively seeking technologies to facilitate the production of wines with lower ethanol content. Nonconventional yeast species, in particular, non-
Saccharomyces
yeasts, have shown potential for producing wines with lower alcohol content. These yeast species, which are largely associated with grapes preharvest, are present in the early stages of fermentation but, in general, are not capable of completing alcoholic fermentation. We have evaluated 50 different non-
Saccharomyces
isolates belonging to 24 different genera for their capacity to produce wine with a lower ethanol concentration when used in sequential inoculation regimes with a
Saccharomyces cerevisiae
wine strain. A sequential inoculation of
Metschnikowia pulcherrima
AWRI1149 followed by an
S. cerevisiae
wine strain was best able to produce wine with an ethanol concentration lower than that achieved with the single-inoculum, wine yeast control. Sequential fermentations utilizing AWRI1149 produced wines with 0.9% (vol/vol) and 1.6% (vol/vol) (corresponding to 7.1 g/liter and 12.6 g/liter, respectively) lower ethanol concentrations in Chardonnay and Shiraz wines, respectively. In Chardonnay wine, the total concentration of esters and higher alcohols was higher for wines generated from sequential inoculations, whereas the total concentration of volatile acids was significantly lower. In sequentially inoculated Shiraz wines, the total concentration of higher alcohols was higher and the total concentration of volatile acids was reduced compared with those in control
S. cerevisiae
wines, whereas the total concentrations of esters were not significantly different.
The Ancient Small GTPase Rab21 Functions in Intermediate Endocytic Steps in Trypanosomes
Authors: Ali Moazzam , Leung Ka Fai , Field Mark C.
Published: December 2013

Endocytosis is an essential process in nearly all eukaryotic cells, including the African trypanosome
Trypanosoma brucei
. Endocytosis in these organisms is exclusively clathrin mediated, although several lineage-specific features indicate that precise mechanisms are distinct from those of higher eukaryotes.
T. brucei
Rab21 is a member of an ancient, pan-eukaryotic, endocytic Rab clade that is retained by trypanosomes. We show that
T. brucei
Rab21 (TbRab21) localizes to endosomes, partially colocalizing with TbRab5A, TbRab28, and TbVps23, the latter two being present at late endosomes. TbRab21 expression is essential for cellular proliferation, and its suppression results in a partial block in traffic to the lysosome. RNA interference (RNAi)-mediated knockdown of TbRab21 had no effect on TbRab5A expression or location but did result in decreased in
trans
expression of ESCRT (trypanosome endosomal sorting complex required for transport) components and TbRab28, while knockdown of ESCRT subunit TbVps23 resulted in decreased TbRab21 expression. These data suggest that TbRab21 acts downstream of TbRab5A and functions in intimate connection with the trypanosome ESCRT system.
Candida albicans Triggers NLRP3-Mediated Pyroptosis in Macrophages
Authors: Wellington Melanie , Koselny Kristy , Sutterwala Fayyaz S. , Krysan Damian J.
Published: December 2013

Pyroptosis is an inflammasome-mediated programmed cell death pathway triggered in macrophages by a variety of stimuli, including intracellular bacterial pathogens. Activation of pyroptosis leads to the secretion of interleukin-1β (IL-1β) and pore-mediated cell lysis. Although not considered an intracellular pathogen,Candida albicansis able to kill and, thereby, escape from macrophages. Here, we show thatC. albicans-infected bone marrow-derived macrophages (BMDM) and murine J774 macrophages undergo pyroptotic cell death that is suppressed by glycine and pharmacologic inhibition of caspase-1. Infection of BMDM harvested from mice lacking components of the inflammasome revealed that pyroptosis was dependent on caspase-1, ASC, and NLRP3 and independent of NLRC4. In contrast to its role during intracellular bacterial infection, pyroptosis does not restrictC. albicansreplication. NonfilamentousCandidaspp. did not trigger pyroptosis, whileCandida krusei, which forms pseudohyphae in macrophages, triggered much lower levels than didC. albicans. Interestingly, aSaccharomyces cerevisiaestrain from the filamentous background Σ1278 also triggered low, but significant, levels of pyroptosis. We have found that deletion of the transcription factorUPC2decreases pyroptosis but has little effect on filamentation in the macrophage. In addition, a gain-of-function mutant ofUPC2induces higher levels of pyroptosis than does a matched control strain. Taken together, these data are most consistent with a model in which filamentation is necessary but not sufficient to trigger NLRP3 inflammasome-mediated pyroptosis. This is the first example of a fungal pathogen triggering pyroptosis and indicates thatC. albicans-mediated macrophage damage is not solely due to hypha-induced physical disruption of cellular integrity.
Physiological Framework for the Regulation of Quorum Sensing-Dependent Public Goods in Pseudomonas aeruginosa
Authors: Mellbye Brett , Schuster Martin
Published: December 2013

Many bacteria possess cell density-dependent quorum-sensing (QS) systems that often regulate cooperative secretions involved in host-microbe or microbe-microbe interactions. These secretions, or “public goods,” are frequently coregulated by stress and starvation responses. Here we provide a physiological rationale for such regulatory complexity in the opportunistic pathogen
Pseudomonas aeruginosa
. Using minimal-medium batch and chemostat cultures, we comprehensively characterized specific growth rate-limiting macronutrients as key triggers for the expression of extracellular enzymes and metabolites directly controlled by the
las
and
rhl
QS systems. Expression was unrelated to cell density, depended on the secreted product's elemental composition, and was induced only when the limiting nutrient was not also a building block of the product;
rhl
-dependent products showed the strongest response, caused by the largely
las
-independent induction of the regulator RhlR and its cognate signal. In agreement with the prominent role of the
rhl
system, slow growth inverted the
las
-to-
rhl
signal ratio, previously considered a characteristic distinguishing between planktonic and biofilm lifestyles. Our results highlight a supply-driven, metabolically prudent regulation of public goods that minimizes production costs and thereby helps stabilize cooperative behavior. Such regulation would be beneficial for QS-dependent public goods that act broadly and nonspecifically, and whose need cannot always be accurately assessed by the producing cell. Clear differences in the capacities of the
las
and
rhl
systems to integrate starvation signals help explain the existence of multiple QS systems in one cell.
mRNA Cap Methylation Influences Pathogenesis of Vesicular Stomatitis VirusIn Vivo
Authors: Ma Yuanmei , Wei Yongwei , Zhang Xiaodong , Zhang Yu , Cai Hui , Zhu Yang , Shilo Konstantin , Oglesbee Michael , Krakowka Steven , Whelan Sean P. J. , Li Jianrong
Published: December 2013

One role of mRNA cap guanine-N-7 (G-N-7) methylation is to facilitate the efficient translation of mRNA. The role of mRNA cap ribose 2′-O methylation is enigmatic, although recent work has implicated this as a signature to avoid detection of RNA by the innate immune system (S. Daffis, K. J. Szretter, J. Schriewer, J. Q. Li, S. Youn, J. Errett, T. Y. Lin, S. Schneller, R. Zust, H. P. Dong, V. Thiel, G. C. Sen, V. Fensterl, W. B. Klimstra, T. C. Pierson, R. M. Buller, M. Gale, P. Y. Shi, M. S. Diamond, Nature 468:452-456, 2010, doi:10.1038/nature09489). Working with vesicular stomatitis virus (VSV), we previously showed that a panel of recombinant VSVs carrying mutations at a predicted methyltransferase catalytic site (rVSV-K1651A, -D1762A, and -E1833Q) orS-adenosylmethionine (SAM) binding site (rVSV-G1670A, -G1672A, and -G4A) were defective in cap methylation and were also attenuated for growth in cell culture. Here, we analyzed the virulence of these recombinants in mice. We found that rVSV-K1651A, -D1762A, and -E1833Q, which are defective in both G-N-7 and 2′-O methylation, were highly attenuated in mice. All three viruses elicited a high level of neutralizing antibody and provided full protection against challenge with the virulent VSV. In contrast, mice inoculated with rVSV-G1670A and -G1672A, which are defective only in G-N-7 methylation, were attenuatedin vivoyet retained a low level of virulence. rVSV-G4A, which is completely defective in both G-N-7 and 2′-O methylation, also exhibited low virulence in mice despite the fact that productive viral replication was not detected in lung and brain. Taken together, our results suggest that abrogation of viral mRNA cap methylation can serve as an approach to attenuate VSV, and perhaps other nonsegmented negative-strand RNA viruses, for potential application as vaccines and viral vectors.

IMPORTANCENonsegmented negative-sense (NNS) RNA viruses include a wide range of significant human, animal, and plant pathogens. For many of these viruses, there are no vaccines or antiviral drugs available. mRNA cap methylation is essential for mRNA stability and efficient translation. Our current understanding of mRNA modifications of NNS RNA viruses comes largely from studies of vesicular stomatitis virus (VSV). In this study, we showed that recombinant VSVs (rVSVs) defective in mRNA cap methylation were attenuatedin vitroandin vivo. In addition, these methyltransferase (MTase)-defective rVSVs triggered high levels of antibody responses and provided complete protection against VSV infection. Thus, this study will not only contribute to our understanding of the role of mRNA cap MTase in viral pathogenesis but also facilitate the development of new live attenuated vaccines for VSV, and perhaps other NNS RNA viruses, by inhibiting viral mRNA cap methylation.
Neighbourhood green space and the odds of having skin cancer: multilevel evidence of survey data from 267072 Australians
Authors: Astell-Burt Thomas , Feng Xiaoqi , Kolt Gregory S
Published: December 2013

Background

If green spaces encourage people to spend more time outdoors in physical, recreational and social activities, this could have unintended but important consequences for health in countries where levels of ultraviolet (UV) radiation are non-trivial. We investigated whether people who lived in neighbourhoods containing lots of green space were likely to spend more time outdoors and, subsequently, were more likely to report a case of skin cancer.

Methods

Multilevel logit regression was used to fit associations between self-reported medically diagnosed skin cancer (melanoma and non-melanoma) and an objective measure of green space. These models were adjusted for measures of susceptibility (skin colour and tanning), socioeconomic variables, demographic and cultural characteristics (eg, ancestry and country of birth). Mediation analyses were conducted using self-reported measures of time spent outdoors and participation in moderate-to-vigorous physical activity (MVPA).

Results

Descriptive analyses reported a positive association between green space and skin cancer (p<0.001). Time outdoors and in MVPA was also higher among people living in greener areas. The association between green space and skin cancer was robust after adjustment. In comparison to people with 0–20% green space, for example, the adjusted odds of having skin cancer were 9% higher among those with >80% green space. Only 1.6% and less than 1% of the association was mediated by MVPA and time spent outdoors.

Conclusions

Neighbourhood green space is associated with higher odds of having skin cancer in Australia. The relationship between green space and health, in its broadest terms, is likely to vary by geographical context.
ON THE DESCRIPTIONAL COMPLEXITY OF THE WINDOW SIZE FOR DELETING RESTARTING AUTOMATA
Authors: KUTRIB MARTIN , OTTO FRIEDRICH
Published: December 2013

The restarting automaton was inspired by the technique of ‘analysis by reduction’ from linguistics. A restarting automaton processes a given input word through a sequence of cycles. In each cycle the current word on the tape is scanned from left to right and a single local simplification (a rewrite) is executed. One of the essential parameters of a restarting automaton is the size of its read/write window. Here we study the impact of the window size on the descriptional complexity of several types of deterministic and nondeterministic restarting automata. For all k ≥ 4, we show that the savings in the economy of descriptions of restarting automata that can only delete symbols but not rewrite them (that is, the so-called R- and RR-automata) cannot be bounded by any recursive function, when changing from window size k to window size k + 1. This holds for deterministic as well as for nondeterministic automata, and for k ≥ 5, it even holds for the stateless variants of these automata. However, the trade-off between window sizes two and one is recursive for deterministic devices. In addition, a polynomial upper bound is given for the trade-off between RRWW-automata with window sizes k + 1 and k for all k ≥ 2.
RESTARTING TILING AUTOMATA
Authors: PRŮŠA DANIEL , MRÁZ FRANTIŠEK
Published: December 2013

We present a new model of a two-dimensional computing device called restarting tiling automaton. The automaton defines a set of tile-rewriting, weight-reducing rules and a scanning strategy by which a tile to rewrite is being searched. We investigate properties of the induced families of picture languages. Special attention is paid to picture languages that can be accepted independently of the scanning strategy. We show that this family strictly includes REC and exhibits similar closure properties. Moreover, we prove that its intersection with the set of one-row languages coincides with the regular languages.
Existence and upper semicontinuity of attractors for stochastic equations with deterministic non-autonomous terms
Authors: Wang Bixiang
Published: December 2013

We prove the existence and uniqueness of tempered random attractors for stochastic Reaction–Diffusion equations on unbounded domains with multiplicative noise and deterministic non-autonomous forcing. We establish the periodicity of the tempered attractors when the stochastic equations are forced by periodic functions. We further prove the upper semicontinuity of these attractors when the intensity of stochastic perturbations approaches zero.
CONTEXTUALIZING YOUTH ENTREPRENEURSHIP: THE CASE OF BOTSWANA'S YOUNG FARMERS FUND
Authors: WILLIAMS MIKE , HOVORKA ALICE J
Published: December 2013

Entrepreneurship is well established as a development strategy to facilitate youth empowerment in Africa. Existing scholarship on youth entrepreneurship, while informative, remains limited given its focus on either normative institutional structures or individual decision-making behaviors. Recent research offers a contextualist approach, featuring the dynamic relationship between individual behavior and structural context. Engaging and building upon a contextualist approach, this paper offers a place-based study of youth entrepreneurship in Botswana. The paper documents empirical findings revealing trends in youth circumstances and experiences, namely empowerment potential, financial strain and knowledge/skill gaps. It then explores the cultural, political and institutional contextual effects shaping youth entrepreneurship within the Young Farmers Fund (YFF). Drawing on elements of 'best practice,' the paper offers suggestions for enhancing practical entrepreneurship in Botswana through educational, technical and operational means. Although the paper contributes a case study of youth and entrepreneurship in Botswana, it also offers and demonstrates the conceptual framework of contextualism as a useful research tool for subsequent place-based studies.
BOUNDARIES OF NETWORK TIES IN ENTREPRENEURSHIP: HOW LARGE IS TOO LARGE?
Authors: QIAN SHANSHAN , KEMELGOR BRUCE H.
Published: December 2013

External environments can require entrepreneurs to adjust and maintain network ties to cope with environmental changes and turbulence. Although network ties can help entrepreneurs gain resources and support, researchers are becoming aware of some negative aspects of networks, such as information redundancy. We used relative weight analysis and identified that environmental munificence and uncertainty influence the size of one's network. In addition, we surveyed 44 entrepreneurial founders of firms in the bio-technology industry regarding their network composition, including number of ties and firm performance. We found that environmental factors led to increases in both business and social network size. In addition, we identified an optimal number of network ties prior to tie-additions becoming negatively related to firm performance.