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Changes of membrane fatty acids and proteins of Shewanella putrefaciens treated with cinnamon oil and gamma irradiation
No full textAbstract
Background
In order to detect the antimicrobial mechanism of combined treatment of cinnamon oil and gamma irradiation (GI), the membrane fatty acids and proteins characteristics of Shewanella putrefaciens ( S. putrefaciens ) treated with cinnamon oil and GI, and the distribution of cinnamon oil in S. putrefaciens were observed in this study.
Results
The membrane lipid profile of S. putrefaciens was notably damaged by treatments of cinnamon oil and the combination of cinnamon oil and GI, with significantly fatty acids decrease in C14:0, C16:0, C16:1, C17:1, C18:1 ( p \ua0<\ua00.05). The SDS-PAGE result showed that GI did not have obvious effect on membrane proteins (MP), but GI combined with cinnamon oil changed the MP subunits. Cinnamaldehyde, the main component of cinnamon oil, can not transport into S. putrefaciens obviously. It was transformed into cinnamyl alcohol in the nutrient broth with the action of S. putrefaciens . This indicated that the antimicrobial action of cinnamon oil mainly happened on the membrane of S. putrefaciens.
Conclusion
Cinnamon oil could act on the membrane of S. putrefaciens with the damage of fatty acids and proteins, and GI would increase the destructive capability of cinnamon oil on the membrane fatty acids and proteins of S. putrefaciens
Genetic analysis of teat number in pigs reveals some developmental pathways independent of vertebra number and several loci which only affect a specific side
No full textAbstract
Background
Number of functional teats is an important trait in commercial swine production. As litter size increases, the number of teats must also increase to supply nutrition to all piglets. Therefore, a genome-wide association analysis was conducted to identify genomic regions that affect this trait in a commercial swine population. Genotypic data from the Illumina Porcine SNP60v1 BeadChip were available for 2951 animals with total teat number (TTN) records. A subset of these animals (n\ua0=\ua01828) had number of teats on each side recorded. From this information, the following traits were derived: number of teats on the left (LTN) and right side (RTN), maximum number of teats on a side (MAX), difference between LTN and RTN (L\ua0\u2212\ua0R) and absolute value of L\ua0\u2212\ua0R (DIF). Bayes C option of GENSEL (version 4.61) and 1-Mb windows were implemented. Identified regions that explained more than 1.5% of the genomic variation were tested in a larger group of animals (n\ua0=\ua05453) to estimate additive genetic effects.
Results
Marker heritabilities were highest for TTN (0.233), intermediate for individual side counts (0.088\ua0to\ua00.115) and virtually nil for difference traits (0.002 for L\ua0\u2212\ua0R and 0.006 for DIF). Each copy of the VRTN mutant allele increased teat count by 0.35 (TTN), 0.16 (LTN and RTN) and 0.19 (MAX). 15, 18, 13 and 18 one-Mb windows were detected that explained more than 1.0% of the genomic variation for TTN, LTN, RTN, and MAX, respectively. These regions cumulatively accounted for over 50% of the genomic variation of LTN, RTN and MAX, but only 30% of that of TTN. Sus scrofa chromosome SSC10:52\ua0Mb was associated with all four count traits, while SSC10:60 and SSC14:54\ua0Mb were associated with three count traits. Thirty-three SNPs accounted for nearly 39% of the additive genetic variation in the validation dataset. No effect of piglet sex or percentage of males in litter was detected, but birth weight was positively correlated with TTN.
Conclusions
Teat number is a heritable trait and use of genetic markers would expedite selection progress. Exploiting genetic variation associated with teat counts on each side would enhance selection focused on total teat counts. These results confirm QTL on SSC4, seven and ten and identify a novel QTL on SSC14
ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana
No full textAbstract
Background
Many eukaryotic RNAs have been considered non-coding as they only contain short open reading frames (sORFs). However, there is increasing evidence for the translation of these sORFs into bioactive peptides with potent signaling, antimicrobial, developmental, antioxidant roles etc. Yet only a few peptides encoded by sORFs are annotated in the model organism Arabidopsis thaliana .
Results
To aid the functional annotation of these peptides, we have developed ARA-PEPs (available at http://www.biw.kuleuven.be/CSB/ARA-PEPs ), a repository of putative peptides encoded by sORFs in the A. thaliana genome starting from in-house Tiling arrays, RNA-seq data and other publicly available datasets. ARA-PEPs currently lists 13,748 sORF-encoded peptides with transcriptional evidence. In addition to existing data, we have identified 100 novel transcriptionally active regions (TARs) that might encode 341 novel stress-induced peptides (SIPs). To aid in identification of bioactivity, we add functional annotation and sequence conservation to predicted peptides.
Conclusion
To our knowledge, this is the largest repository of plant peptides encoded by sORFs with transcript evidence, publicly available and this resource will help scientists to effortlessly navigate the list of experimentally studied peptides, the experimental and computational evidence supporting the activity of these peptides and gain new perspectives for peptide discovery
Effects of Pleistocene sea-level fluctuations on mangrove population dynamics: a lesson from Sonneratia alba
No full textAbstract
Background
A large-scale systematical investigation of the influence of Pleistocene climate oscillation on mangrove population dynamics could enrich our knowledge about the evolutionary history during times of historical climate change, which in turn may provide important information for their conservation.
Results
In this study, phylogeography of a mangrove tree Sonneratia alba was studied by sequencing three chloroplast fragments and seven nuclear genes. A low level of genetic diversity at the population level was detected across its range, especially at the range margins, which was mainly attributed to the steep sea-level drop and associated climate fluctuations during the Pleistocene glacial periods. Extremely small effective population size (Ne) was inferred in populations from both eastern and western Malay Peninsula (44 and 396, respectively), mirroring the fragility of mangrove plants and their paucity of robustness against future climate perturbations and human activity. Two major genetic lineages of high divergence were identified in the two mangrove biodiversity centres: the Indo-Malesia and Australasia regions. The estimated splitting time between these two lineages was 3.153 million year ago (MYA), suggesting a role for pre-Pleistocene events in shaping the major diversity patterns of mangrove species. Within the Indo-Malesia region, a subdivision was implicated between the South China Sea (SCS) and the remaining area with a divergence time of 1.874 MYA, corresponding to glacial vicariance when the emerged Sunda Shelf halted genetic exchange between the western and eastern coasts of the Malay Peninsula during Pleistocene sea-level drops. Notably, genetic admixture was observed in populations at the boundary regions, especially in the two populations near the Malacca Strait, indicating secondary contact between divergent lineages during interglacial periods. These interregional genetic exchanges provided ample opportunity for the re-use of standing genetic variation, which could facilitate mangrove establishment and adaptation in new habitats, especially in the context of global climate changes.
Conclusion
Phylogeogrpahic analysis in this study reveal that Pleistocene sea-level fluctuations had profound influence on population differentiation of the mangrove tree S. alba . Our study highlights the fragility of mangrove plants and offers a guide for the conservation of coastal mangrove communities experiencing ongoing changes in sea-level
Phylogenomic analysis of Copepoda (Arthropoda, Crustacea) reveals unexpected similarities with earlier proposed morphological phylogenies
No full textAbstract
Background
Copepods play a critical role in marine ecosystems but have been poorly investigated in phylogenetic studies. Morphological evidence supports the monophyly of copepods, whereas interordinal relationships continue to be debated. In particular, the phylogenetic position of the order Harpacticoida is still ambiguous and inconsistent among studies. Until now, a small number of molecular studies have been done using only a limited number or even partial genes and thus there is so far no consensus at the order-level.
Results
This study attempted to resolve phylogenetic relationships among and within four major copepod orders including Harpacticoida and the phylogenetic position of Copepoda among five other crustacean groups (Anostraca, Cladocera, Sessilia, Amphipoda, and Decapoda) using 24 nuclear protein-coding genes. Phylogenomics has confirmed the monophyly of Copepoda and Podoplea. However, this study reveals surprising differences with the majority of the copepod phylogenies and unexpected similarities with postembryonic characters and earlier proposed morphological phylogenies; More precisely, Cyclopoida is more closely related to Siphonostomatoida than to Harpacticoida which is likely the most basally-branching group of Podoplea. Divergence time estimation suggests that the origin of Harpacticoida can be traced back to the Devonian, corresponding well with recently discovered fossil evidence. Copepoda has a close affinity to the clade of Malacostraca and Thecostraca but not to Branchiopoda. This result supports the hypothesis of the newly proposed clades, Communostraca, Multicrustacea, and Allotriocarida but further challenges the validity of Hexanauplia and Vericrustacea.
Conclusions
The first phylogenomic study of Copepoda provides new insights into taxonomic relationships and represents a valuable resource that improves our understanding of copepod evolution and their wide range of ecological adaptations
Prediction of ineffective elective cardioversion of atrial fibrillation: a retrospective multi-center patient cohort study
No full textAbstract
Background
Elective cardioversion (ECV) of atrial fibrillation (AF) is a standard procedure to restore sinus rhythm. However, predictors for ineffective ECV (failure of ECV or recurrence of AF within 30\ua0days) are unknown.
Methods
We investigated 1998 ECVs performed for AF lasting >48\ua0h in 1,342 patients in a retrospective multi-center study. Follow-up data were collected from 30\ua0days after ECV.
Results
Median number of cardioversions was one per patient with a range of 1\u201310. Altogether 303/1998 (15.2%) ECVs failed. Long (>5\ua0years) AF history and over 30\ua0days duration of the index AF episode were independent predictors for ECV failure and low (<60/min) ventricular rate of AF predicted success of ECV. In patients with successful ECVs an early recurrence of AF was detected in 549 (32.4%) cases. Female gender, high (>60/min) ventricular rate, renal failure and antiarrhythmic agents at discharge were the independent predictors for recurrence. In total ECV was ineffective in 852 (42.6%) cases. Female gender (OR 1.44, CI95% 1.15\u20131.80, p \u2009<\u20090.01), young (<65\ua0years) age (OR 1.31, CI95% 1.07\u20131.62, p \u2009=\u20090.01), ventricular rate >60/min (OR 1.92, CI95% 1.08\u20133.41, p \u2009=\u20090.03), antiarrhythmic medication at discharge (OR 1.48, CI95% 1.14\u20131.93, p \u2009<\u20090.01) and low (<60/ml/min) estimated glomerular filtration rate (OR 1.59, CI95% 1.08\u20132.33, p \u2009=\u20090.02) were predictors of ineffective ECV.
Conclusions
Female gender, use of antiarrhythmic drug therapy and renal failure predicted both recurrence of AF and the composite end point. For the first time in a large real-life study several clinical predictors for clinically ineffective ECV were identified
Dietary treatment of Crohn\u2019s disease: perceptions of families with children treated by exclusive enteral nutrition, a questionnaire survey
No full textAbstract
Background
Diet is strongly associated with the aetiology of Crohn\u2019s Disease (CD) and exclusive enteral nutrition (EEN) is the primary induction treatment in paediatric CD. This study explored opinions around the use of EEN and alternative novel, solid food-based diets (SFDs) expressed by paediatric patients with CD, previously treated with EEN and their parents.
Methods
This anonymous questionnaire surveyed families of CD patients treated with EEN over 1\ua0year. Two questionnaire forms were completed; one asking the patients\u2019 opinions and another referring to their main carer. This questionnaire explored participants\u2019 demographic characteristics; acceptability of a repeat EEN course to treat a future flare (EEN repeat); their opinion on how difficult EEN would be compared to an example SFD; and their intention to participate in a future clinical trial assessing the therapeutic efficacy of an SFD in CD.
Results
Forty-one families of CD patients were approached with 29 sending replies (71%). Most of our participants were positive on completing another EEN course, however the majority would choose an SFD alternative (Patients:66, Parents:72%). Both patients and their parents rated EEN to be more difficult to adhere to compared to an example SFD ( p \u2009<\u20090.05), and their ratings were strongly correlated (EEN: r \u2009=\u20090.83, SFD: r \u2009=\u20090.75, p \u2009<\u20090.001). The majority of our respondents would agree to participate in a clinical trial assessing an SFD\u2019s effectiveness (Patients:79, Parents:72%) for the management of active CD.
Conclusions
While patients with CD and their families would accept an EEN repeat, the majority would prefer an SFD alternative. CD families surveyed are supportive of the development of solid food-based dietary treatments
The effects of habitual functional training on physical functioning in patients after hip fracture: the protocol of the HIPFRAC study
No full textAbstract
Background
The survivors after hip fracture often report severe pain and loss of physical functioning. The poor outcomes cause negative impact on the person\u2019s physical functioning and quality of life and put a financial burden on society. Rehabilitation is important to improve physical functioning after hip fracture. To maintain the continuity in rehabilitation we have an assumption that it is of utmost importance to continue and progress the functional training that already started at the hospital, while the patients are transferred to short-term stays in a nursing home before they are returning to home. The aim presently is to examine the effects of a functional training program, initiated by the physiotherapist and performed by the nurses, on physical functioning while the patients are at short term stays in primary health care.
Methods/design
Inclusion and randomization will take place during hospital stay. All patients 65\ua0years or above who have sustained a hip fracture are eligible, except if they have a score on Mini Mental State (MMS-E) of less than 15, could walk less than 10 m prior to the fracture, or are terminally ill. The intervention consists of additional functional training as part of the habitual daily routine during short term stays at nursing homes after discharge from hospital. The primary outcome is physical functioning measured by the Short Physical Performance Battery (SPPB). Secondary outcomes are Timed \u201cUp & Go\u201d (TUG), hand grip strength, activPAL accelerometer, and self-reported measures like new Mobility Score (NMS), Walking Habits, University of California Los Angeles (UCLA) activity scale, Fall efficacy scale (FES), EuroQol health status measure (EQ-5D-5\ua0L), and pain.
Discussion
Issues related to internal and external validity in the study are discussed. The outline for the arguments in this protocol is organized according to the guidelines of the Medical Research Council (MRC) guidance on how to develop and evaluate complex interventions.
Trial registration
ClinicalTrials.gov NCT02780076
Prioritizing problems in and solutions to homecare safety of people with dementia: supporting carers, streamlining care
No full textAbstract
Background
Dementia care is predominantly provided by carers in home settings. We aimed to identify the priorities for homecare safety of people with dementia according to dementia health and social care professionals using a novel priority-setting method.
Methods
The project steering group determined the scope, the context and the criteria for prioritization. We then invited 185 North-West London clinicians via an open-ended questionnaire to identify three main problems and solutions relating to homecare safety of people with dementia. 76 clinicians submitted their suggestions which were thematically synthesized into a composite list of 27 distinct problems and 30 solutions. A group of 49 clinicians arbitrarily selected from the initial cohort ranked the composite list of suggestions using predetermined criteria.
Results
Inadequate education of carers of people with dementia (both family and professional) is seen as a key problem that needs addressing in addition to challenges of self-neglect, social isolation, medication nonadherence. Seven out of top 10 problems related to patients and/or carers signalling clearly where help and support are needed. The top ranked solutions focused on involvement and education of family carers, their supervision and continuing support. Several suggestions highlighted a need for improvement of recruitment, oversight and working conditions of professional carers and for different home safety-proofing strategies.
Conclusions
Clinicians identified a range of suggestions for improving homecare safety of people with dementia. Better equipping carers was seen as fundamental for ensuring homecare safety. Many of the identified suggestions are highly challenging and not easily changeable, yet there are also many that are feasible, affordable and could contribute to substantial improvements to dementia homecare safety
Depression, alcohol use, and intimate partner violence among outpatients in rural Uganda: vulnerabilities for HIV, STIs and high risk sexual behavior
No full textAbstract
Background
Intimate partner violence (IPV), alcohol use, and depression are key vulnerabilities for HIV in Uganda, and taken together may have a synergistic effect on risk. Our objective was to investigate the associations between depression, IPV, and alcohol use and HIV-risk indicators among a sample of outpatients in rural Uganda, and the effect of co-occurrence of these factors on HIV-risk indicators.
Methods
In a structured interview we collected data on high-risk sexual behavior, depression symptoms, emotional and physical IPV, and alcohol use, as well as a blood sample for HIV and syphilis tests and a urine sample for chlamydia and gonorrhea tests from 325 male and female outpatients receiving provider-initiated HIV testing and counseling (PITC) at a public hospital outpatient clinic in rural Uganda. We used logistic regression and generalized linear modeling to test independent associations between depression, IPV, and alcohol use and HIV-risk indicators, as well as the effect of co-occurrence on HIV-risk indicators.
Results
Twelve percent of men and 15% of women had two or more of the following conditions: depression, IPV, and alcohol use; another 29% of men and 33% of women had 1 condition. Each condition was independently associated with HIV risk behavior for men and women, and for women, depression was associated with testing positive for HIV or a sexually transmitted infection (STI). Men with one condition (AOR 2.32, 95% CI 1.95\u20132.77) and two or more conditions (AOR 12.77, 95% CI 7.97\u201320.47) reported more high risk sex acts compared to those with no potential co-occurring conditions. For men, experiencing two or more conditions increased risky sex more than one alone ( \u3c7
2
24.68, p \u2009<\u20090.001). Women experiencing one condition (AOR 3.33, 95% CI 137\u20138.08) and two co-occurring conditions (AOR 5.87, 95% CI 1.99\u201317.35) were more likely to test positive for HIV or an STI and women with two co-occurring conditions were also at increased risk for risky sex (AOR 2.18, 95% CI 1.64\u20132.91). We also found preliminary evidence suggesting synergistic effects between depression and emotional IPV and between alcohol use and depression.
Conclusions
This study demonstrates the co-occurrence of depression, IPV, and alcohol use in men and women in an outpatient setting in rural Uganda. The co-occurrence of these factors was associated with greater HIV risk, highlighting the need for a more holistic approach to HIV prevention and care research and programming