Temporal fermentation and microbial community dynamics in rumens of sheep grazing a ryegrass-based pasture offered either in the morning or in the afternoon.

Eight ruminally-fistulated wethers were used to examine the temporal effects of afternoon (PM; 1600h) v. morning (AM; 0800 h) allocation of fresh spring herbage from a perennial ryegrass (Lolium perenne L.)-based pasture on fermentation and microbial community dynamics. Herbage chemical composition was minimally affected by time of allocation, but daily mean ammonia concentrations were greater for the PM group. The 24-h pattern of ruminal fermentation (i.e. time of sampling relative to time of allocation), however, varied considerably for all fermentation variables (P⩽0.001). Most notably amongst ruminal fermentation characteristics, ammonia concentrations showed a substantial temporal variation; concentrations of ammonia were 1.7-, 2.0- and 2.2-fold greater in rumens of PM wethers at 4, 6 and 8h after allocation, respectively, compared with AM wethers. The relative abundances of archaeal and ciliate protozoal taxa were similar across allocation groups. In contrast, the relative abundances of members of the rumen bacterial community, like Prevotella 1 (P=0.04), Bacteroidales RF16 group (P=0.005) and Fibrobacter spp. (P=0.008) were greater for the AM group, whereas the relative abundance of Kandleria spp. was greater (P=0.04) for the PM group. Of these taxa, only Prevotella 1 (P=0.04) and Kandleria (P<0.001) showed a significant interaction between time of allocation and time of sampling relative to feed allocation. Relative abundances of Prevotella 1 were greater at 2h (P=0.05), 4h (P=0.003) and 6h (P=0.01) after AM allocation of new herbage, whereas relative abundances of Kandleria were greater at 2h (P=0.003) and 4h (P<0.001) after PM allocation. The early post-allocation rise in ammonia concentrations in PM rumens occurred simultaneously with sharp increases in the relative abundance of Kandleria spp. and with a decline in the relative abundance of Prevotella. All measures of fermentation and most microbial community composition data showed highly dynamic changes in concentrations and genus abundances, respectively, with substantial temporal changes occurring within the first 8h of allocating a new strip of herbage. The dynamic changes in the relative abundances of certain bacterial groups, in synchrony with a substantial diurnal variation in ammonia concentrations, has potential effects on the efficiency by which N is utilised by the grazing ruminant.

The body composition phenotype of Irish adults aged 18-81 years.

BACKGROUND: Regional distribution of adiposity and lean tissue mass are predictors of health risk that cannot be defined by body mass index but can be attained by dual-energy X-ray absorptiometry (DXA). Age and sex-related adult ranges of whole-body and regional adiposity and lean tissue are not available for Irish men and women. AIMS: The aim of this study was to construct a DXA-based body composition profile of Irish adults, focusing on age- and sex-related difference in total and regional adiposity and lean tissue mass. METHODS: The study population comprised a convenience sample of 1606 participants, aged 18-81 years participating in the University of Limerick Body Composition study. Data were analysed to construct stature-normalised indices of body fat mass (BFMI), site-specific visceral adiposity, lean tissue mass (LTMI) and appendicular lean tissue mass (ALTMI). RESULTS: Compared to the young adult (18-29 years), BFMI was higher in women (p < 0.001) but plateaued in men aged >50 years. For men, age-related difference in LTMI was not evident but ALTMI was significantly lower in those >50 years. For women, there was evidence of significantly lower LTMI with advancing age and, similar to men, significantly lower ALTMI in those >50 years. CONCLUSIONS: These data provide an insight into the age-related anthropometric phenotype of Irish adults. Centile data have been constructed that provide informative data of the age and sex-specific range of adiposity and lean tissue mass. These data may assist in identification of those at risk of aberrant, body composition-related disease.

Prevalence and correlates of diagnosed and undiagnosed type 2 diabetes mellitus and pre-diabetes in older adults: Findings from the Irish Longitudinal Study on Ageing (TILDA).

AIMS: The prevalence of type 2 diabetes and pre-diabetes has increased rapidly in recent decades and this trend will continue as the global population ages. This study investigates the prevalence of, and factors associated with, diagnosed and undiagnosed type 2 diabetes mellitus and pre-diabetes in older adults in Ireland. METHODS: Cross-sectional data from 5377 men and women aged 50 and over from Wave 1 of the Irish Longitudinal Study on Ageing (TILDA) was analysed. Diagnosed diabetes was defined using self-reported doctors' diagnosis and medications data. Glycated haemoglobin (HbA1c) analysis was used to identify undiagnosed and pre-diabetes. Age and sex-specific prevalence estimates were generated. Logistic regression was used to investigate the association between diabetes classification and the demographic, health and lifestyle characteristics of the population. RESULTS: The prevalence of diagnosed and undiagnosed type 2 diabetes was 8.6% (95% confidence interval (CI): 7.6-9.5%) and 0.9% (95% CI: 0.6-1.1%) respectively. Diabetes was more prevalent in men than women and increased with age. The prevalence of pre-diabetes was 5.5% (95% CI: 4.8-6.3%) and increased with age. Diabetes and pre-diabetes were independently associated with male sex, central obesity and a history of hypertension, while undiagnosed diabetes was associated with geographic location and medical costs cover. CONCLUSION: Despite high rates of obesity and other undiagnosed health conditions, the prevalence of undiagnosed and pre-diabetes is relatively low in community-dwelling older adults in Ireland. Addressing lifestyle factors in this population may help to further reduce the prevalence of pre-diabetes and improve outcomes for those with a previous diagnosis.

Plant trait expression responds to establishment timing.

Trait divergence between co-occurring individuals could decrease the strength of competition between these individuals, thus promoting their coexistence. To test this hypothesis, we manipulated establishment timing for four congeneric pairs of perennial plants and assessed trait plasticity. Because soil conditions can affect trait expression and competition, we grew the plants in field-collected soil from each congener. Competition was generally weak across species, but the order of establishment affected divergence in biomass between potmates for three congeneric pairs. The type of plastic response differed among genera, with trait means of early-establishing individuals of Rumex and Solanum spp. differing from late-establishing individuals, and trait divergence between potmates of Plantago and Trifolium spp. depending on which species established first. Consistent with adaptive trait plasticity, higher specific leaf area (SLA) and root-shoot ratio in Rumex spp. established later suggest that these individuals were maximizing their ability to capture light and soil resources. Greater divergence in SLA correlated with increased summed biomass of competitors, which is consistent with trait divergence moderating the strength of competition for some species. Species did not consistently perform better in conspecific or congener soil, but soil type influenced the effect of establishment order. For example, biomass divergence between Rumex potmates was greater in R. obtusifolius soil regardless of which species established first. These results suggest that plant responses to establishment timing act in a species-specific fashion, potentially enhancing coexistence in plant communities.

The Complete Genome Sequence of Methanobrevibacter sp. AbM4.

Methanobrevibacter sp. AbM4 was originally isolated from the abomasal contents of a sheep and was chosen as a representative of the Methanobrevibacter wolinii clade for genome sequencing. The AbM4 genome is smaller than that of the rumen methanogen M. ruminantium M1 (2.0 Mb versus 2.93 Mb), encodes fewer open reading frames (ORFs) (1,671 versus 2,217) and has a lower G+C percentage (29% versus 33%). Overall, the composition of the AbM4 genome is very similar to that of M1 suggesting that the methanogenesis pathway and central metabolism of these strains are highly similar, and both organisms are likely to be amenable to inhibition by small molecule inhibitors and vaccine-based methane mitigation technologies targeting these conserved features. The main differences compared to M1 are that AbM4 has a complete coenzyme M biosynthesis pathway and does not contain a prophage or non-ribosomal peptide synthase genes. However, AbM4 has a large CRISPR region and several type I and type II restriction-modification system components. Unusually, DNA-directed RNA polymerase B' and B'' subunits of AbM4 are joined, a feature only previously observed in some thermophilic archaea. AbM4 has a much reduced complement of genes encoding adhesin-like proteins which suggests it occupies a ruminal niche different from that of M1.

Genome sequencing of rumen bacteria and archaea and its application to methane mitigation strategies.

Ruminant-derived methane (CH4), a potent greenhouse gas, is a consequence of microbial fermentation in the digestive tract of livestock. Development of mitigation strategies to reduce CH4 emissions from farmed animals is currently the subject of both scientific and environmental interest. Methanogens are the sole producers of ruminant CH4, and therefore CH4 abatement strategies can either target the methanogens themselves or target the other members of the rumen microbial community that produce substrates necessary for methanogenesis. Understanding the relationship that methanogens have with other rumen microbes is crucial when considering CH4 mitigation strategies for ruminant livestock. Genome sequencing of rumen microbes is an important tool to improve our knowledge of the processes that underpin those relationships. Currently, several rumen bacterial and archaeal genome projects are either complete or underway. Genome sequencing is providing information directly applicable to CH4 mitigation strategies based on vaccine and small molecule inhibitor approaches. In addition, genome sequencing is contributing information relevant to other CH4 mitigation strategies. These include the selection and breeding of low CH4-emitting animals through the interpretation of large-scale DNA and RNA sequencing studies and the modification of other microbial groups within the rumen, thereby changing the dynamics of microbial fermentation.

Progress in the development of vaccines against rumen methanogens.

Vaccination against rumen methanogens offers a practical approach to reduce methane emissions in livestock, particularly ruminants grazing on pasture. Although successful vaccination strategies have been reported for reducing the activity of the rumen-dwelling organism Streptococcus bovis in sheep and S. bovis and Lactobacillus spp. in cattle, earlier approaches using vaccines based on whole methanogen cells to reduce methane production in sheep have produced less promising results. An anti-methanogen vaccine will need to have broad specificity against methanogens commonly found in the rumen and induce antibody in saliva resulting in delivery of sufficiently high levels of antibodies to the rumen to reduce methanogen activity. Our approach has focussed on identifying surface and membrane-associated proteins that are conserved across a range of rumen methanogens. The identification of potential vaccine antigens has been assisted by recent advances in the knowledge of rumen methanogen genomes. Methanogen surface proteins have been shown to be immunogenic in ruminants and vaccination of sheep with these proteins induced specific antibody responses in saliva and rumen contents. Current studies are directed towards identifying key candidate antigens and investigating the level and types of salivary antibodies produced in sheep and cattle vaccinated with methanogen proteins, stability of antibodies in the rumen and their impact on rumen microbial populations. In addition, there is a need to identify adjuvants that stimulate high levels of salivary antibody and are suitable for formulating with protein antigens to produce a low-cost and effective vaccine.

Prophage-like elements in bifidobacteria: insights from genomics, transcription, integration, distribution, and phylogenetic analysis.

So far, there is only fragmentary and unconfirmed information on bacteriophages infecting the genus Bifidobacterium. In this report we analyzed three prophage-like elements that are present in the genomes of Bifidobacterium breve UCC 2003, Bifidobacterium longum NCC 2705, and Bifidobacterium longum DJO10A, designated Bbr-1, Bl-1, and Blj-1, respectively. These prophagelike elements exhibit homology with genes of double-stranded DNA bacteriophages spanning a broad phylogenetic range of host bacteria and are surprisingly closely related to bacteriophages infecting low-G+C bacteria. All three prophage-like elements are integrated in a tRNA(Met) gene, which appears to be reconstructed following phage integration. Analysis of the distribution of this integration site in many bifidobacterial species revealed that the attB sites are well conserved. The Blj-1 prophage is 36.9 kb long and was induced when a B. longum DJO10A culture was exposed to mitomycin C or hydrogen peroxide. The Bbr-1 prophage-like element appears to consist of a noninducible 28.5-kb chimeric DNA fragment composed of a composite mobile element inserted into prophage-like sequences, which do not appear to be widely distributed among B. breve strains. Northern blot analysis of the Bbr-1 prophage-like element showed that large parts of its genome are transcriptionally silent. Interestingly, a gene predicted to encode an extracellular beta-glucosidase carried within the Bbr-1 prophage-like element was shown to be transcribed.

Magnetic resonance image tissue classification using a partial volume model.

We describe a sequence of low-level operations to isolate and classify brain tissue within T1-weighted magnetic resonance images (MRI). Our method first removes nonbrain tissue using a combination of anisotropic diffusion filtering, edge detection, and mathematical morphology. We compensate for image nonuniformities due to magnetic field inhomogeneities by fitting a tricubic B-spline gain field to local estimates of the image nonuniformity spaced throughout the MRI volume. The local estimates are computed by fitting a partial volume tissue measurement model to histograms of neighborhoods about each estimate point. The measurement model uses mean tissue intensity and noise variance values computed from the global image and a multiplicative bias parameter that is estimated for each region during the histogram fit. Voxels in the intensity-normalized image are then classified into six tissue types using a maximum a posteriori classifier. This classifier combines the partial volume tissue measurement model with a Gibbs prior that models the spatial properties of the brain. We validate each stage of our algorithm on real and phantom data. Using data from the 20 normal MRI brain data sets of the Internet Brain Segmentation Repository, our method achieved average kappa indices of kappa = 0.746 +/- 0.114 for gray matter (GM) and kappa = 0.798 +/- 0.089 for white matter (WM) compared to expert labeled data. Our method achieved average kappa indices kappa = 0.893 +/- 0.041 for GM and kappa = 0.928 +/- 0.039 for WM compared to the ground truth labeling on 12 volumes from the Montreal Neurological Institute's BrainWeb phantom.

Variable presentation of parvovirus B19 in a family.

This case report of the sequential presentation of parvovirus B19 in a family describes a 38-year-old woman initially presenting with 'gloves and socks' syndrome, along with her husband and five children who were also affected. A high clinical attack rate with prolonged illness and variable clinical presentations was demonstrated, including polyarthritis, erythema infectiosum and symptoms of a respiratory tract infection. In addition, the range of syndromes and clinical features of parvovirus B19 are presented.

Clinical management of pain in children with cancer: selected approaches and innovative strategies.

More than 50% of children with cancer experience some type of cancer-related pain. Yet many children with cancer do not receive the benefit of current knowledge or innovative techniques in pain management. The authors review specific types of pain observed in children with cancer. The case studies are examples of clinical situations in which the child with cancer experiences pain. Each case study is followed by a discussion of appropriate pain management strategies. Approaches to pain management discussed in this article emphasize several of the new techniques that are now being used for pediatric cancer pain management.

Familial occurrence of multiple nonmelanoma skin cancer.

A survey of patients with histologically confirmed nonmelanoma skin cancer (NMSC) found 12 families in which several members developed skin cancers. The prevalence of NMSC in these families was far greater than in the normal population. The trait appeared to be dominantly inherited, and NMSC developed at an earlier age in succeeding generations, possibly because of a change in sun exposure habits.

Squamous cell carcinoma in southern and northern Australia.

Squamous cell carcinoma (scc) of the skin was studied in two similar populations, one living in the temperate zone of Australia, the other living in the tropics. In the tropics, the patients were significantly younger, the man to woman ratio approached unity, and women had significantly more sccs on the legs. In the temperate zone, men had significantly more on the head and neck, but women had significantly more on the upper and lower limbs.

Basal-cell carcinoma in temperate and tropical Australia.

The clinical features of patients with basal-cell carcinoma (BCC) living in temperate and tropical Australia were studied. In the temperate zone the patients were considerably older on average, men outnumbered women and there were differences between the sexes in the site of the prevalent BCC. In the tropics the patients were significantly younger on average, the male-to-female ratio approached unity and there were no differences between the sexes with regard to the site of the BCC.

Skin cancers and HLA frequencies in renal transplant recipients.

An association between HLA DR7 and the development of multiple non-melanoma skin cancer was detected in immunosuppressed patients in southern Australia. The relative risk was 2.6 which was lower than for immunocompetent patients with the same skin cancers. HLA frequencies of renal transplant recipients with multiple skin cancers were determined. The types HLA B27 and HLA Dr7 were found in significantly higher frequency, and there was no absence of HLA A11.