bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reducing Salt in Raw Pork Sausages Increases Spoilage and Correlates with Reduced Bacterial Diversity
Authors: Fougy Lysiane , Desmonts Marie-Hélène , Coeuret Gwendoline , Fassel Christine , Hamon Erwann , Hézard Bernard , Champomier-Vergès Marie-Christine , Chaillou Stéphane 
Published: April 2016

ABSTRACT

Raw sausages are perishable foodstuffs; reducing their salt content raises questions about a possible increased spoilage of these products. In this study, we evaluated the influence of salt reduction (from 2.0% to 1.5% [wt/wt]), in combination with two types of packaging (modified atmosphere [50% mix of CO
2
-N
2
] and vacuum packaging), on the onset of spoilage and on the diversity of spoilage-associated bacteria. After 21 days of storage at 8°C, spoilage was easily observed, characterized by noticeable graying of the products and the production of gas and off-odors defined as rancid, sulfurous, or sour. At least one of these types of spoilage occurred in each sample, and the global spoilage intensity was more pronounced in samples stored under modified atmosphere than under vacuum packaging and in samples with the lower salt content. Metagenetic 16S rRNA pyrosequencing revealed that vacuum-packaged samples contained a higher total bacterial richness (
n
= 69 operational taxonomic units [OTUs]) than samples under the other packaging condition (
n
= 46 OTUs). The core community was composed of 6 OTUs (
Lactobacillus sakei
,
Lactococcus piscium
,
Carnobacterium divergens
,
Carnobacterium maltaromaticum
,
Serratia proteamaculans
, and
Brochothrix thermosphacta
), whereas 13 OTUs taxonomically assigned to the
Enterobacteriaceae
,
Enterococcaceae
, and
Leuconostocaceae
families comprised a less-abundant subpopulation. This subdominant community was significantly more abundant when 2.0% salt and vacuum packaging were used, and this correlated with a lower degree of spoilage. Our results demonstrate that salt reduction, particularly when it is combined with CO
2
-enriched packaging, promotes faster spoilage of raw sausages by lowering the overall bacterial diversity (both richness and evenness).

IMPORTANCE
Our study takes place in the context of raw meat product manufacturing and is linked to a requirement for salt reduction. Health guidelines are calling for a reduction in dietary salt intake. However, salt has been used for a very long time as a hurdle technology, and salt reduction in meat products raises the question of spoilage and waste of food. The study was conceived to assess the role of sodium chloride reduction in meat products, both at the level of spoilage development and at the level of bacterial diversity, using 16S rRNA amplicon sequencing and raw pork sausage as a meat model.
Detection and Molecular Characterization of Hepatitis A Virus from Tunisian Wastewater Treatment Plants with Different Secondary Treatments
Authors: Ouardani Imen , Turki Syrine , Aouni Mahjoub , Romalde Jesús L. 
Published: April 2016

ABSTRACT

Hepatitis A virus (HAV) is the main causative agent of hepatitis infection associated with waterborne outbreaks worldwide. In Tunisia, there is no specific surveillance system for HAV and current secondary wastewater treatment processes are unable to remove viral particles, which present a potential public health problem. Qualitative and quantitative analysis of HAV in 271 raw and treated wastewater samples from five sewage treatment plants (STPs) during 13 months was performed. Moreover, the efficiency of three secondary wastewater treatment processes (conventional activated sludge, extended aeration, and oxidation ditch activated sludge) was evaluated. Data obtained demonstrated that HAV is endemic in Tunisia and circulates with high prevalence in both raw (66.9%) and treated (40.7%) wastewater. HAV circulates throughout the year in the coastal areas, with the highest rates found during summer and autumn, whereas in central Tunisia, high levels were shown in autumn and winter. Total virus removal was not achieved, since no difference in mean HAV loads was observed in effluents (6.0 × 10
3
genome copies [GC]/ml) and influents (2.7 × 10
3
GC/ml). The comparison of the HAV removal values of the three different wastewater treatment methods indicates that extended aeration and oxidation ditch activated sludge had better efficiency in removing viruses than conventional activated sludge did. Molecular characterization revealed that the vast majority of HAV strains belonged to subgenotype IA, with the cocirculation of subgenotype IB in wastewater treatment plants that collect tourism wastewater.

IMPORTANCE
This report provides important data on the incidence, behavior, seasonality, and genotype distribution of HAV in the environment in Tunisia, as well as the risk of infection derived from its occurrence in effluents due to inadequate wastewater treatment. In addition, these findings seem to confirm that the prevalence of HAV depends on socioeconomic level, sanitary conditions in the communities, sewage facilities, the locality, and the climate. The wide dispersion of HAV in effluents proves the inefficacity of the current wastewater treatment processes used in Tunisia to remove virus; therefore, establishment of tertiary treatment processes or replacement of the medium-charge activated sludge (conventional activated sludge) by the low-charge version (oxidation ditch activated sludge) is absolutely needed. Rapid detection of the HAV genome in wastewater may provide a timely warning sign to health authorities to implement population protection measures.
Transcriptome and Secretome Analyses of the Wood Decay Fungus Wolfiporia cocos Support Alternative Mechanisms of Lignocellulose Conversion
Authors: Gaskell Jill , Blanchette Robert A. , Stewart Philip E. , BonDurant Sandra Splinter , Adams Marie , Sabat Grzegorz , Kersten Phil , Cullen Dan 
Published: April 2016

ABSTRACT

Certain wood decay basidiomycetes, collectively referred to as brown rot fungi, rapidly depolymerize cellulose while leaving behind the bulk of cell wall lignin as a modified residue. The mechanism(s) employed is unclear, but considerable evidence implicates the involvement of diffusible oxidants generated via Fenton-like chemistry. Toward a better understanding of this process, we have examined the transcriptome and secretome of
Wolfiporia cocos
when cultivated on media containing glucose, purified crystalline cellulose, aspen (
Populus grandidentata
), or lodgepole pine (
Pinus contorta
) as the sole carbon source. Compared to the results obtained with glucose, 30, 183, and 207 genes exhibited 4-fold increases in transcript levels in cellulose, aspen, and lodgepole pine, respectively. Mass spectrometry identified peptides corresponding to 64 glycoside hydrolase (GH) proteins, and of these, 17 corresponded to transcripts upregulated on one or both woody substrates. Most of these genes were broadly categorized as hemicellulases or chitinases. Consistent with an important role for hydroxyl radical in cellulose depolymerization, high transcript levels and upregulation were observed for genes involved in iron homeostasis, iron reduction, and extracellular peroxide generation. These patterns of regulation differ markedly from those of the closely related brown rot fungus
Postia placenta
and expand the number of enzymes potentially involved in the oxidative depolymerization of cellulose.

IMPORTANCE
The decomposition of wood is an essential component of nutrient cycling in forest ecosystems. Few microbes have the capacity to efficiently degrade woody substrates, and the mechanism(s) is poorly understood. Toward a better understanding of these processes, we show that when grown on wood as a sole carbon source the brown rot fungus
W. cocos
expresses a unique repertoire of genes involved in oxidative and hydrolytic conversions of cell walls.
A β-Alanine Catabolism Pathway Containing a Highly Promiscuous ω-Transaminase in the 12-Aminododecanate-Degrading Pseudomonas sp. Strain AAC
Authors: Wilding Matthew , Peat Thomas S. , Newman Janet , Scott Colin 
Published: April 2016

ABSTRACT

We previously isolated the transaminase KES23458 from
Pseudomonas
sp. strain AAC as a promising biocatalyst for the production of 12-aminododecanoic acid, a constituent building block of nylon-12. Here, we report the subsequent characterization of this transaminase. It exhibits activity with a broad substrate range which includes α-, β-, and ω-amino acids, as well as α,ω-diamines and a number of other industrially relevant compounds. It is therefore a prospective candidate for the biosynthesis of a range of polyamide monomers. The crystal structure of KES23458 revealed that the protein forms a dimer containing a large active site pocket and unusual phosphorylated histidine residues. To infer the physiological role of the transaminase, we expressed, purified, and characterized a dehydrogenase from the same operon, KES23460. Unlike the transaminase, the dehydrogenase was shown to be quite selective, catalyzing the oxidation of malonic acid semialdehyde, formed from β-alanine transamination via KES23458. In keeping with previous reports, the dehydrogenase was shown to catalyze both a coenzyme A (CoA)-dependent reaction to form acetyl-CoA and a significantly slower CoA-independent reaction to form acetate. These findings support the original functional assignment of KES23458 as a β-alanine transaminase. However, a seemingly well-adapted active site and promiscuity toward unnatural compounds, such as 12-aminododecanoic acid, suggest that this enzyme could perform multiple functions for
Pseudomonas
sp. strain AAC.

IMPORTANCE
We describe the characterization of an industrially relevant transaminase able to metabolize 12-aminododecanoic acid, a constituent building block of the widely used polymer nylon-12, and we report the biochemical and structural characterization of the transaminase protein. A physiological role for this highly promiscuous enzyme is proposed based on the characterization of a related gene from the host organism. Molecular dynamics simulations were carried out to compare the conformational changes in the transaminase protein to better understand the determinants of specificity in the protein. This study makes a substantial contribution that is of interest to the broad biotechnology and enzymology communities, providing insights into the catalytic activity of an industrially relevant biocatalyst as well as the biological function of this operon.
Alternative Biotransformation of Retinal to Retinoic Acid or Retinol by an Aldehyde Dehydrogenase from Bacillus cereus
Authors: Hong Seung-Hye , Ngo Ho-Phuong-Thuy , Nam Hyun-Koo , Kim Kyoung-Rok , Kang Lin-Woo , Oh Deok-Kun 
Published: April 2016

ABSTRACT

A novel bacterial aldehyde dehydrogenase (ALDH) that converts retinal to retinoic acid was first identified in
Bacillus cereus
. The amino acid sequence of ALDH from
B. cereus
(
Bc
ALDH) was more closely related to mammalian ALDHs than to bacterial ALDHs. This enzyme converted not only small aldehydes to carboxylic acids but also the large aldehyde all-
trans
-retinal to all-
trans
-retinoic acid with NAD(P)
+
. We newly found that
Bc
ALDH and human ALDH (ALDH1A1) could reduce all-
trans
-retinal to all-
trans
-retinol with NADPH. The catalytic residues in
Bc
ALDH were Glu266 and Cys300, and the cofactor-binding residues were Glu194 and Glu457. The E266A and C300A variants showed no oxidation activity. The E194S and E457V variants showed 15- and 7.5-fold higher catalytic efficiency (
k
cat
/

K
m

) for the reduction of all-
trans
-retinal than the wild-type enzyme, respectively. The wild-type, E194S variant, and E457V variant enzymes with NAD
+
converted 400 μM all-
trans
-retinal to 210 μM all-
trans
-retinoic acid at the same amount for 240 min, while with NADPH, they converted 400 μM all-
trans
-retinal to 20, 90, and 40 μM all-
trans
-retinol, respectively. These results indicate that
Bc
ALDH and its variants are efficient biocatalysts not only in the conversion of retinal to retinoic acid but also in its conversion to retinol with a cofactor switch and that retinol production can be increased by the variant enzymes. Therefore,
Bc
ALDH is a novel bacterial enzyme for the alternative production of retinoic acid and retinol.

IMPORTANCE
Although mammalian ALDHs have catalyzed the conversion of retinal to retinoic acid with NAD(P)
+
as a cofactor, a bacterial ALDH involved in the conversion is first characterized. The biotransformation of all-
trans
-retinal to all-
trans
-retinoic acid by
Bc
ALDH and human ALDH was altered to the biotransformation to all-
trans
-retinol by a cofactor switch using NADPH. Moreover, the production of all-
trans
-retinal to all-
trans
-retinol was changed by mutations at positions 194 and 457 in
Bc
ALDH. The alternative biotransformation of retinoids was first performed in the present study. These results will contribute to the biotechnological production of retinoids, including retinoic acid and retinol.
Activation of an Otherwise Silent Xylose Metabolic Pathway in Shewanella oneidensis
Authors: Sekar Ramanan , Shin Hyun Dong , DiChristina Thomas J. 
Published: April 2016

ABSTRACT

Shewanella oneidensis
is unable to metabolize the sugar xylose as a carbon and energy source. In the present study, an otherwise silent xylose catabolic pathway was activated in
S. oneidensis
by following an adaptive evolution strategy. Genome-wide scans indicated that the
S. oneidensis
genome encoded two proteins similar to the xylose oxido-reductase pathway enzymes xylose reductase (SO_0900) and xylulokinase (SO_4230), and purified SO_0900 and SO_4230 displayed xylose reductase and xylulokinase activities, respectively. The
S. oneidensis
genome was missing, however, an
Escherichia coli
XylE-like xylose transporter. After 12 monthly transfers in minimal growth medium containing successively higher xylose concentrations, an
S. oneidensis
mutant (termed strain XM1) was isolated for the acquired ability to grow aerobically on xylose as a carbon and energy source. Whole-genome sequencing indicated that strain XM1 contained a mutation in an unknown membrane protein (SO_1396) resulting in a glutamine-to-histidine conversion at amino acid position 207. Homology modeling demonstrated that the Q207H mutation in SO_1396 was located at the homologous xylose docking site in XylE. The expansion of the
S. oneidensis
metabolic repertoire to xylose expands the electron donors whose oxidation may be coupled to the myriad of terminal electron-accepting processes catalyzed by
S. oneidensis
. Since xylose is a lignocellulose degradation product, this study expands the potential substrates to include lignocellulosic biomass.

IMPORTANCE
The activation of an otherwise silent xylose metabolic system in
Shewanella oneidensis
is a powerful example of how accidental mutations allow microorganisms to adaptively evolve. The expansion of the
S. oneidensis
metabolic repertoire to xylose expands the electron donors whose oxidation may be coupled to the myriad of terminal electron-accepting processes catalyzed by
S. oneidensis
. Since xylose is a lignocellulose degradation product, this study expands the potential substrates to include lignocellulosic biomass.
Recreational drug use in the Oslo nightlife setting: study protocol for a cross-sectional time series using biological markers, self-reported and qualitative data
Authors: Nordfjærn Trond , Edland-Gryt Marit , Bretteville-Jensen Anne Line , Buvik Kristin , Gripenberg Johanna 
Published: April 2016

IntroductionRecreational drug use in the nightlife setting carries the risk of many negative consequences, such as violence, injuries, aberrant driving and sexual risk-taking. The aim of this study is to investigate recreational drug use and user characteristics among people visiting licensed premises, for example, nightclubs and bars, by using self-reports and biological markers. Staff of licensed premises will be asked to report drug use observations. Further, by using qualitative data, we will examine the motives, consequences and culture associated with recreational drug use. An additional aim is to compare self-reported drug use with oral fluid test (OFT) results in order to validate the different measurement methods in this context.Methods and analysesData collection will be conducted among patrons (n=1000) outside licensed premises. On consent, patrons will be asked to anonymously complete a questionnaire, a breath alcohol concentration test and an OFT. Patrons who report use of recreational drugs in the previous 12 months will be asked to leave their contact information for a subsequent qualitative in-depth interview (n=30–40). Staff from licensed premises (n=500) will be invited during Responsible Beverage Service Training to participate in an anonymous survey. Survey data will be analysed by univariate and multivariate statistical methods and the oral fluids will be analysed for a large number of drugs using biochemical methods. Cohen's κ will be used as a measure of agreement between self-reported drug use and OFT. In-depth interviews will be coded in HyperRESEARCH and analysed using an inductive approach. Data collection will be repeated on a biannual basis until at least 2020, allowing for examination of trends in recreational drug use.Ethics and disseminationThis study has been approved by the Regional Committee for Medical and Health Research Ethics. Results will be disseminated in research journals, conferences and the media.
Assisted reproductive technology and risk of asthma and allergy in the offspring: protocol for a systematic review and meta-analysis
Authors: Nwaru Bright I , McCleary Nicola , Erkkola Maijaliisa , Kaila Minna , Virtanen Suvi M , Sheikh Aziz 
Published: April 2016

IntroductionThe use of assisted reproductive technology (ART) procedures has increased globally over the last three decades. Recent observational studies suggest that children conceived through ART may be at increased risk of asthma and atopic disease compared with children conceived naturally, but findings are mixed. We aim to synthesise the evidence on the impact of ART on the risk of asthma and atopic disease in the offspring.Methods and analysisWe will identify relevant studies by searching MEDLINE, EMBASE, Cochrane Library, ISI Web of Science, CINAHL, Scopus, Google Scholar, AMED, Global Health, PsychINFO, CAB International and the WHO Global Health Library from 1978 to 2016. We will locate additional studies through searching databases of the proceedings of international conferences, contacting international experts in the field, and searching the references cited in identified studies. We will include analytic observational studies (cohort studies, case–control studies and cross-sectional studies) that have investigated the impact of any type of ART on offspring's asthma and atopic disease. Screening of identified records, data extraction from eligible studies and risk of bias assessment of eligible studies will be independently undertaken by two reviewers, with arbitration by a third reviewer. The Effective Public Health Practice Project will be employed for risk of bias assessment. Estimates from studies judged to be clinically, methodologically and statistically homogeneous will be synthesised using random-effects meta-analysis.Ethics and disseminationAs this study is based solely on the published literature, no ethics approval is required. We will publish our findings in a peer-reviewed scientific journal and present the results at national and international scientific conferences.Protocol registrationWe will register a detailed protocol for the review with the International Prospective Register of Systematic Reviews (PROSPERO) prior to starting the review.
Protocol for systematic review and meta-analysis: hop (Humulus lupulusL.) for menopausal vasomotor symptoms
Authors: Abdi Fatemeh , Kazemi Farideh , Ramezani Tehrani Fahimeh , Roozbeh Nasibeh 
Published: April 2016

IntroductionMenopause is a critical stage in every woman's life. It can cause a distressing time for women by creating various vasomotor symptoms (VMS). Phytoestrogens can potentially exert various favourable effects and alleviate VMS in postmenopausal women. The hop (Humulus lupulusL.) contains 8-prenylnaringenin (8-PN), the most potent phytoestrogen known to date. The hop is eight times stronger than any other herbal oestrogens. This study aims to conduct a comprehensive systematic review and a meta-analysis survey of the effects of hop in the management of VMS in postmenopausal women.MethodsOnly randomised controlled clinical trials, with cluster randomisation and crossover, blinded and non-blinded designs, conducted between 2000 and 2015, will be included in this review. Quasi-experimental and observational studies as well as case reports will be excluded. The studies will be selected if their participants were aged 40–60 years, had elevated follicle-stimulating hormone (FSH) levels and/or menstrual irregularities, and experienced discomforting VMS (at least hot flashes or night sweats). The primary outcome will be the rate of response to treatment, such as changes in frequency and intensity of symptoms in the intervention and placebo groups. ‘Hop’, ‘Humulus’, ‘menopause’, ‘vasomotor’, ‘hot flashes’, ‘phytoestrogen’ and ‘night sweats’ will be used as search key words. Prior to their inclusion in the review, the selected papers will be assessed by two independent reviewers for methodological validity. Any disagreements will be resolved through a third reviewer. The risk of bias will be independently determined using the Cochrane Risk of Bias Tool. The quality of the papers will be assessed based on the CONSORT checklist.Ethics and disseminationResults will be disseminated through traditional academic literature. Dissemination of results will occur by peer-reviewed publications. The results of our project can help reproductive health researchers when evaluating the discomforts of research procedures described in study protocols or when designing a study. Information on experiences of menopausal women involved in previous studies may also help in future research. The expected dissemination actions are effective treatment in designing strategies that aim to develop women's health and healthcare providers when offering treatment for women with vasomotor symptoms.