ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis

peer-reviewedCrAssphages are an extensive and ubiquitous family of tailed bacteriophages, predicted to infect bacteria of the order Bacteroidales. Despite being found in ~50% of individuals and representing up to 90% of human gut viromes, members of this viral family have never been isolated in culture and remain understudied. Here, we report the isolation of a CrAssphage (ΦCrAss001) from human faecal material. This bacteriophage infects the human gut symbiont Bacteroides intestinalis, confirming previous in silico predictions of the likely host. DNA sequencing demonstrates that the bacteriophage genome is circular, 102 kb in size, and has unusual structural traits. In addition, electron microscopy confirms that ΦcrAss001 has a podovirus-like morphology. Despite the absence of obvious lysogeny genes, ΦcrAss001 replicates in a way that does not disrupt proliferation of the host bacterium, and is able to maintain itself in continuous host culture during several weeks

How much variation in oocyte yield after controlled ovarian stimulation can be explained? A multilevel modelling study

How much variation in oocyte yield after controlled ovarian stimulation (COS) can be accounted for by known patient and treatment characteristics

Materials for phantoms for terahertz pulsed imaging

Phantoms are commonly used in medical imaging for quality assurance, calibration, research and teaching. They may include test patterns or simulations of organs, but in either case a tissue substitute medium is an important component of the phantom. The aim of this work was to identify materials suitable for use as tissue substitutes for the relatively new medical imaging modality terahertz pulsed imaging. Samples of different concentrations of the candidate materials TX151 and napthol green dye were prepared, and measurements made of the frequency-dependent absorption coefficient (0.5 to 1.5 THz) and refractive index (0.5 to 1.0 THz). These results were compared qualitatively with measurements made in a similar way on samples of excised human tissue (skin, adipose tissue and striated muscle). Both materials would be suitable for phantoms where the dominant mechanism to be simulated is absorption (similar to ∼100 cm(-1) at 1 THz) and where simulation of the strength of reflections from boundaries is not important; for example, test patterns for spatial resolution measurements. Only TX151 had a frequency-dependent refractive index close to that of tissue, and could therefore be used to simulate the layered structure of skin, the complexity of microvasculature or to investigate frequency-dependent interference effects that have been noted in terahertz images

Influence of Community‐Based Dental Education on Dental Students’ Preparation and Intent to Treat Underserved Populations

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/153622/1/jddj002203372012765tb05286x.pd

Methanosarcina play an important role in anaerobic co-digestion of the seaweed Ulva lactuca: metagenomics structure and predicted metabolism of functional microbial communities.

Macro-algae represent an ideal resource of third generation biofuels, but their use necessitates a refinement of commonly used anaerobic digestion processes. In a previous study, contrasting mixes of dairy slurry and the macro-alga Ulva lactuca were anaerobically digested in mesophilic continuously stirred tank reactors for 40 weeks. Higher proportions of U. lactuca in the feedstock led to inhibited digestion and rapid accumulation of volatile fatty acids, requiring a reduced organic loading rate. In this study, 16S pyrosequencing was employed to characterise the microbial communities of both the weakest (R1) and strongest (R6) performing reactors from the previous work as they developed over a 39 and 27-week period respectively. Comparing the reactor communities revealed clear differences in taxonomy, predicted metabolic orientation and mechanisms of inhibition, while constrained canonical analysis (CCA) showed ammonia and biogas yield to be the strongest factors differentiating the two reactor communities. Significant biomarker taxa and predicted metabolic activities were identified for viable and failing anaerobic digestion of U. lactuca. Acetoclastic methanogens were inhibited early in R1 operation, followed by a gradual decline of hydrogenotrophic methanogens. Near-total loss of methanogens led to an accumulation of acetic acid that reduced performance of R1, while a slow decline in biogas yield in R6 could be attributed to inhibition of acetogenic rather than methanogenic activity. The improved performance of R6 is likely to have been as a result of the large Methanosarcina population, which enabled rapid removal of acetic acid, providing favourable conditions for substrate degradation

Psychometric Evaluation of a 13‐Point Measure of Students’ Overall Competence in Community‐Based Dental Education Programs

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/153670/1/jddj0022033720168010tb06207x.pd

Risk factors associated with detailed reproductive phenotypes in dairy and beef cows

peer-reviewedThis article was first published in animal, Volume 8, Issue 05, May 2014, pp 695-703, © The Animal Consortium 2014The objective of this study was to identify detailed fertility traits in dairy and beef cattle from transrectal ultrasonography records and quantify the associated risk factors. Data were available on 148 947 ultrasound observations of the reproductive tract from 75 949 cows in 843 Irish dairy and beef herds between March 2008 and October 2012. Traits generated included (1) cycling at time of examination, (2) cystic structures, (3) early ovulation, (4) embryo death and (5) uterine score; the latter was measured on a scale of 1 (good) to 4 (poor) characterising the tone of the uterine wall and fluid present in the uterus. After editing, 72 773 records from 44 415 dairy and beef cows in 643 herds remained. Factors associated with the logit of the probability of a positive outcome for each of the binary fertility traits were determined using generalised estimating equations; linear mixed model analysis was used for the analysis of uterine score. The prevalence of cycling, cystic structures, early ovulation and embryo death was 84.75%, 3.87%, 7.47% and 3.84%, respectively. The occurrence of the uterine heath score of 1, 2, 3 and 4 was 70.63%, 19.75%, 8.36% and 1.26%, respectively. Cows in beef herds had a 0.51 odds (95% CI = 0.41 to 0.63, P<0.001) of cycling at the time of examination compared with cows in dairy herds; stage of lactation at the time of examination was the same in both herd types. Furthermore, cows in dairy herds had an inferior uterine score (indicating poorer tone and a greater quantity of uterine fluid present) compared with cows in beef herds. The likelihood of cycling at the time of examination increased with parity and stage of lactation, but was reduced in cows that had experienced dystocia in the previous calving. The presence of cystic structures on the ovaries increased with parity and stage of lactation. The likelihood of embryo/foetal death increased with parity and stage of lactation. Dystocia was not associated with the presence of cystic structures or embryo death. Uterine score improved with parity and stage of lactation, while cows that experienced dystocia in the previous calving had an inferior uterine score. Heterosis was the only factor associated with increased likelihood of early ovulation. The fertility traits identified, and the associated risk factors, provide useful information on the reproductive status of dairy and beef cows.Funding from the Department of Agriculture, Food and Marine Research Stimulus Fund (RSF 11/S/133) and the OptiMIR project is gratefully acknowledged

Detecting microRNA activity from gene expression data

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression by binding to the messenger RNA (mRNA) of protein coding genes. They control gene expression by either inhibiting translation or inducing mRNA degradation. A number of computational techniques have been developed to identify the targets of miRNAs. In this study we used predicted miRNA-gene interactions to analyse mRNA gene expression microarray data to predict miRNAs associated with particular diseases or conditions.</p> <p>Results</p> <p>Here we combine correspondence analysis, between group analysis and co-inertia analysis (CIA) to determine which miRNAs are associated with differences in gene expression levels in microarray data sets. Using a database of miRNA target predictions from TargetScan, TargetScanS, PicTar4way PicTar5way, and miRanda and combining these data with gene expression levels from sets of microarrays, this method produces a ranked list of miRNAs associated with a specified split in samples. We applied this to three different microarray datasets, a papillary thyroid carcinoma dataset, an in-house dataset of lipopolysaccharide treated mouse macrophages, and a multi-tissue dataset. In each case we were able to identified miRNAs of biological importance.</p> <p>Conclusions</p> <p>We describe a technique to integrate gene expression data and miRNA target predictions from multiple sources.</p

High Surface Area and Z′ in a Thermally Stable 8-fold Polycatenated Hydrogen-bonded Framework

1,3,5-Tris(4-carboxyphenyl)benzene assembles into an intricate 8-fold polycatenated assembly of (6,3) hexagonal nets formed through hydrogen bonds and π-stacking. One polymorph features 56 independent molecules in the asymmetric unit, the largest Z′ reported to date. The framework is permanently porous, with a BET surface area of 1095 m2 g−1 and readily adsorbs N2, H2 and CO2