Low genotyping error rates in non-invasively collected samples from roe deer of the Bavarian Forest National Park

Genetic wildlife monitoring is increasingly carried out on the basis of non-invasively collected samples, whereby the most commonly used DNA sources are skin appendages (hairs, feathers) and faeces. In order to guide decisions regarding future adequate ways to monitor the roe deer (Capreolus capreolus) population of the Bavarian Forest National Park in Germany, we tested these two different types of DNA source materials to compare their suitability for genetic monitoring. We determined the haplotypes (d-loop) of 19 roe deer and genotyped each individual (tissue, hairs, faeces) across 12 microsatellite loci. The amount of missing and erroneous microsatellite alleles obtained from hair and faeces samples, respectively, was estimated based on comparisons with the corresponding tissue sample control. We observed no missing alleles in hair samples, but in fecal samples PCR failed in 30 out of 228 instances (19 individuals x 12 loci), corresponding to a frequency of missing alleles of 13.2% across all loci and individuals. In genotypes generated from hairs erroneous alleles were detected in 2 out of 228 instances (0.9%), while genotypes retrieved from fecal samples displayed erroneous alleles in 6 out of 198 remaining instances (3%). We conclude that both hair and fecal samples are generally well suited for genetic roe deer monitoring, but that fecal sample based analyses require a larger sample size to account for higher PCR failure rates.     

Criteria Used in Clinical Practice to Guide Immunosuppressive Treatment in Patients with Primary Sclerosing Cholangitis

Background & Aims

Current guidelines recommend immunosuppressive treatment (IT) in patients with primary sclerosing cholangitis (PSC) and elevated aminotransferase levels more than five times the upper limit of normal and elevated serum IgG-levels above twice the upper limit of normal. Since there is no evidence to support this recommendation, we aimed to assess the criteria that guided clinicians in clinical practice to initiate IT in patients with previously diagnosed PSC.

Methods

This is a retrospective analysis of 196 PSC patients from seven German hepatology centers, of whom 36 patients had received IT solely for their liver disease during the course of PSC. Analyses were carried out using methods for competing risks.

Results

A simplified autoimmune hepatitis (AIH) score >5 (HR of 36, p<0.0001) and a modified histological activity index (mHAI) greater than 3/18 points (HR 3.6, p = 0.0274) were associated with the initiation of IT during the course of PSC. Of note, PSC patients who subsequently received IT differed already at the time of PSC diagnosis from those patients, who did not receive IT during follow-up: they presented with increased levels of IgG (p = 0.004) and more frequently had clinical signs of cirrhosis (p = 0.0002).

Conclusions

This is the first study which investigates the parameters associated with IT in patients with PSC in clinical practice. A simplified AIH score >5 and a mHAI score >3, suggesting concomitant features of AIH, influenced the decision to introduce IT during the course of PSC. In German clinical practice, the cutoffs used to guide IT may be lower than recommended by current guidelines.     

The predictive value of trill performance in a large repertoire songbird,the nightingale Luscinia megarhynchos

In animal communication, elaborate signals have been shown to be under sexual selection and often to reliably indicate a signaler's quality, condition, or motivation. For instance, the performance of physically challenging signals such as trills – i.e. rapidly repeated elements of broad frequency bandwidth – is considered to reflect signaler quality. Nightingales Luscinia megarhynchos are renowned for their outstanding song repertoire sizes, and most songs include a variety of complex trills. In the present study, we examined whether performance of trills can reliably reflect male quality. We show that vocal performance of trills predicts the age of a male. Older males sang trills that were closer to the performance limit than did younger males. Moreover, males with narrower beaks sang more consistent trills than did males with wider beaks. Vocal performance of trills, however, did not significantly predict other measures of biometric quality such as body size or body condition of the males. The findings suggest that receivers could benefit from the predictive value of physically demanding song traits in assessing age as an important quality component of potential mates or rivals. Particularly in species with high singing versatility, signaler assessment based on readily assessable structures may be adaptive, as this will allow receivers to quickly gather relevant information about the singer without attending to the full song repertoire.     

Antifungal and physicochemical properties of Ocimum essential oil loaded in poly(lactic acid) nanofibers

Poly(lactic acid) (PLA) nanofibres containing different proportions of the essential oils from Ocimum basilicum L. and Ocimum gratissimum L. were prepared by solution blow spinning method. The essential oils were extracted by hydrodistillation and characterized by gas chromatography. MEV, contact angle, DSC and FTIR were used to characterize the nanofibres. The effect of bioative nanofibres on the growth of the fungus and on the production of ochratoxin A were evaluated using the fumigation test. Linalool, 1·8-cineole and camphor were the principal components of the essential oil from O. basilicum, and eugenol was the principal constituent in the oil from O. gratissimum. An increase in the average diameter of the nanofibres was observed with the addition of the essential oils. The essential oils acted as a plasticizer, resulting in a reduction in the crystallinity of the PLA. The encapsulation of essential oils in PLA nanofibres was verified by FTIR. An effective antifungal and antimicotoxygenic activity against Aspergillus ochraceus and Aspergillus westerdjikiae was observed for the bioative nanofibres. These results confirm the potential of PLA nanofibres containing the essential oils for the control of toxigenic fungi that cause the deterioration of food and are harmful to human health.     

The DcMaster Transposon Display maps polymorphic insertion sites in the carrot (Daucus carota L.) genome

DcMaster is a family of PIF/Harbinger-like class II transposable elements identified in carrot. We present a modified Transposon Display molecular marker system allowing amplification of genomic regions containing DcMaster elements. We scored 77 DcMaster Transposon Display (DcMTD) amplicons, of which 54 (70%) were segregating in the F₂ progeny from the cross between wild and cultivated carrot. Segregating amplicons were incorporated into a previously developed molecular linkage map of carrot. Twenty-eight markers were attributed to the wild parent, 23 originated from the cultivated parent, and three markers remained unlinked. The markers were evenly distributed among the nine linkage groups. However, differences in the distribution pattern of DcMaster insertion sites in the genomes of the wild and cultivated parent were observed. Specificity of the obtained amplicons was confirmed by sequencing and three putative DcMaster subfamilies, differing in the sequence of their terminal inverted repeats, were revealed.     

Interpretability of bi-level variable selection methods

Variable selection is usually performed to increase interpretability, as sparser models are easier to understand than full models. However, a focus on sparsity is not always suitable, for example, when features are related due to contextual similarities or high correlations. Here, it may be more appropriate to identify groups and their predictive members, a task that can be accomplished with bi-level selection procedures. To investigate whether such techniques lead to increased interpretability, group exponential LASSO (GEL), sparse group LASSO (SGL), composite minimax concave penalty (cMCP), and least absolute shrinkage, and selection operator (LASSO) as reference methods were used to select predictors in time-to-event, regression, and classification tasks in bootstrap samples from a cohort of 1001 patients. Different groupings based on prior knowledge, correlation structure, and random assignment were compared in terms of selection relevance, group consistency, and collinearity tolerance. The results show that bi-level selection methods are superior to LASSO in all criteria. The cMCP demonstrated superiority in selection relevance, while SGL was convincing in group consistency. An all-round capacity was achieved by GEL: the approach jointly selected correlated and content-related predictors while maintaining high selection relevance. This method seems recommendable when variables are grouped, and interpretation is of primary interest.     

Mikroskopische Studien zur Innervation des Magen-Darmkanales V.

Zusammenfassung Die interstitielle Zelle läßt sich vielleicht als die kleinste Form einer vegetativen Ganglienzelle betrachten.Im Auerbachschen Plexus des menschlichen Colons kommen Zellen vom Typus 1 und 2 nach Dogiel und viele kleine und mittelgroße, der Form nach sehr mannigfache Gnanglienzellan vor.Der Auerbachsche Plexus zeigt eine Gliederung in ein Primär-, Sekundär- und Tertiärgeflecht. Der mit dem Auerbachschen Plexus kontinuierlich zusammenhängende Plexus muscularis profundus besitzt in verhältnismäßig spärlicher, aber gleichmäßiger Verteilung Ganglienzellen.Die großen Ganglienzellen des Meissnerschen Plexus gehören vorwiegend dem Typus 2 nach Dogiel an; daneben gibt es noch eine Fülle kleiner, teils multipolarer, teils der Form nach schwer bestimmbarer Ganglienzellen.Die an die Muscularis mucosae grenzenden Maschen des Meissnerschen Plexus sind von außerordentlicher Feinheit und enthalten auch interstitielle Zellen.Der Meissnersche Plexus geht mit feinsten, netzartigen Faserzügen ohne scharfe Grenze in den in der Schleimhaut ausgebreiteten Plexus mucosus über. Letzterer enthält zwar in seinem an die Submucosa grenzenden Gebiet noch vereinzelte kleine multipolare Ganglienzellen, weist jedoch in seinen übrigen, dem Epithel genäherten Lagen nur noch interstitielle Zellen auf.Der Plexus mucosus besitzt die Form des Terminalretikulums, den Charakter einer netzartigen Endformation des vegetativen Nervensystems, das hier afferente, efferente und (Sekretorische Nervenelemente in einer gemeinsamen plasmodialen Leitbahn beherbergt.In der Schleimhaut des Processus vermiformis entwickelt der dort ausgebreitete Plexus mucosus eine außerordentliche Zartheit und Reichhaltigkeit seiner nervösen Elemente.In einem Falle von rein neurogener Appandizitis kommen im Plexus mucosus des menschlichen Processus vermiformis bei sonst intakter Schleimhaut neuromatöse Gewebsneubildungen vor, die als das Resultat eines im Terminalretikulum zutage tretenden Wucherungsprozesses gedeutet werden können.In einem Falle von Megacolon werden schwere pathologische Veränderungen, vor allem an den Zellen und Fasern des Auerbachschen Plexus und des Plexus muscularis profundus beschrieben.     

Predictors of Raised Viral Load during Antiretroviral Therapy in Patients with and without Prior Antiretroviral Use: A Cross-Sectional Study

Objectives

In Lagos, Nigeria, Médecins Sans Frontières (MSF) and the Ministry of Health (MoH) commenced free antiretroviral treatment (ART) in a hospital-based clinic. We performed a cross-sectional study to compare factors associated with raised viral load between patients with (“experienced”) and without (“naïve”) prior antiretroviral (ARV) exposure at commencement of ART at the clinic. We also examined factors influencing ARV adherence in experienced patients prior to clinic entry.

Methods

We included adult patients receiving ART from MSF who answered a questionnaire about previous antiretroviral use. Multivariate logistic regression was used to estimate odds ratios (OR) for raised viral load (≥1000 copies/mL).

Results

1246 (96%) patients answered: 1075 (86%) reported no, and 171 (14%) some, prior ARV exposure. ARV-naïve patients were more immunosuppressed at baseline: 65% vs 37% (p<0.001) had CD4<200; 17% vs 9% (p = 0.013) were WHO stage 4. Proportionately more experienced than naïve patients had raised viral loads (20% vs 9%, p<0.001) on ART in the MSF/MoH clinic. Raised viral load was associated with prior ARV experience (adjusted OR = 3.74, 95%CI 2.09–6.70, p<0.001) and complete interruption of current ART (adjusted OR = 3.71, 95%CI 2.06–6.68, p<0.001). Higher CD4 at time of VL and a higher self-rated score of recent adherence were associated with lower OR of a raised viral load. Among experienced patients who missed pills before joining MSF/MoH, most common reasons were because ARVS were not affordable (58%) or available (33%), with raised viral load associated with being unsure how to take them (OR = 3.16, 95%CI 1.10–9.12, p = 0.033).

Conclusions

Patients previously exposed to ARVs had increased OR of raised viral load. The cost and availability of ARVs were common reasons for missing ARVs before joining the MSF/MoH clinic, and inadequate patient knowledge was associated with raised viral load.