16S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus

The EU-protected slug Geomalacus maculosus Allman occurs only in the West of Ireland and in northern Spain and Portugal. We explored the microbial community found within the faeces of Irish specimens with a view to determining whether a core microbiome existed among geographically isolated slugs which could give insight into the adaptations of G. maculosus to the available food resources within its habitat. Faecal samples of 30 wild specimens were collected throughout its Irish range and the V3 region of the bacterial 16S rRNA gene was sequenced using Illumina MiSeq. To investigate the influence of diet on the microbial composition, faecal samples were taken and sequenced from six laboratory reared slugs which were raised on two different foods. We found a widely diverse microbiome dominated by Enterobacteriales with three core OTUs shared between all specimens. While the reared specimens appeared clearly separated by diet in NMDS plots, no significant difference between the slugs fed on the two different diets was found. Our results indicate that while the majority of the faecal microbiome of G. maculosus is probably dependent on the microhabitat of the individual slugs, parts of it are likely selected for by the host

The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool

Background: Amplicon sequencing methods targeting the 16S rRNA gene have been used extensively to investigate microbial community composition and dynamics in anaerobic digestion. These methods successfully characterize amplicons but do not distinguish micro-organisms that are actually responsible for the process. In this research, the archaeal and bacterial community of 48 full-scale anaerobic digestion plants were evaluated on DNA (total community) and RNA (active community) level via 16S rRNA (gene) amplicon sequencing. Results: A significantly higher diversity on DNA compared with the RNA level was observed for archaea, but not for bacteria. Beta diversity analysis showed a significant difference in community composition between the DNA and RNA of both bacteria and archaea. This related with 25.5 and 42.3% of total OTUs for bacteria and archaea, respectively, that showed a significant difference in their DNA and RNA profiles. Similar operational parameters affected the bacterial and archaeal community, yet the differentiating effect between DNA and RNA was much stronger for archaea. Co-occurrence networks and functional prediction profiling confirmed the clear differentiation between DNA and RNA profiles. Conclusions: In conclusion, a clear difference in active (RNA) and total (DNA) community profiles was observed, implying the need for a combined approach to estimate community stability in anaerobic digestion

Weathering of the Ethiopian volcanic province: a new weathering index to characterize and compare soils

© Walter de Gruyter Berlin/Boston 2015.Soil formation occurs through numerous physical and chemical weathering processes acting to alter the parent rock on the Earths surface. Samples of surface soils were collected over a range of elevations (2000-3600 m) from profiles directly overlying basaltic to more felsic parent rocks, over a region in NW Ethiopia. The soils were investigated to determine their chemical composition and X-ray diffraction was used to identify and quantify individual mineral phases. The data set was analyzed using non-parametric statistics (Spearmans Rank and Mann-Whitney U tests) to compare the soils forming over the two parent rocks. Principal component analysis (PCA) was used to identify the mineral alteration assemblage and formation during pedogenesis. The extent of alteration was quantified using several chemical weathering indices (Chemical Index of Alteration = CIA; Chemical Index of Weathering = CIW), including an index calculated by multivariate analyses of the soil chemical composition data (weathering W index). Further to this we devised and tested a new weathering index (Wmin) using multivariate analysis of the soil mineralogy, to estimate the extent of weathering and physico-chemical proprieties of the parent rock from which the soil formed. The soils present a fair to advanced stage of alteration, with abundant iron (Fe) oxides (up to 40 wt%) and phyllosilicates (up to 57 wt%), including kaolinite-smectite (K-S) mixed-layer phases. The K-S was composed of either 30-50% kaolinite or 94-98% kaolinite layers. Discrete kaolinite was also present. The bimodal K-S mineralogical composition is likely due to two precursor phases: feldspar for the kaolinite-rich K-S and volcanic glass for the smectite-rich K-S. K-S with intermediate composition (50-94% kaolinite) was rare, due to its instability. Statistical analysis showed significant differences between the chemical compositions of the soils developed on the two different parent volcanic compositions. The soils overlying the more felsic parent rocks were less altered than those overlying the flood basalt. When comparing the weathering indices calculated in this study, we conclude that while the CIA and CIW may be more readily determined, the W and Wmin indices can elucidate information on the composition of the original rock from which they formed. The W index is more sensitive to certain variables when compared with the newly derived mineralogical Wmin index; however the Wmin index takes into account mineral phases within the sample, which provides a more detailed interpretation of weathering rates than chemistry alone. In addition the Wmin index correlated with meteorological variables, such as elevation (and consequently temperature and precipitation), known to influence the degree of pedogenesis. The Wmin index can be used to enhance our understanding of the processes that occur during weathering processes to supplement information gained from traditional chemical weathering indices

Use of Tranexamic acid is a cost effective method in preventing blood loss during and after total knee replacement

<p>Abstract</p> <p>Background & Purpose</p> <p>Allogenic blood transfusion in elective orthopaedic surgery is best avoided owing to its associated risks. Total knee replacement often requires blood transfusion, more so when bilateral surgery is performed. Many strategies are currently being employed to reduce the amount of peri-operative allogenic transfusions. Anti-fibrinolytic compounds such as aminocaproic acid and tranexamic acid have been used systemically in perioperative settings with promising results. This study aimed to evaluate the effectiveness of tranexamic acid in reducing allogenic blood transfusion in total knee replacement surgery.</p> <p>Methodology</p> <p>This was a retrospective cohort study conducted on patients undergoing total knee replacement during the time period November 2005 to November 2008. Study population was 99 patients, of which 70 underwent unilateral and 29 bilateral knee replacement. Forty-seven patients with 62 (49.5%) knees (group-I) had received tranexamic acid (by surgeon preference) while the remaining fifty-two patients with 66 (51.5%) knees (group-II) had did not received any tranexamic acid either pre- or post-operatively.</p> <p>Results</p> <p>The mean drop in the post-operative haemoglobin concentration in Group-II for unilateral and bilateral cases was 1.79 gm/dl and 2.21 gm/dl, with a mean post-operative drainage of 1828 ml (unilateral) and 2695 ml (bilateral). In comparison, the mean drop in the post-op haemoglobin in Group-I was 1.49 gm/dl (unilateral) and 1.94 gm/dl (bilateral), with a mean drainage of 826 ml (unilateral) and 1288 ml (bilateral) (p-value < 0.001).</p> <p>Interpretation</p> <p>Tranexamic acid is effective in reducing post-operative drainage and requirement of blood transfusion after knee replacement.</p

Differential ratio amplicons (Ramp) for the evaluation of RNA integrity extracted from complex environmental samples

Reliability and reproducibility of transcriptomics‐based studies are dependent on RNA integrity. In microbial ecology, microfluidics‐based techniques, such as the Ribosomal Integrity Number (RIN), targeting rRNA are currently the only approaches to evaluate RNA integrity. However, the relationship between rRNA and mRNA integrity is unknown. Here we present an integrity index, the Ratio Amplicon, Ramp, adapted from human clinical studies, to directly monitor mRNA integrity from complex environmental samples. We show, in a suite of experimental degradations of RNA extracted from sediment, that while the RIN generally reflected the degradation status of RNA the Ramp mapped mRNA degradation better. Furthermore, we examined the effect of degradation on transcript community structure by amplicon sequencing of 16S rRNA, amoA and glnA transcripts. We successfully sequenced transcripts for all three targets even from highly‐degraded RNA samples. While RNA degradation changed the community structure of the mRNA profiles, no changes were observed for the 16S rRNA transcript profiles. Since both RT‐Q‐PCR and sequencing results were obtained, even from highly degraded samples, we strongly recommend evaluating RNA integrity prior to downstream processing to ensure meaningful results. For this both the RIN and Ramp are useful, with the Ramp better evaluating mRNA integrity in this study

Ordering of droplets and light scattering in polymer dispersed liquid crystal films

We study the effects of droplet ordering in initial optical transmittance through polymer dispersed liquid crystal (PDLC) films prepared in the presence of an electrical field. The experimental data are interpreted by using a theoretical approach to light scattering in PDLC films that explicitly relates optical transmittance and the order parameters characterizing both the orientational structures inside bipolar droplets and orientational distribution of the droplets. The theory relies on the Rayleigh-Gans approximation and uses the Percus-Yevick approximation to take into account the effects due to droplet positional correlations.Comment: revtex4, 18 pages, 8 figure

Bioreactor scalability: laboratory-scale bioreactor design influences performance, ecology, and community physiology in expanded granular sludge bed bioreactors

Studies investigating the feasibility of new, or improved, biotechnologies, such as wastewater treatment digesters, inevitably start with laboratory-scale trials. However, it is rarely determined whether laboratory-scale results reflect full-scale performance or microbial ecology. The Expanded Granular Sludge Bed (EGSB) bioreactor, which is a high-rate anaerobic digester configuration, was used as a model to address that knowledge gap in this study. Two laboratory-scale idealizations of the EGSB—a one-dimensional and a three- dimensional scale-down of a full-scale design—were built and operated in triplicate under near-identical conditions to a full-scale EGSB. The laboratory-scale bioreactors were seeded using biomass obtained from the full-scale bioreactor, and, spent water from the distillation of whisky from maize was applied as substrate at both scales. Over 70 days, bioreactor performance, microbial ecology, and microbial community physiology were monitored at various depths in the sludge-beds using 16S rRNA gene sequencing (V4 region), specific methanogenic activity (SMA) assays, and a range of physical and chemical monitoring methods. SMA assays indicated dominance of the hydrogenotrophic pathway at full-scale whilst a more balanced activity profile developed during the laboratory-scale trials. At each scale, Methanobacterium was the dominant methanogenic genus present. Bioreactor performance overall was better at laboratory-scale than full-scale. We observed that bioreactor design at laboratory-scale significantly influenced spatial distribution of microbial community physiology and taxonomy in the bioreactor sludge-bed, with 1-D bioreactor types promoting stratification of each. In the 1-D laboratory bioreactors, increased abundance of Firmicutes was associated with both granule position in the sludge bed and increased activity against acetate and ethanol as substrates. We further observed that stratification in the sludge-bed in 1-D laboratory-scale bioreactors was associated with increased richness in the underlying microbial community at species (OTU) level and improved overall performance

Lymphangiosarcoma of the arm presenting with lymphedema in a woman 16 years after mastectomy: a case report

Lymphangiosarcoma following breast cancer is a relatively rare entity, with around 300 cases so far reported worldwide. Affecting the long term survivors of breast cancer, lymphangiosarcoma (Stewart-Traves Syndrome) has a high mortality rate. Since lympedema following radical mastectomy or axillary clearance and radiotherapy seems to be the main predisposing factor, further research regarding modifications in the surgical technique of axillary nodes dissection as well as the development of new chemotherapeutic agents effective in lymphangiosarcoma are required