bluuebunny/crossref_metadata_2025 huggingface dataset:
Examining the impact of regular aspirin use and PIK3CA mutations on survival in stage 2 colon cancer
Authors: Murphy Caitlin , Turner Natalie , Wong Hui‐Li , Sinnathamby Mathu , Tie Jeanne , Lee Belinda , Desai Jayesh , Skinner Iain , Christie Michael , Hutchinson Ryan , Lunke Sebastian , Waring Paul , Gibbs Peter , Tran Ben
Published: November 2016

Background/Aim

Data suggest aspirin improves survival in colorectal cancer (CRC) harbouring
PIK3CA
mutations. The impact of aspirin is thought predominantly to be through an anti‐inflammatory effect. The aim of this study is to explore the effect of aspirin use on survival in a real‐world cohort of stage 2 colon cancer (CC) patients.

Methods

A prospective CRC database identified patients diagnosed with stage 2 CC between 2000 and 2011.
PIK3CA
mutation status was determined by next generation sequencing. Neutrophil‐lymphocyte ratio greater than 5 at diagnosis represented systemic inflammation. Chart review was used to record regular aspirin use at diagnosis. Clinico‐pathological features and survival data were available. Survival analyses used the Cox proportional hazards method.

Results

Of 488 patients with stage 2 CC, 95 patients were aspirin users and 70 patients had
PIK3CA
mutations. Aspirin users were more likely to be older (median: 76.4 years vs 68.3 years, P < 0.001), to be less fit (American Society of Anaesthetists Score 3–4: 58% vs 31%, P < 0.001) and to have systemic inflammation (neutrophil‐lymphocyte ratio > 5: 39% vs 27%, P = 0.027). Regular aspirin use did not significantly improve recurrence‐free survival. In the
PIK3CA
mutated group, there was a trend towards improved recurrence‐free survival (hazard ratio: 0.45, P = 0.42).

Conclusions

Our study did not demonstrate a significant survival advantage from aspirin use in stage 2
PIK3CA
mutated CC. The ‘real‐world’ nature of our cohort and the subsequent uncontrolled differences in age and fitness in aspirin users are likely to have contributed to this result. Defining the true impact of aspirin in CRC requires prospective randomised clinical trials.
Associations of changes in psychosocial factors and their interactions with diabetes distress in patients with type 2 diabetes: a longitudinal study
Authors: Wang Ruey‐Hsia , Hsu Hui‐Chun , Kao Chia‐Chan , Yang Yung‐Mei , Lee Yau‐Jiunn , Shin Shyi‐Jang
Published: November 2016

Aim

To assess the associations of changes in self‐management behaviours, diabetes self‐efficacy, resilience, social support, patient empowerment and their interactions with changes in diabetes distress in patients with type 2 diabetes mellitus.

Background

Many patients with type 2 diabetes mellitus experience diabetes distress. Few longitudinal studies have investigated the associations of changes in various psychosocial factors with changes in diabetes distress in patients with type 2 diabetes mellitus.

Design

This study adopted a longitudinal design. Data were collected at baseline and 12 months later.

Methods

Overall, 304 patients with type 2 diabetes were recruited from four hospitals in southern Taiwan by convenience sampling. A self‐report questionnaire and medical record were used to collect demographic data, clinical indicators, self‐management behaviours, diabetes self‐efficacy, resilience, social support, patient empowerment, and diabetes distress. Data were collected from February 2014–March 2015.

Results/Findings

An increase in resilience or diabetes self‐efficacy significantly associated with a decrease in diabetes distress, whereas an increase in patient empowerment significantly associated with an increase in diabetes distress. The interactions between increase in patient empowerment and increase in self‐management behaviours significantly associated with decrease in diabetes distress.

Conclusion

Nurses could endeavour to improve the diabetes self‐efficacy and resilience to reducing diabetes distress. Arbitrarily empowering patients may increase diabetes distress. Increasing self‐care management behaviours and patient empowerment might need to be simultaneously addressed to reduce the diabetes distress in patients with type 2 diabetes.
A Randomized controlled trial to evaluate the impact of a Nurse Navigator Programme on outcomes of people with breast cancer: study protocol
Authors: Chillakunnel Hussain Rawther Shejila , Pai Mamatha Shivananda , Fernandes Donald J , Mathew Stanley , Binu V S , Chakrabarty Jyothi , Devi Elsa Sanatombi , George Anice , Nayak Baby S
Published: November 2016

Aim

To evaluate the effectiveness of a Nurse Navigator Programme on anxiety, psychological distress and quality of life in people with breast cancer.

Background

Breast cancer is the most frequently detected malignancy and a major cause of cancer death among women around the world. The lengthy course of illness from initial diagnosis to treatment and subsequent follow‐up causes deterioration in physical, psychological and social status among patients. Nurses have a major role in cancer care. As women with breast cancer have to undergo various treatment modalities, continued care by a pivot nurse is thought to enhance treatment adherence. Limited studies have been reported from developing countries on Nurse Navigation Programmes.

Design

A Stratified Randomized controlled trial with repeated measures.

Methods

One hundred and twenty newly diagnosed women with breast cancer admitted to surgery wards of a tertiary care hospital in South India will be recruited. (Project funded in Octo"ber 2014). Women are randomly allocated to a control and intervention group. The outcome variables are anxiety, psychological distress and quality of life. Data on outcome measures will be collected at five different time points: before surgery, at discharge, beginning of adjuvant therapy, middle of adjuvant therapy and at the end of adjuvant therapy.

Discussion

This study may give evidence on the effectiveness of a Nurse Navigator Programme for women with breast cancer. If significant effects were detected, the programme could be integrated into hospital services to improve the patient care.
Systematic review of measurement properties of self‐reported instruments for evaluating self‐care in adults
Authors: Matarese Maria , Lommi Marzia , De Marinis Maria Grazia
Published: November 2016

Aims

The aims of this study were as follows: to identify instruments developed to assess self‐care in healthy adults; to determine the theory on which they were based; their validity and reliability properties and to synthesize the evidence on their measurement properties.

Background

Many instruments have been developed to assess self‐care in many different populations and conditions. Clinicians and researchers should select the most appropriate self‐care instrument based on the knowledge of their measurement properties.

Design

Systematic review of measurement instruments according to the protocol recommended by the COnsensus‐based Standards for the selection of health Measurement INstruments (COSMIN) panel.

Data sources

PubMed, Embase, PsycINFO, Scopus and CINAHL databases were searched from inception to December 2015.

Review methods

Studies testing measurement properties of self‐report instruments assessing self‐care in healthy adults, published in the English language and in peer review journals were selected. Two reviewers independently appraised the methodological quality of the studies with the COSMIN checklist and the quality of results using specific quality criteria.

Results

Twenty‐six articles were included in the review testing the measurement properties of nine instruments. Seven instruments were based on Orem's Self‐care theory. Not all the measurement properties were evaluated for the identified instruments. No self‐care instrument showed strong evidence supporting the evaluated measurement properties.

Conclusion

Despite the development of several instruments to assess self‐care in the adult population, no instrument can be fully recommended to clinical nurses and researchers. Further studies of high methodological quality are needed to confirm the measurement properties of these instruments.
Influence of habitat patchiness on diversity patterns of a habitat specialist plant community
Authors: Gil‐López Manuel J. , Segarra‐Moragues José G. , Ojeda Fernando
Published: November 2016

Question

Does the number and relative abundance of sandstone specialist woody species in Mediterranean heathland (herriza) communities of the Strait of Gibraltar decrease with increasing sandstone patch isolation? If so, does this reduction suggest deterministic (ecological filtering) or random (ecological drift) effects?

Location

Strait of Gibraltar region.

Methods

We recorded the identity and relative abundance of sandstone specialist and generalist woody plant species in 26 herriza samples. We then calculated the degree of sandstone patch isolation of each herriza sample and used generalized linear regression models to examine the effect of sandstone patch isolation on species richness and relative abundance of woody species in the herriza communities, separately for sandstone specialist and generalist species. We finally compared beta‐diversity values among herriza samples from the two sides of the Strait of Gibraltar.

Results

Increasing sandstone patch isolation determined a loss of sandstone specialist species in herriza communities. This loss of sandstone specialist species is more pronounced in the African side of the Strait, where overall sandstone patch isolation is higher, suggesting that this is a random process (ecological drift) that resulted in higher beta‐diversity between herrizas in Tangier.

Conclusions

This study highlights the high vulnerability of the highly biodiverse herriza or Mediterranean heathland in the African side of the Strait of Gibraltar as a consequence of its overall higher sandstone patchiness.
Barriers and facilitators to initial and continued attendance at community‐based lifestyle programmes among families of overweight and obese children: a systematic review
Authors: Kelleher E. , Davoren M. P. , Harrington J. M. , Shiely F. , Perry I. J. , McHugh S. M.
Published: November 2016

The success of childhood weight management programmes relies on family engagement. While attendance offers many benefits including the support to make positive lifestyle changes, the majority of families referred to treatment decline. Moreover, for those who do attend, benefits are often compromised by high programme attrition. This systematic review investigated factors influencing attendance at community‐based lifestyle programmes among families of overweight or obese children. A narrative synthesis approach was used to allow for the inclusion of quantitative, qualitative and mixed‐method study designs. Thirteen studies met the inclusion criteria. Results suggest that parents provided the impetus for programme initiation, and this was driven largely by a concern for their child's psychological health and wellbeing. More often than not, children went along without any real reason or interest in attending. Over the course of the programme, however, children's positive social experiences such as having fun and making friends fostered the desire to continue. The stigma surrounding excess weight and the denial of the issue amongst some parents presented barriers to enrolment and warrant further study. This study provides practical recommendations to guide future policy makers, programme delivery teams and researchers in developing strategies to boost recruitment and minimise attrition.
Correlation between chemical-bonding states and fixed-charge states of Sr-silicate film on Si(100) substrate
Authors: Taniwaki Shota , Yoshida Haruhiko , Arafune Koji , Ogura Atsushi , Satoh Shin-ichi , Hotta Yasushi
Published: November 2016

The authors studied the correlation between the chemical bonding (CB) states and fixed charge (FC) states of Sr-silicate films grown on Si(100) substrates [Sr-silicate/Si(100)]. The Sr-silicate/Si(100) samples were synthesized by silicate reaction of SrO layers on the Si substrates through the diffusion of Si atoms from the substrates by thermal annealing in oxygen atmosphere. The CB states and the FC states of the Sr-silicate/Si(100) samples were obtained from their O 1s core-level x-ray photoemission spectra and the shift in voltage from the flat band state in their capacitance–voltage curves, respectively. Peak fittings of the O 1s core-level spectra for each sample were carried out with the three components of Si–O, Si–O–Sr, and Sr–O bonds to determine the CB state. The thin Sr-silicate layers were mainly constructed of the Si-O-Sr component. With increasing thickness, the amount of Si-O-Sr component decreased while that of Sr-O increased. The thickness dependency of the FC density showed a good agreement with that of the Si-O-Sr component, revealing a clear correlation between FC and Sr–O–Si bonding. Our results suggest that silicate bonding plays an important role in FC generation in Sr-silicate systems.
Identifying the dominating perceptual differences in headphone reproduction
Authors: Volk Christer P. , Lavandier Mathieu , Bech Søren , Christensen Flemming
Published: November 2016

The perceptual differences between the sound reproductions of headphones were investigated in a pair-wise comparison study. Two musical excerpts were reproduced over 21 headphones positioned on a mannequin and recorded. The recordings were then processed and reproduced over one set of headphones to listeners, who were asked to evaluate their perceived degree of dissimilarity. The two musical excerpts were used in separate experiments. The processing of the recordings consisted of compensating for the influences of the playback headphones worn by the listeners as well as for the mannequin's ear canals. A multidimensional scaling analysis revealed two dominating perceptual dimensions used by the listeners to differentiate the reproductions of the headphones. These dimensions were similar for the two musical excerpts. Objective metrics are proposed to describe them, leading to correlations ranging from 0.89 to 0.97 between the dimensions and metrics. The first perceptual dimension was associated with the relative strength of bass, while the second dimension was related to the relative strength of the lower midrange.
Computational multiheterodyne spectroscopy
Authors: Burghoff David , Yang Yang , Hu Qing
Published: November 2016

A computationally enabled approach is used to perform dual-comb spectroscopy without a phase reference.
Blind protein structure prediction using accelerated free-energy simulations
Authors: Perez Alberto , Morrone Joseph A. , Brini Emiliano , MacCallum Justin L. , Dill Ken A.
Published: November 2016

Protein structures can be predicted by combining atomistic simulations and coarse information.
Molecular structure of bottlebrush polymers in melts
Authors: Paturej Jarosław , Sheiko Sergei S. , Panyukov Sergey , Rubinstein Michael
Published: November 2016

Steric repulsion between grafted side chains inhibits interpenetration of bottlebrushes, transforming them into flexible filaments.
Overcoming a nucleosomal barrier to replication
Authors: Chang Han-Wen , Pandey Manjula , Kulaeva Olga I. , Patel Smita S. , Studitsky Vasily M.
Published: November 2016

Nucleosomes present a strong, sequence-dependent barrier for moving replisomes and can survive during DNA replication in vitro.
Multistrain Infections with Lyme Borreliosis Pathogens in the Tick Vector
Authors: Durand Jonas , Herrmann Coralie , Genné Dolores , Sarr Anouk , Gern Lise , Voordouw Maarten J.
Published: November 2016

Mixed or multiple-strain infections are common in vector-borne diseases and have important implications for the epidemiology of these pathogens. Previous studies have mainly focused on interactions between pathogen strains in the vertebrate host, but little is known about what happens in the arthropod vector.
Borrelia afzelii
and
Borrelia garinii
are two species of spirochete bacteria that cause Lyme borreliosis in Europe and that share a tick vector,
Ixodes ricinus
. Each of these two tick-borne pathogens consists of multiple strains that are often differentiated using the highly polymorphic
ospC
gene. For each
Borrelia
species, we studied the frequencies and abundances of the
ospC
strains in a wild population of
I. ricinus
ticks that had been sampled from the same field site over a period of 3 years. We used quantitative PCR (qPCR) and 454 sequencing to estimate the spirochete load and the strain diversity within each tick. For
B. afzelii
, there was a negative relationship between the two most common
ospC
strains, suggesting the presence of competitive interactions in the vertebrate host and possibly the tick vector. The flat relationship between total spirochete abundance and strain richness in the nymphal tick indicates that the mean abundance per strain decreases as the number of strains in the tick increases. Strains with the highest spirochete load in the nymphal tick were the most common strains in the tick population. The spirochete abundance in the nymphal tick appears to be an important life history trait that explains why some strains are more common than others in nature.

IMPORTANCE
Lyme borreliosis is the most common vector-borne disease in the Northern Hemisphere and is caused by spirochete bacteria that belong to the
Borrelia burgdorferi
sensu lato
species complex. These tick-borne pathogens are transmitted among vertebrate hosts by hard ticks of the genus
Ixodes
. Each
Borrelia
species can be further subdivided into genetically distinct strains. Multiple-strain infections are common in both the vertebrate host and the tick vector and can result in competitive interactions. To date, few studies on multiple-strain vector-borne pathogens have investigated patterns of cooccurrence and abundance in the arthropod vector. We demonstrate that the abundance of a given strain in the tick vector is negatively affected by the presence of coinfecting strains. In addition, our study suggests that the spirochete abundance in the tick is an important life history trait that can explain why some strains are more common in nature than others.
Elimination of a Free Cysteine by Creation of a Disulfide Bond Increases the Activity and Stability of Candida boidinii Formate Dehydrogenase
Authors: Zheng Junxian , Yang Taowei , Zhou Junping , Xu Meijuan , Zhang Xian , Rao Zhiming
Published: November 2016

NAD+-dependent formate dehydrogenase (FDH; EC 1.2.1.2) is an industrial enzyme widely used for NADH regeneration. However, enzyme inactivation caused by the oxidation of cysteine residues is a flaw of native FDH. In this study, we relieved the oxidation of the free cysteine of FDH fromCandida boidinii(CboFDH) through the construction of disulfide bonds between A10 and C23 as well as I239 and C262. Variants A10C, I239C, and A10C/I239C were obtained by the site-directed mutagenesis and their properties were studied. Results showed that there were no significant changes in the optimum temperature and pH between variants and wild-typeCboFDH. However, the stabilities of all variant enzymes were improved. Specifically, theCboFDH variant A10C (A10Cfdh) showed a significant increase in copper ion resistance and acid resistance, a 6.7-fold increase in half-life at 60°C, and a 1.4-fold increase in catalytic efficiency compared with the wild type. Asymmetric synthesis ofl-tert-leucine indicated that the process time was reduced by 40% with variant A10Cfdh, which benefited from the increase in catalytic efficiency. Circular dichroism analysis and molecular dynamics simulation indicated that variants that contained disulfide bonds lowered the overall root mean square deviation (RMSD) and consequently increased the protein rigidity without affecting the secondary structure of enzyme. This work is expected to provide a viable strategy to avoid the microbial enzyme inactivation caused by the oxidation of the free cysteine residues and improving their performances.

IMPORTANCEFDH is widely used for NADH regeneration in dehydrogenase-based synthesis of optically active compounds to decrease the cost of production. This study highlighted a viable strategy that was used to eliminate the oxidation of free cysteine residues of FDH fromCandida boidiniiby the introduction of disulfide bonds. Using this strategy, we obtained a variant FDH with improved activity and stability. The improvement of activity and stability of FDH is expected to reduce its price and then further to decrease the cost of its application.
Season-Specific Occurrence of Potentially Pathogenic Vibrio spp. on the Southern Coast of South Korea
Authors: Di Doris Y. W. , Lee Anna , Jang Jeonghwan , Han Dukki , Hur Hor-Gil
Published: November 2016

Vibrio
species are widely distributed in warm estuarine and coastal environments, and they can infect humans through the consumption of raw and mishandled contaminated seafood. In this study, we aimed to isolate and observe the distribution of enteropathogenic
Vibrio
spp. from environments of the southern coast of South Korea over a season cycle. A total of 10,983 isolates of
Vibrio
spp. were obtained from tidal water and mud samples over a 1-year period from five sampling sites along the southwest coast of South Korea. We found that
Vibrio alginolyticus
(
n
= 6,262) and
Vibrio parahaemolyticus
(
n
= 1,757) were ubiquitous in both tidal water and mud year round, whereas
Vibrio cholerae
(
n
= 24) and
Vibrio vulnificus
(
n
= 130) were seasonally specific to summer. While all
V. cholerae
isolates were nontoxigenic (non-O1 and non-O139), more than 88% of
V. vulnificus
isolates possessed the virulence factor elastolytic protease (encoded by
vvp
). Interestingly,
V. parahaemolyticus
, which was omnipresent in all seasons, contained the virulence factors thermostable direct hemolysin (encoded by
tdh
) and thermostable direct hemolysin-related hemolysin (encoded by
trh
) in larger amounts in June (29
trh
-positive strains) and September (14
tdh
-, 36
trh
-, and 12
tdh
- and
trh
-positive strains) than in December (4
trh
-positive strains) and February (3
tdh
-positive strains), and virulence factors were absent from isolates detected in April. To understand why virulence factors were detected only in the warm season and were absent in the cold season although the locations are static, long-term monitoring and particularly seasonal study are necessary.

IMPORTANCE
The presence of enteropathogenic
Vibrio
species (
Vibrio cholerae
,
Vibrio parahaemolyticus
, and
Vibrio vulnificus
), which cause acute diarrheal infection, septicemia, and wound infections upon ingestion through food and water, is usually associated with temperature. The World Health Organization (WHO) has estimated that there are 1.4 to 4.3 million cases and 28,000 to 142,000 deaths per year worldwide caused by cholera disease. In South Korea alone, consumption is as much as 52.4 kg of fish and shellfish per year per capita. Our findings suggested that seasonally specific acceleration of these possible pathogenic
Vibrio
spp. may threaten seafood safety and increase the risk of illness in South Korea, where local people consume raw fish during warmer months.
Inactivation of Cellobiose Dehydrogenases Modifies the Cellulose Degradation Mechanism of Podospora anserina
Authors: Tangthirasunun Narumon , Navarro David , Garajova Sona , Chevret Didier , Tong Laetitia Chan Ho , Gautier Valérie , Hyde Kevin D. , Silar Philippe , Berrin Jean-Guy
Published: November 2016

Conversion of biomass into high-value products, including biofuels, is of great interest to developing sustainable biorefineries. Fungi are an inexhaustible source of enzymes to degrade plant biomass. Cellobiose dehydrogenases (CDHs) play an important role in the breakdown through synergistic action with fungal lytic polysaccharide monooxygenases (LPMOs). The three CDH genes of the model fungus
Podospora anserina
were inactivated, resulting in single and multiple CDH mutants. We detected almost no difference in growth and fertility of the mutants on various lignocellulose sources, except on crystalline cellulose, on which a 2-fold decrease in fertility of the mutants lacking
P. anserina CDH1
(
PaCDH1
) and
PaCDH2
was observed. A striking difference between wild-type and mutant secretomes was observed. The secretome of the mutant lacking all CDHs contained five beta-glucosidases, whereas the wild type had only one.
P. anserina
seems to compensate for the lack of CDH with secretion of beta-glucosidases. The addition of
P. anserina
LPMO to either the wild-type or mutant secretome resulted in improvement of cellulose degradation in both cases, suggesting that other redox partners present in the mutant secretome provided electrons to LPMOs. Overall, the data showed that oxidative degradation of cellulosic biomass relies on different types of mechanisms in fungi.

IMPORTANCE
Plant biomass degradation by fungi is a complex process involving dozens of enzymes. The roles of each enzyme or enzyme class are not fully understood, and utilization of a model amenable to genetic analysis should increase the comprehension of how fungi cope with highly recalcitrant biomass. Here, we report that the cellobiose dehydrogenases of the model fungus
Podospora anserina
enable it to consume crystalline cellulose yet seem to play a minor role on actual substrates, such as wood shavings or miscanthus. Analysis of secreted proteins suggests that
Podospora anserina
compensates for the lack of cellobiose dehydrogenase by increasing beta-glucosidase expression and using an alternate electron donor for LPMO.
Waterborne Viruses and F-Specific Coliphages in Mixed-Use Watersheds: Microbial Associations, Host Specificities, and Affinities with Environmental/Land Use Factors
Authors: Jones Tineke H. , Brassard Julie , Topp Edward , Wilkes Graham , Lapen David R.
Published: November 2016

From the years 2008 to 2014, a total of 1,155 water samples were collected (spring to fall) from 24 surface water sampling sites located in a mixed-used but predominantly agricultural (i.e., dairy livestock production) river basin in eastern Ontario, Canada. Water was analyzed for viable F-specific DNA (F-DNA) and F-specific RNA (F-RNA) (genogroup I [GI] to GIV) coliphage and a suite of molecularly detected viruses (norovirus [GI to GIV], torque teno virus [TTV], rotavirus, kobuvirus, adenovirus, astrovirus, hepatitis A, and hepatitis E). F-DNA and F-RNA coliphage were detected in 33 and 28% of the samples at maximum concentrations of 2,000 and 16,300 PFU · 100 ml
−1
, respectively. Animal TTV, human TTV, kobuvirus, astrovirus, and norovirus GIII were the most prevalent viruses, found in 23, 20, 13, 12, and 11% of samples, respectively. Viable F-DNA coliphage was found to be a modest positive indicator of molecularly detected TTV. F-RNA coliphage, unlike F-DNA coliphage, was a modest positive predictor of norovirus and rotavirus. There were, however, a number of significant negative associations among F-specific coliphage and viruses. F-DNA coliphage densities of >142 PFU · 100 ml
−1
delineated conditions when ∼95% of water samples contained some type of virus. Kobuvirus was the virus most strongly related to detection of any other virus. Land use had some associations with virus/F-specific coliphage detection, but season and surface water flow were the variables that were most important for broadly delineating detection. Higher relative levels of detection of human viruses and human F-RNA coliphage were associated with higher relative degrees of upstream human land development in a catchment.

IMPORTANCE
This study is one of the first, to our knowledge, to evaluate relationships among F-specific coliphages and a large suite of enteric viruses in mixed-use but agriculturally dominated surface waters in Canada. This study suggested that relationships between viable F-specific coliphages and molecularly detected viruses do exist, but they are not always positive. Caution should be employed if viable F-specific coliphages are to be used as indicators of virus presence in surface waters. This study elucidates relative effects of agriculture, wildlife, and human activity on virus and F-specific coliphage detection. Seasonal and meteorological attributes play a strong role in the detection of most virus and F-specific coliphage targets.
A System Model for Understanding the Role of Animal Feces as a Route of Contamination of Leafy Greens before Harvest
Authors: Mishra Abhinav , Pang Hao , Buchanan Robert L. , Schaffner Donald W. , Pradhan Abani K.
Published: November 2016

The majority of foodborne outbreaks in the United States associated with the consumption of leafy greens contaminated with
Escherichia coli
O157:H7 have been reported during the period of July to November. A dynamic system model consisting of subsystems and inputs to the system (soil, irrigation, cattle, wild pig, and rainfall) simulating a hypothetical farm was developed. The model assumed two crops of lettuce in a year and simulated planting, irrigation, harvesting, ground preparation for the new crop, contamination of soil and plants, and survival of
E. coli
O157:H7. As predicted by the baseline model for crops harvested in different months from conventional fields, an estimated 13 out of 257 (5.05%) first crops harvested in July would have at least one plant with at least 1 CFU of
E. coli
O157:H7. Predictions indicate that no first crops would be contaminated with at least 1 CFU of
E. coli
O157:H7 for other months (April to June). The maximum
E. coli
O157:H7 concentration in a plant was higher in the second crop (27.10 CFU) than in the first crop (9.82 CFU). For the second crop, the probabilities of having at least one plant with at least 1 CFU of
E. coli
O157:H7 in a crop were predicted as 15/228 (6.6%), 5/333 (1.5%), 14/324 (4.3%), and 6/115 (5.2%) in August, September, October, and November, respectively. For organic fields, the probabilities of having at least one plant with ≥1 CFU of
E. coli
O157:H7 in a crop (3.45%) were predicted to be higher than those for the conventional fields (2.15%).

IMPORTANCE
This study is the first attempt toward developing a mathematical system model to understand the pathway of
E. coli
O157:H7 in the production of leafy greens. Results of the presented system model indicate that the seasonality of outbreaks of
E. coli
O157:H7-associated contamination of leafy greens was in good agreement with the prevalence of this pathogen in cattle and wild pig feces in a major leafy greens-producing region in California. On the basis of comparisons among the results of different scenarios, it can be recommended that the concentration of
E. coli
O157:H7 in leafy greens can be reduced considerably if contamination of soil with wild pig and cattle feces is mitigated.
The Behavior of Staphylococcus aureus Dual-Species Biofilms Treated with Bacteriophage phiIPLA-RODI Depends on the Accompanying Microorganism
Authors: González Silvia , Fernández Lucía , Campelo Ana Belén , Gutiérrez Diana , Martínez Beatriz , Rodríguez Ana , García Pilar
Published: November 2016

The use of bacteriophages as antimicrobials against pathogenic bacteria offers a promising alternative to traditional antibiotics and disinfectants. Significantly, phages may help to remove biofilms, which are notoriously resistant to commonly used eradication methods. However, the successful development of novel antibiofilm strategies must take into account that real-life biofilms usually consist of mixed-species populations. Within this context, this study aimed to explore the effectiveness of bacteriophage-based sanitation procedures for removing polymicrobial biofilms from food industry surfaces. We treated dual-species biofilms formed by the food pathogenic bacterium
Staphylococcus aureus
in combination with
Lactobacillus plantarum
,
Enterococcus faecium
, or
Lactobacillus pentosus
with the staphylococcal phage phiIPLA-RODI. Our results suggest that the impact of bacteriophage treatment on
S. aureus
mixed-species biofilms varies depending on the accompanying species and the infection conditions. For instance, short treatments (4 h) with a phage suspension under nutrient-limiting conditions reduced the number of
S. aureus
cells in 5-h biofilms by ∼1 log unit without releasing the nonsusceptible species. In contrast, longer infection periods (18 h) with no nutrient limitation increased the killing of
S. aureus
cells by the phage (decrease of up to 2.9 log units). However, in some cases, these conditions promoted the growth of the accompanying species. For example, the
L. plantarum
cell count in the treated sample was up to 2.3 log units higher than that in the untreated control. Furthermore, phage propagation inside dual-species biofilms also depended greatly on the accompanying species, with the highest rate detected in biofilms formed by
S. aureus
-
L. pentosus
. Scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM) also showed changes in the three-dimensional structures of the mixed-species biofilms after phage treatment. Altogether, the results presented here highlight the need to study the impact of phage therapy on microbial communities that reflect a more realistic setting.

IMPORTANCE
Biofilms represent a major source of contamination in industrial and hospital settings. Therefore, developing efficient strategies to combat bacterial biofilms is of the utmost importance from medical and economic perspectives. Bacteriophages have shown potential as novel antibiofilm agents, but further research is still required to fully understand the interactions between phages and biofilm-embedded bacteria. The results presented in this study contribute to achieving a better understanding of such interactions in a more realistic context, considering that most biofilms in the environment consist of mixed-species populations.
Genome Sequence of a Potential New Benyvirus Isolated from Mango RNA-seq Data
Authors: Sela Noa , Luria Neta , Yaari Mor , Prusky Dov , Dombrovsky Aviv
Published: November 2016

We report here the sequence of a new benyvirus found through mango cultivar Shelly RNA-seq analysis in Israel. This is the first virus strain reported in mango trees.
Alternative route for biosynthesis of amino sugars in Escherichia coli K-12 mutants by means of a catabolic isomerase
Authors: Vogler A P , Trentmann S , Lengeler J W
Published: November 2016

By inserting a lambda placMu bacteriophage into gene glmS encoding glucosamine 6-phosphate synthetase (GlmS), the key enzyme of amino sugar biosynthesis, a nonreverting mutant of Escherichia coli K-12 that was strictly dependent on exogenous N-acetyl-D-glucosamine or D-glucosamine was generated. Analysis of suppressor mutations rendering the mutant independent of amino sugar supply revealed that the catabolic enzyme D-glucosamine-6-phosphate isomerase (deaminase), encoded by gene nagB of the nag operon, was able to fulfill anabolic functions in amino sugar biosynthesis. The suppressor mutants invariably expressed the isomerase constitutively as a result of mutations in nagR, the locus for the repressor of the nag regulon. Suppression was also possible by transformation of glmS mutants with high-copy-number plasmids expressing the gene nagB. Efficient suppression of the glmS lesion, however, required mutations in a second locus, termed glmX, which has been localized to 26.8 min on the standard E. coli K-12 map. Its possible function in nitrogen or cell wall metabolism is discussed.
Regulator and enzyme specificities of the TOL plasmid-encoded upper pathway for degradation of aromatic hydrocarbons and expansion of the substrate range of the pathway
Authors: Abril M A , Michan C , Timmis K N , Ramos J L
Published: November 2016

The TOL plasmid upper pathway operon encodes enzymes involved in the catabolism of aromatic hydrocarbons such as toluene and xylenes. The regulator of the gene pathway, the XylR protein, exhibits a very broad effector specificity, being able to recognize as effectors not only pathway substrates but also a wide variety of mono- and disubstituted methyl-, ethyl-, and chlorotoluenes, benzyl alcohols, and p-chlorobenzaldehyde. Benzyl alcohol dehydrogenase and benzaldehyde dehydrogenase, two upper pathway enzymes, exhibit very broad substrate specificities and transform unsubstituted substrates and m- and p-methyl-, m- and p-ethyl-, and m- and p-chloro-substituted benzyl alcohols and benzaldehydes, respectively, at a high rate. In contrast, toluene oxidase only oxidizes toluene, m- and p-xylene, m-ethyltoluene, and 1,2,4-trimethylbenzene [corrected], also at a high rate. A biological test showed that toluene oxidase attacks m- and p-chlorotoluene, albeit at a low rate. No evidence for the transformation of p-ethyltoluene by toluene oxidase has been found. Hence, toluene oxidase acts as the bottleneck step for the catabolism of p-ethyl- and m- and p-chlorotoluene through the TOL upper pathway. A mutant toluene oxidase able to transform p-ethyltoluene was isolated, and a mutant strain capable of fully degrading p-ethyltoluene was constructed with a modified TOL plasmid meta-cleavage pathway able to mineralize p-ethylbenzoate. By transfer of a TOL plasmid into Pseudomonas sp. strain B13, a clone able to slowly degrade m-chlorotoluene was also obtained.
The GLN3 gene product is required for transcriptional activation of allantoin system gene expression in Saccharomyces cerevisiae
Authors: Cooper T G , Ferguson D , Rai R , Bysani N
Published: November 2016

We show that mutation at the GLN3 locus results in decreased steady-state levels of DAL7, DUR1,2, CAR1, and URA3 mRNAs derived from cultures grown in the presence of inducer. Basal levels of these RNA species, however, were not significantly affected by a gln3 mutation. The GLN3 product appears to affect gene expression in two ways. The pleiotropic requirement of GLN3 for induced gene expression probably derives from the need of the GLN3 product for inducer uptake into the cell and its loss in gln3 mutants. We also demonstrate that transcriptional activation, mediated by the DAL5 and DAL7 upstream activation sequences, requires a functional GLN3 gene product. This observation identified transcriptional activation as the most likely point of GLN3 participation in the expression of allantoin system genes.
Genetic mapping of the structural gene for phospholipase C of Pseudomonas aeruginosa PAO
Authors: Lindgren V , Ostroff R M , Vasil M L , Wretlind B
Published: November 2016

An insertion mutation constructed by gene replacement methods was used to map the gene corresponding to the hemolytic phospholipase C (plcS gene) in Pseudomonas aeruginosa PAO1 by R68.45-mediated conjugation. plcS mapped approximately at 67 min on the 75-min chromosomal map (B. W. Holloway, K. O'Hoy, and H. Matsumoto, p. 213-221, in S. J. O'Brien, ed., Genetic Maps 1987, vol. 4, 1987), between the markers pur-67 and pru-375 and considerably distal to the regulatory genes plcA and plcB, which are located at approximately 12 min.
Chromosome engineering in Saccharomyces cerevisiae by using a site-specific recombination system of a yeast plasmid
Authors: Matsuzaki H , Nakajima R , Nishiyama J , Araki H , Oshima Y
Published: November 2016

We have developed an effective method to delete or invert a chromosomal segment and to create reciprocal recombination between two nonhomologous chromosomes in Saccharomyces cerevisiae, using the site-specific recombination system of pSR1, a circular cryptic DNA plasmid resembling 2 microns DNA of S. cerevisiae but originating from another yeast, Zygosaccharomyces rouxii. A 2.1-kilobase-pair DNA fragment bearing the specific recombination site on the inverted repeats of pSR1 was inserted at target sites on a single or two different chromosomes of S. cerevisiae by using integrative vectors. The cells were then transformed with a plasmid bearing the R gene of pSR1, which encodes the site-specific recombination enzyme and is placed downstream of the GAL1 promoter. When the transformants were cultivated in galactose medium, the recombination enzyme produced by expression of the R gene created the modified chromosome(s) by recombination between two specific recombination sites inserted on the chromosome(s).
Presence of chromosomal elements resembling the composite structure Tn3701 in streptococci
Authors: Le Bouguénec C , de Cespédès G , Horaud T
Published: November 2016

Tn3701, carried by Streptococcus pyogenes A454, is the first chromosomal composite element to be described; it contains in its central region Tn3703, a transposon similar to Tn916. A comparison by DNA-DNA hybridization of Tn3701 with omega(cat-tet) and Tn3951, carried by Streptococcus pneumoniae BM6001 and by Streptococcus agalactiae B109, respectively, revealed that the two latter structures are also Tn3701-like composite elements. The DNAs of 27 other antibiotic-resistant group A, B, C, and G streptococci and of S. pneumoniae BM4200 showed sequence homologies to Tn3701 (14 strains, including BM4200), to the regions of Tn3701 outside of Tn3703 (5 strains), and to Tn916 alone (8 strains). The DNAs of five strains did not detectably hybridize with any probe. The tetM gene was identified in most chromosomal genetic elements coding for tetracycline-minocycline resistance. Since Tn3701-like elements are widely disseminated among antibiotic-resistant streptococci (47% of the 34 strains studied), we propose that Tn3701 be considered the prototype of chromosomal composite elements.
Structural and chemical characterization of the S layer of a Pseudomonas-like bacterium
Authors: Austin J W , Stewart M , Murray R G
Published: November 2016

Sections and freeze-fractured preparations showed an S layer on the surface of Pseudomonas-like strain EU2. Polyacrylamide gel electrophoresis of cell envelopes extracted with 1% sodium dodecyl sulfate (SDS) at room temperature showed three proteins (45K, 55K, and 110K). The 55K protein was identified as the S-layer protein. Incubation in 1.5 M guanidine hydrochloride removed the S layer from cell envelopes and dissociated the structure into subunits. The soluble 55K protein reassembled into planar sheets upon removal of the guanidine hydrochloride by dialysis. Electron microscopy and image processing indicated that these sheets had p4 symmetry in projection with a lattice constant of 13.2 +/- 0.1 nm (corresponding to 9.3 nm between adjacent fourfold axes). In some instances these reassemblies appeared to form small three-dimensional crystals which gave particularly clear views of the structure in projection because of the superimposition of information from a number of layers. A model is proposed with molecules having rounded lobes connected by a narrower linker region and joining at the lobes to form the fourfold axes of the array. The pattern superficially resembles those of other bacterial S layers, such as those of Aeromonas salmonicida, Aeromonas hydrophila, and Azotobacter vinelandii. Extraction of cell envelopes with 1% SDS at 50 degrees C released the 110K protein from the envelopes and removed an amorphous backing layer from the S layer. The 45K protein displayed heat-modifiable migration in SDS-polyacrylamide gel electrophoresis and was insoluble in SDS at 50 degrees C or in high concentrations of guanidine hydrochloride, suggesting that it was associated with the peptidoglycan.
Purification and characterization of fatty acid beta-oxidation enzymes from Caulobacter crescentus
Authors: O'Connell M A , Orr G , Shapiro L
Published: November 2016

Acetoacetyl coenzyme A (acetoacetyl-CoA) thiolase, an enzyme required for short-chain fatty acid degradation, has been purified to near homogeneity from Caulobacter crescentus. The relative heat stability of this enzyme allowed it to be separated from beta-ketoacyl-CoA thiolase. The purification scheme minus the heating step also permitted the copurification of crotonase and 3-hydroxyacyl-CoA dehydrogenase. These activities are in a multienzyme complex in Escherichia coli, but a similar complex was not observed in C. crescentus. Instead, separate proteins differing in enzymatic activity were detected, analogous to the beta-oxidation enzymes that have been isolated from Clostridium acetobutylicum and from mitochondria of higher eucaryotes. In these cells, as appears to be the case with C. crescentus, the individual enzymes form multimers of identical subunits.
Identification of an Escherichia coli genetic locus involved in thermoregulation of the pap operon
Authors: White-Ziegler C A , Blyn L B , Braaten B A , Low D A
Published: November 2016

We previously showed, using a single-copy papBAp-lac fusion (previously designated papBA-lac), that pyelonephritis-associated pili (pap) pilin gene transcription is subject to both phase variation and thermoregulatory control mechanisms (L. B. Blyn, B. A. Braaten, C. A. White-Ziegler, D. H. Rolfson, and D. A. Low, EMBO J. 8:613-620, 1989). At 37 degrees C, Escherichia coli strains carrying the papBAp-lac fusion displayed both Lac+ and Lac- colony phenotypes. In contrast, at 23 degrees C, colonies displayed a uniform Lac- phenotype, suggesting that pilin was not transcribed at this temperature. In this study, a strain carrying the papBAp-lac fusion was subjected to mini-Tn10 (mTn10) mutagenesis to isolate mutants that could initiate transcription of pilin at the nonpermissive temperature. Two classes of thermoregulatory mutants were identified in which the mTn10 mutation was linked to the mutant phenotype. Class I mutants displayed a phase variation phenotype at both 37 degrees C and 23 degrees C, whereas class II mutants displayed a uniform Lac+ colony phenotype at both temperatures. Preliminary analysis of these mutants showed that the mTn10 insertions in the class I mutants were chromosomally located, whereas the mTn10 insertions in the class II mutants were located within the papBAp-lac fusion phage. Southern blot analysis of the class I mutants demonstrated that mTn10 was present in the same 5.9-kilobase SalI DNA fragment in each mutant. Two of the class I mTn10 mutations were mapped to approximately 23.4 min on the E. coli K-12 chromosome. The locus defined by the class I mTn10 mutations was designated tcp, for thermoregulatory control of pap. Analysis of phase transition rates of the class I mutants showed that the phase-off (Lac-)----phase-on (Lac+) transition rates were higher than those observed with the nonmutant E. coli strain.
The HtrA (DegP) protein, essential for Escherichia coli survival at high temperatures, is an endopeptidase
Authors: Lipinska B , Zylicz M , Georgopoulos C
Published: November 2016

As a preliminary step in the understanding of the function of the Escherichia coli HtrA (DegP) protein, which is indispensable for bacterial survival only at elevated temperatures, the protein was purified and partially characterized. The HtrA protein was purified from cells carrying the htrA gene cloned into a multicopy plasmid, resulting in its overproduction. The sequence of the 13 N-terminal amino acids of the purified HtrA protein was determined and was identical to the one predicted for the mature HtrA protein by the DNA sequence of the cloned gene. Moreover, the N-terminal sequence showed that the 48-kilodalton HtrA protein is derived by cleavage of the first 26 amino acids of the pre-HtrA precursor polypeptide and that the point of cleavage follows a typical target sequence recognized by the leader peptidase enzyme. The HtrA protein was shown to be a specific endopeptidase which was inhibited by diisopropylfluorophosphate, suggesting that HtrA is a serine protease.