Journals
2012 EN
Fernando Gómez · Gabriela C. Monsalve · Vincent Tse
+6 more
Background Studies with the nematode model Caenorhabditis elegans have identified conserved biochemical pathways that act to modulate life span. Life span can also be influenced by the composition of the intestinal microbiome, and C . elegans life span can be dramatically influenced by its diet of Escherichia coli . Although C . elegans is typically fed the standard OP50 strain of E . coli , nematodes fed E . coli strains rendered respiratory deficient, either due to a lack coenzyme Q or the absence of ATP synthase, show significant life span extension. Here we explore the mechanisms accounting for the enhanced nematode life span in response to these diets. Results The intestinal load of E . coli was monitored by determination of worm-associated colony forming units (cfu/worm or coliform counts) as a function of age. The presence of GFP-expressing E . coli in the worm intestine was also monitored by fluorescence microscopy. Worms fed the standard OP50 E . coli strain have high cfu and GFP-labeled bacteria in their guts at the L4 larval stage, and show saturated coliform counts by day five of adulthood. In contrast, nematodes fed diets of respiratory deficient E . coli lacking coenzyme Q lived significantly longer and failed to accumulate bacteria within the lumen at early ages. Animals fed bacteria deficient in complex V showed intermediate coliform numbers and were not quite as long-lived. The results indicate that respiratory deficient Q-less E . coli are effectively degraded in the early adult worm, either at the pharynx or within the intestine, and do not accumulate in the intestinal tract until day ten of adulthood. Conclusions The findings of this study suggest that the nematodes fed the respiratory deficient E . coli diet live longer because the delay in bacterial colonization of the gut subjects the worms to less stress compared to worms fed the OP50 E . coli diet. This work suggests that bacterial respiration can act as a virulence factor, influencing the ability of bacteria to colonize and subsequently harm the animal host. Respiratory deficient bacteria may pose a useful model for probing probiotic relationships within the gut microbiome in higher organisms.
Journals
2012 EN
Ganwu Li · Subhashinie Kariyawasam · Kelly A. Tivendale
+5 more
Background Extraintestinal pathogenic Escherichia coli are important pathogens of human and animal hosts. Some human and avian extraintestinal pathogenic E. coli are indistinguishable on the basis of diseases caused, multilocus sequence and phylogenetic typing, carriage of large virulence plasmids and traits known to be associated with extraintestinal pathogenic E. coli virulence. Results The gene tkt1 identified by a previous signature-tagged transposon mutagenesis study, was found on a 16-kb genomic island of avian pathogenic Escherichia coli (APEC) O1, the first pathogenic Escherichia coli strain whose genome has been completely sequenced. tkt1 was present in 39.6% (38/96) of pathogenic Escherichia coli strains, while only 6.25% (3/48) of E. coli from the feces of apparently healthy chickens was positive. Further, tkt1 was predominantly present in extraintestinal pathogenic E. coli belonging to the B2 phylogenetic group, as compared to extraintestinal pathogenic E. coli of other phylogenetic groups. The tkt1 -containing genomic island is inserted between the metE and ysgA genes of the E. coli K12 genome. Among different extraintestinal pathogenic E. coli of the B2 phylogenetic group, 61.7% of pathogenic Escherichia coli , 80.6% of human uropathogenic E.coli and 94.1% of human neonatal meningitis-causing E. coli , respectively, harbor a complete copy of this island; whereas, only a few avian fecal E. coli strains contained the complete island. Functional analysis showed that Tkt1 confers very little transketolase activity but is involved in peptide nitrogen metabolism. Conclusion These results suggest tkt1 and its corresponding genomic island are frequently associated with avian and human ExPEC and are involved in bipeptide metabolism.
Journals
2012 EN
Catherine BloisHeulin · Mélodie Crével · Martin Böye
+1 more
Background Many studies of cerebral asymmetries in different species lead, on the one hand, to a better understanding of the functions of each cerebral hemisphere and, on the other hand, to develop an evolutionary history of hemispheric laterality. Our animal model is particularly interesting because of its original evolutionary path, i.e. return to aquatic life after a terrestrial phase. The rare reports concerning visual laterality of marine mammals investigated mainly discrimination processes. As dolphins are migrant species they are confronted to a changing environment. Being able to categorize new versus familiar objects would allow dolphins a rapid adaptation to novel environments. Visual laterality could be a prerequisite to this adaptability. To date, no study, to our knowledge, has analyzed the environmental factors that could influence their visual laterality. Results We investigated visual laterality expressed spontaneously at the water surface by a group of five common bottlenose dolphins ( Tursiops truncatus ) in response to various stimuli. The stimuli presented ranged from very familiar objects (known and manipulated previously) to familiar objects (known but never manipulated) to unfamiliar objects (unknown, never seen previously). At the group level, dolphins used their left eye to observe very familiar objects and their right eye to observe unfamiliar objects. However, eyes are used indifferently to observe familiar objects with intermediate valence. Conclusion Our results suggest different visual cerebral processes based either on the global shape of well-known objects or on local details of unknown objects. Moreover, the manipulation of an object appears necessary for these dolphins to construct a global representation of an object enabling its immediate categorization for subsequent use. Our experimental results pointed out some cognitive capacities of dolphins which might be crucial for their wild life given their fission-fusion social system and migratory behaviour.
Journals
2012 EN
Catherine Bodénès · Émilie Chancerel · Oliver Gailing
+15 more
Background Genetic markers and linkage mapping are basic prerequisites for comparative genetic analyses, QTL detection and map-based cloning. A large number of mapping populations have been developed for oak, but few gene-based markers are available for constructing integrated genetic linkage maps and comparing gene order and QTL location across related species. Results We developed a set of 573 expressed sequence tag-derived simple sequence repeats (EST-SSRs) and located 397 markers (EST-SSRs and genomic SSRs) on the 12 oak chromosomes (2n = 2x = 24) on the basis of Mendelian segregation patterns in 5 full-sib mapping pedigrees of two species: Quercus robur (pedunculate oak) and Quercus petraea (sessile oak). Consensus maps for the two species were constructed and aligned. They showed a high degree of macrosynteny between these two sympatric European oaks. We assessed the transferability of EST-SSRs to other Fagaceae genera and a subset of these markers was mapped in Castanea sativa , the European chestnut. Reasonably high levels of macrosynteny were observed between oak and chestnut. We also obtained diversity statistics for a subset of EST-SSRs, to support further population genetic analyses with gene-based markers. Finally, based on the orthologous relationships between the oak, Arabidopsis , grape, poplar, Medicago , and soybean genomes and the paralogous relationships between the 12 oak chromosomes, we propose an evolutionary scenario of the 12 oak chromosomes from the eudicot ancestral karyotype. Conclusions This study provides map locations for a large set of EST-SSRs in two oak species of recognized biological importance in natural ecosystems. This first step toward the construction of a gene-based linkage map will facilitate the assignment of future genome scaffolds to pseudo-chromosomes. This study also provides an indication of the potential utility of new gene-based markers for population genetics and comparative mapping within and beyond the Fagaceae.
Journals
2012 EN
Jan Bartoš · Čestmı́r Vlček · Frédéric Choulet
+11 more
Background Polyploidization is considered one of the main mechanisms of plant genome evolution. The presence of multiple copies of the same gene reduces selection pressure and permits sub-functionalization and neo-functionalization leading to plant diversification, adaptation and speciation. In bread wheat, polyploidization and the prevalence of transposable elements resulted in massive gene duplication and movement. As a result, the number of genes which are non-collinear to genomes of related species seems markedly increased in wheat. Results We used new-generation sequencing (NGS) to generate sequence of a Mb-sized region from wheat chromosome arm 3DS. Sequence assembly of 24 BAC clones resulted in two scaffolds of 1,264,820 and 333,768 bases. The sequence was annotated and compared to the homoeologous region on wheat chromosome 3B and orthologous loci of Brachypodium distachyon and rice. Among 39 coding sequences in the 3DS scaffolds, 32 have a homoeolog on chromosome 3B. In contrast, only fifteen and fourteen orthologs were identified in the corresponding regions in rice and Brachypodium , respectively. Interestingly, five pseudogenes were identified among the non-collinear coding sequences at the 3B locus, while none was found at the 3DS locus. Conclusion Direct comparison of two Mb-sized regions of the B and D genomes of bread wheat revealed similar rates of non-collinear gene insertion in both genomes with a majority of gene duplications occurring before their divergence. Relatively low proportion of pseudogenes was identified among non-collinear coding sequences. Our data suggest that the pseudogenes did not originate from insertion of non-functional copies, but were formed later during the evolution of hexaploid wheat. Some evidence was found for gene erosion along the B genome locus.
Journals
2012 EN
Romain Monclus · JeanCharles Leplé · Catherine Bastien
+5 more
Background Hybrid poplars species are candidates for biomass production but breeding efforts are needed to combine productivity and water use efficiency in improved cultivars. The understanding of the genetic architecture of growth in poplar by a Quantitative Trait Loci (QTL) approach can help us to elucidate the molecular basis of such integrative traits but identifying candidate genes underlying these QTLs remains difficult. Nevertheless, the increase of genomic information together with the accessibility to a reference genome sequence ( Populus trichocarpa Nisqually-1) allow to bridge QTL information on genetic maps and physical location of candidate genes on the genome. The objective of the study is to identify QTLs controlling productivity, architecture and leaf traits in a P. deltoides x P. trichocarpa F1 progeny and to identify candidate genes underlying QTLs based on the anchoring of genetic maps on the genome and the gene ontology information linked to genome annotation. The strategy to explore genome annotation was to use Gene Ontology enrichment tools to test if some functional categories are statistically over-represented in QTL regions. Results Four leaf traits and 7 growth traits were measured on 330 F1 P. deltoides x P. trichocarpa progeny. A total of 77 QTLs controlling 11 traits were identified explaining from 1.8 to 17.2% of the variation of traits. For 58 QTLs, confidence intervals could be projected on the genome. An extended functional annotation was built based on data retrieved from the plant genome database Phytozome and from an inference of function using homology between Populus and the model plant Arabidopsis . Genes located within QTL confidence intervals were retrieved and enrichments in gene ontology (GO) terms were determined using different methods. Significant enrichments were found for all traits. Particularly relevant biological processes GO terms were identified for QTLs controlling number of sylleptic branches: intervals were enriched in GO terms of biological process like ‘ripening’ and ‘adventitious roots development’. Conclusion Beyond the simple identification of QTLs, this study is the first to use a global approach of GO terms enrichment analysis to fully explore gene function under QTLs confidence intervals in plants. This global approach may lead to identification of new candidate genes for traits of interest.
Journals
2012 EN
Francesco Fabbrini · Muriel Gaudet · Catherine Bastien
+7 more
Background The genetic control of important adaptive traits, such as bud set, is still poorly understood in most forest trees species. Poplar is an ideal model tree to study bud set because of its indeterminate shoot growth. Thus, a full-sib family derived from an intraspecific cross of P. nigra with 162 clonally replicated progeny was used to assess the phenotypic plasticity and genetic variation of bud set in two sites of contrasting environmental conditions. Results Six crucial phenological stages of bud set were scored. Night length appeared to be the most important signal triggering the onset of growth cessation. Nevertheless, the effect of other environmental factors, such as temperature, increased during the process. Moreover, a considerable role of genotype × environment (G × E) interaction was found in all phenological stages with the lowest temperature appearing to influence the sensitivity of the most plastic genotypes. Descriptors of growth cessation and bud onset explained the largest part of phenotypic variation of the entire process. Quantitative trait loci (QTL) for these traits were detected. For the four selected traits (the onset of growth cessation (date2.5), the transition from shoot to bud (date1.5), the duration of bud formation (subproc1) and bud maturation (subproc2)) eight and sixteen QTL were mapped on the maternal and paternal map, respectively. The identified QTL, each one characterized by small or modest effect, highlighted the complex nature of traits involved in bud set process. Comparison between map location of QTL and P. trichocarpa genome sequence allowed the identification of 13 gene models, 67 bud set-related expressional and six functional candidate genes (CGs). These CGs are functionally related to relevant biological processes, environmental sensing, signaling, and cell growth and development. Some strong QTL had no obvious CGs, and hold great promise to identify unknown genes that affect bud set. Conclusions This study provides a better understanding of the physiological and genetic dissection of bud set in poplar. The putative QTL identified will be tested for associations in P. nigra natural populations. The identified QTL and CGs will also serve as useful targets for poplar breeding.
Journals
2012 EN
Nadine Berndt · Catherine Bolman · Lilian Lechner
+3 more
Background There is no more effective intervention for secondary prevention of coronary heart disease than smoking cessation. Yet, evidence about the (cost-)effectiveness of smoking cessation treatment methods for cardiac inpatients that also suit nursing practice is scarce. This protocol describes the design of a study on the (cost-)effectiveness of two intensive smoking cessation interventions for hospitalised cardiac patients as well as first results on the inclusion rates and the characteristics of the study population. Methods/design An experimental study design is used in eight cardiac wards of hospitals throughout the Netherlands to assess the (cost-)effectiveness of two intensive smoking cessation counselling methods both combined with nicotine replacement therapy. Randomization is conducted at the ward level (cross-over). Baseline and follow-up measurements after six and 12 months are obtained. Upon admission to the cardiac ward, nurses assess patients’ smoking behaviour, ensure a quit advice and subsequently refer patients for either telephone counselling or face-to-face counselling. The counselling interventions have a comparable structure and content but differ in provider and delivery method, and in duration. Both counselling interventions are compared with a control group receiving no additional treatment beyond the usual care. Between December 2009 and June 2011, 245 cardiac patients who smoked prior to hospitalisation were included in the usual care group, 223 in the telephone counselling group and 157 in the face-to-face counselling group. Patients are predominantly male and have a mean age of 57 years. Acute coronary syndrome is the most frequently reported admission diagnosis. The ultimate goal of the study is to assess the effects of the interventions on smoking abstinence and their cost-effectiveness. Telephone counselling is expected to be more (cost-)effective in highly motivated patients and patients with high SES, whereas face-to-face counselling is expected to be more (cost-)effective in less motivated patients and patients with low SES. Discussion This study examines two intensive smoking cessation interventions for cardiac patients using a multi-centre trial with eight cardiac wards. Although not all eligible patients could be included and the distribution of patients is skewed in the different groups, the results will be able to provide valuable insight into effects and costs of counselling interventions varying in delivery mode and intensity, also concerning subgroups. Trial registration Dutch Trial Register NTR2144
Journals
2012 EN
Clare Liddy · Jatinderpreet Singh · William Hogg
+6 more
Background Primary care plays a key role in the prevention and management of cardiovascular disease (CVD). We examined primary care practice adherence to recommended care guidelines associated with the prevention and management of CVD for high risk patients. Methods We conducted a secondary analysis of cross-sectional baseline data collected from 84 primary care practices participating in a large quality improvement initiative in Eastern Ontario from 2008 to 2010. We collected medical chart data from 4,931 patients who either had, or were at high risk of developing CVD to study adherence rates to recommended guidelines for CVD care and to examine the proportion of patients at target for clinical markers such as blood pressure, lipid levels and hemoglobin A1c. Results Adherence to preventive care recommendations was poor. Less than 10% of high risk patients received a waistline measurement, half of the smokers received cessation advice, and 7.7% were referred to a smoking cessation program. Gaps in care exist for diabetes and kidney disease as 54.9% of patients with diabetes received recommended hemoglobin-A1c screenings, and only 55.8% received an albumin excretion test. Adherence rates to recommended guidelines for coronary artery disease, hypertension, and dyslipidemia were high (>75%); however <50% of patients were at target for blood pressure or LDL-cholesterol levels (37.1% and 49.7% respectively), and only 59.3% of patients with diabetes were at target for hemoglobin-A1c. Conclusions There remain significant opportunities for primary care providers to engage high risk patients in prevention activities such as weight management and smoking cessation. Despite high adherence rates for hypertension, dyslipidemia, and coronary artery disease, a significant proportion of patients failed to meet treatment targets, highlighting the complexity of caring for people with multiple chronic conditions. Trial Registration NCT00574808
Journals
2012 EN
Marjolein Gysels · Catherine Evans · Irene J Higginson
Background The development of the evidence-base informing end of life (EoL) care is hampered by the assumption that patients at the EoL are too vulnerable to participate in research. This study aims to systematically and critically review the evidence regarding the experiences and views of patients, caregivers, professionals and researchers about participation in EoL care research, and to identify best practices in research participation. Methods We searched seven electronic databases, and hand searched three journals and the bibliographies of relevant papers. Inclusion criteria were original research papers on involvement in EoL care research or its impact on participants. Critical interpretive synthesis was used to integrate the whole body of empirical evidence on this topic and generate theoretical categories from the evidence. Results Of a total of 239 identified studies, 20 studies met the inclusion criteria, from: the US (11), the UK (6) and Australia (3). Most focused on patients with cancer (12) and were conducted in hospices (9) or hospitals (7). Studies enquired about issues related to: EoL care research in general (5), specific research methods (13), and trial research (2). The studies evaluating willingness to participate in EoL care research showed positive outcomes across the different parties involved in research. Factors influencing willingness were mainly physical and cognitive impairment. Participating in research was a positive experience for most patients and carers but a minority experienced distress. This was related to: characteristics of the participants; the type of research; or the way it was conducted. Participatory study designs were found particularly suitable for enabling the inclusion of a wide range of participants. Conclusion The evidence explored within this study demonstrates that the ethical concerns regarding patient participation in EoL care research are often unjustified. However, research studies in EoL care require careful design and execution that incorporates sensitivity to participants’ needs and concerns to enable their participation. An innovative conceptual model for research participation relevant for potentially vulnerable people was developed.