Predictive Models of Genetic Redundancy in Arabidopsis thaliana.

Genetic redundancy refers to a situation where an individual with a loss-of-function mutation in one gene (single mutant) does not show an apparent phenotype until one or more paralogs are also knocked out (double/higher-order mutant). Previous studies have identified some characteristics common among redundant gene pairs, but a predictive model of genetic redundancy incorporating a wide variety of features derived from accumulating omics and mutant phenotype data is yet to be established. In addition, the relative importance of these features for genetic redundancy remains largely unclear. Here, we establish machine learning models for predicting whether a gene pair is likely redundant or not in the model plant Arabidopsis thaliana based on six feature categories: functional annotations, evolutionary conservation including duplication patterns and mechanisms, epigenetic marks, protein properties including posttranslational modifications, gene expression, and gene network properties. The definition of redundancy, data transformations, feature subsets, and machine learning algorithms used significantly affected model performance based on holdout, testing phenotype data. Among the most important features in predicting gene pairs as redundant were having a paralog(s) from recent duplication events, annotation as a transcription factor, downregulation during stress conditions, and having similar expression patterns under stress conditions. We also explored the potential reasons underlying mispredictions and limitations of our studies. This genetic redundancy model sheds light on characteristics that may contribute to long-term maintenance of paralogs, and will ultimately allow for more targeted generation of functionally informative double mutants, advancing functional genomic studies.

Gut microbiota composition correlates with diet and health in the elderly.

Alterations in intestinal microbiota composition are associated with several chronic conditions, including obesity and inflammatory diseases. The microbiota of older people displays greater inter-individual variation than that of younger adults. Here we show that the faecal microbiota composition from 178 elderly subjects formed groups, correlating with residence location in the community, day-hospital, rehabilitation or in long-term residential care. However, clustering of subjects by diet separated them by the same residence location and microbiota groupings. The separation of microbiota composition significantly correlated with measures of frailty, co-morbidity, nutritional status, markers of inflammation and with metabolites in faecal water. The individual microbiota of people in long-stay care was significantly less diverse than that of community dwellers. Loss of community-associated microbiota correlated with increased frailty. Collectively, the data support a relationship between diet, microbiota and health status, and indicate a role for diet-driven microbiota alterations in varying rates of health decline upon ageing.

Composition, variability, and temporal stability of the intestinal microbiota of the elderly.

Alterations in the human intestinal microbiota are linked to conditions including inflammatory bowel disease, irritable bowel syndrome, and obesity. The microbiota also undergoes substantial changes at the extremes of life, in infants and older people, the ramifications of which are still being explored. We applied pyrosequencing of over 40,000 16S rRNA gene V4 region amplicons per subject to characterize the fecal microbiota in 161 subjects aged 65 y and older and 9 younger control subjects. The microbiota of each individual subject constituted a unique profile that was separable from all others. In 68% of the individuals, the microbiota was dominated by phylum Bacteroides, with an average proportion of 57% across all 161 baseline samples. Phylum Firmicutes had an average proportion of 40%. The proportions of some phyla and genera associated with disease or health also varied dramatically, including Proteobacteria, Actinobacteria, and Faecalibacteria. The core microbiota of elderly subjects was distinct from that previously established for younger adults, with a greater proportion of Bacteroides spp. and distinct abundance patterns of Clostridium groups. Analyses of 26 fecal microbiota datasets from 3-month follow-up samples indicated that in 85% of the subjects, the microbiota composition was more like the corresponding time-0 sample than any other dataset. We conclude that the fecal microbiota of the elderly shows temporal stability over limited time in the majority of subjects but is characterized by unusual phylum proportions and extreme variability.

Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy.

OBJECTIVES: The human intestinal microbiota composition alters naturally with age, but is unusually perturbed by antibiotic therapy. The impact of antibiotic therapy on the composition of the intestinal microbiota of a cross-section of elderly Irish subjects (n = 185, ≥ 65 years) was investigated, taking into consideration their residence location. METHODS: Forty-two of the 185 elderly subjects were treated with at least one antibiotic within 1 month prior to faecal microbiota profiling. The residence locations of the subjects varied from long-term nursing care and rehabilitation wards to day hospitals and the community. RESULTS: Culture-dependent methods indicated that faecal Bifidobacterium spp. numbers were significantly reduced following antibiotic treatment (P = 0.004, 7-fold reduction), while levels of Lactobacillus spp. and Enterobacteriaceae were unaffected. The largest decrease in Bifidobacterium spp. numbers was linked to the administration of nucleic acid synthesis inhibitors (P = 0.004, 23-fold reduction). Microbiota profiling revealed a significant compositional change across nine genera following antibiotic therapy, including a relative increase in Lactobacillus spp. (P = 0.031), as well as a decrease in the number of genera identified in the antibiotic-treated subjects (n = 58), when compared with untreated subjects (n = 79). More alterations in the intestinal microbiota were observed post-nucleic acid synthesis inhibitor therapy, most notably a decrease in relative Faecalibacterium spp. numbers (P < 0.001). CONCLUSIONS: The impact of antibiotic therapy on the intestinal microbiota in the elderly should be considered for long-term health effects, and differential susceptibility may require the development of products (e.g. prebiotics and probiotics) for at-risk subjects.

Challenges and implications for biomedical research and intervention studies in older populations: insights from the ELDERMET study.

Older people constitute a growing proportion of the worldwide population. Despite this, older people are often excluded from clinical research and are generally underrepresented in intervention studies. This severely restricts the ability to generalise outcomes from research involving younger populations, which may impact on the progression of knowledge and the development of best practice guidelines for the care of older people. This opinion piece outlines the challenges and practical difficulties experienced and overcome by the ELDERMET project. The ELDERMET project has recruited almost 500 subjects, aged 65 years and older, across a range of health states from the very frail to the very fit, half of whom have been studied at multiple time points. All ELDERMET subjects have participated in an extensive protocol and supplied multiple biological sample types. The challenges and obstacles faced by both researchers in recruiting older subjects and older people engaging with research and intervention studies are set out. Strategies are discussed for: the recruitment and retention of older subjects; recruiting subjects with physical or cognitive impairment; recruitment from specific locations; collecting accurate and robust data, particularly from subjects with mild to severe cognitive impairment; intervention product design, delivery and compliance. Practical and realistic solutions for maximising the engagement of older people with research and intervention studies are offered. The increased benefit brought by the generalisation and application of research and intervention outcomes to older populations is discussed.

Probing the physiological role of the plastid outer-envelope membrane using the oemiR plasmid collection.

Plastids are the site of complex biochemical pathways, most prominently photosynthesis. The organelle evolved through endosymbiosis with a cyanobacterium, which is exemplified by the outer envelope membrane that harbors more than 40 proteins in Arabidopsis. Their evolutionary conservation indicates high significance for plant cell function. While a few proteins are well-studied as part of the protein translocon complex the majority of outer envelope protein functions is unclear. Gaining a deeper functional understanding has been complicated by the lack of observable loss-of-function mutant phenotypes, which is often rooted in functional genetic redundancy. Therefore, we designed outer envelope-specific artificial micro RNAs (oemiRs) capable of downregulating transcripts from several loci simultaneously. We successfully tested oemiR function by performing a proof-of-concept screen for pale and cold-sensitive mutants. An in-depth analysis of pale mutant alleles deficient in the translocon component TOC75 using proteomics provided new insights into putative compensatory import pathways. The cold stress screen not only recapitulated 3 previously known phenotypes of cold-sensitive mutants but also identified 4 mutants of additional oemiR outer envelope loci. Altogether our study revealed a role of the outer envelope to tolerate cold conditions and showcasts the power of the oemiR collection to research the significance of outer envelope proteins.

Older people and laxative use: comparison between community and long-term care settings.

Constipation is a common problem affecting many older people's quality of life. The aim of the study was to describe and compare the frequency of use of laxative medication in Irish adults, aged 65 years and older, from the community and a long-term care setting. Participants (n=207) were part of the Irish ELDERMET project. The project aims to find out how diet and lifestyle influence, and are influenced by, the bacteria in the gut, and how this knowledge can be used to promote health in older Irish people. It has recruited over 450 people, aged 65 and older, and will use the information gathered from the extensive proforma to develop recommendations, as well as functional foods/functional food ingredients specifically designed to promote and support health in older populations. Data were collected between June 2008 and April 2010 using a survey questionnaire. A quantitative descriptive correlational design was used. Analysis was conducted using PASW Statistics 18.0. Participants in long-term care received a greater number of both laxatives and prescribed medications than community-dwelling participants. Increased polypharmacy was also seen in participants taking laxatives, with participants in long-term care significantly (p<0.001) more likely to take multiple laxatives. Nurses are in a key position to develop proactive approaches to the prevention and treatment of constipation.

Vitamin D and estrogen receptor-alpha genotype and indices of bone mass and bone turnover in Danish girls.

Peak bone mass is a major determinant of osteoporosis risk in later life. It is under strong genetic control; however, little is known about the identity of the genes involved. In the present study, we investigated the relationship between polymorphisms in the genes encoding the vitamin D receptor (VDR) (FokI, TaqI) and estrogen receptor-alpha (ERalpha) (PvuII, XbaI), and bone mineral density (BMD), bone mineral content (BMC), and markers of bone turnover in 224 Danish girls aged 11-12 years. BMD and BMC were measured by dual-energy X-ray absorptiometry. Serum osteocalcin, 25(OH)D, and parathyroid hormone (PTH) were measured by ELISA assays and urinary pyridinium cross-links by HPLC. Physical activity, dietary calcium, and Tanner stage were assessed by questionnaire. In general, there were no significant differences in anthropometrical variables, physical activity, dietary calcium, serum 25(OH)D, or PTH among genotype groups. BMD or BMC of lumbar spine or whole body (adjusted for body and bone size and pubertal status) were not associated with VDR or ERalpha genotypes or the combination of these genotypes. This lack of association remained even after adjustment for dietary and environmental factors. VDR genotypes had no effect on bone turnover markers. XX and PP ERalpha genotypes were associated (P < 0.05) with reduced levels of urinary pyridinium cross-links, whereas serum osteocalcin was similar among genotypes. These findings suggest that the rate of bone resorption was influenced by ERalpha genotypes, even though these biochemical differences were not evident in bone mass indices.

Impact of genetic variation on metabolic response of bone to diet.

There is compelling evidence to suggest that both the development of bone to peak bone mass at maturity and subsequent loss depend on the interaction between genetic, hormonal, environmental and nutritional factors. The major part (< or = 80%) of the age-specific variation in bone turnover and bone density is genetically determined. However, the notion of genetic determinant is of little value unless the specific genes that are involved can be identified. Most work in this area of osteoporosis research has focused on the candidate gene approach, which has identified several candidate genes for osteoporosis, including genes encoding the vitamin D receptor (VDR), oestrogen receptors (alpha and beta), apolipoprotein E, collagen type I alpha 1 and methylenetetrahydrofolate reductase, amongst many others. However, in general, findings from numerous studies of the association between such genes and various bone variables have been inconsistent. In addition to possible gene-gene interactions it is likely that there are interactions between these genes and certain environmental factors, especially nutrition, that may mediate expression of bone-related phenotypes. While these potential interactions add a level of complexity to our understanding of these apparent genetic effects on bone, identification of a role for genetic factors without knowledge of their interaction with nutrients can do little to advance prevention and treatment of osteoporosis. This information is especially important because, unlike genotype, diet and nutrition can be modified. The aim of the present review is to critically evaluate current knowledge relating to candidate genes for osteoporosis, with particular emphasis on their interaction with nutrients and dietary factors in determining bone health.

The effect of polyunsaturated fatty acids, including conjugated linoleic acid, on calcium absorption and bone metabolism and composition in young growing rats.

The effect of polyunsaturated fatty acids (PUFA), in particular conjugated linoleic acid (CLA), on Ca and bone metabolism is unclear. In a 2x2 factorial design study, forty male 4-week-old rats were fed a control diet containing 70 g added fat (soyabean oil (SBO; n-6 PUFA-rich diet) or menhaden oil-safflower oil (MSO; n-3 PUFA-rich diet))/kg diet with 0 or 10 g CLA/kg for 8 weeks. Ex vivo prostaglandin E2 biosynthesis by bone organ culture was significantly higher (P<0.001) in rats consuming SBO compared with MSO, irrespective of CLA. Addition of the CLA treatment to either diet further lowered (P<0.05) ex vivo prostaglandin E2 production. Neither PUFA type nor CLA altered circulating or femoral mRNA levels of osteocalcin (a marker of bone formation) or insulin-like growth factor-I (a mediator of bone metabolism). While urinary pyridinium crosslinks levels (markers of bone resorption) were unaffected by CLA irrespective of PUFA type, they were significantly higher (P<0.05) in rats consuming SBO compared with MSO irrespective of CLA. Net fractional (%) and absolute (mg) Ca absorption were significantly (P<0.01 and P<0.05 respectively) higher in CLA-supplemented than unsupplemented animals fed on the n-3 PUFA-rich diet, whereas CLA had no effect in animals fed the n-6 PUFA-rich diet. There was no effect of CLA supplementation on bone mineral mass. In conclusion, CLA supplementation over 8 weeks appeared to enhance Ca absorption in young growing rats fed an n-3 PUFA-rich diet, but had no measurable effect on bone metabolism or bone mass over this time frame.

The effect of bovine whey protein on ectopic bone formation in young growing rats.

The beneficial effect of bovine whey protein (WP) on bone metabolism has been shown in adult human subjects and ovariectomised rats. However, its effect on bone formation in earlier life, particularly during periods of bone mineral accrual, has not been investigated. Twenty-one male rats (4 weeks old, Wistar strain) were randomised by weight into three groups of seven rats each and fed ad libitum on a semi-purified low-Ca diet (3.0 g Ca/kg diet) containing 0 (control), 10 (diet WP1) or 20 (diet WP2) g bovine WP/kg for 47 d. On day 34 of the dietary intervention, all rats had two gelatine capsules containing demineralised bone powder implanted subcutaneously in the thorax region (a well-established in vivo model of ectopic bone formation). At 14 d after implantation, alkaline phosphatase activity (reflective of bone formation) in the bone implants from animals fed WP1 and -2 diets was almost 2-fold (P<0.01) that of control animals. Insulin-like growth factor (IGF)-I mRNA levels were about 3-fold (P<0.05) higher in implants from animals fed the WP diets compared with those from control animals. Serum- and urine-based biomarkers of bone metabolism and bone mineral composition in intact femora were unaffected by WP supplementation. In conclusion, the present findings suggest that bovine WP can enhance the rate of ectopic bone formation in young growing rats fed a Ca-restricted diet. This effect may be mediated by an increased synthesis of IGF-I in growing bone. The effect of WP on bone formation warrants further investigation.