Classification of non-coding variants with high pathogenic impact

Whole genome sequencing is increasingly used to diagnose medical conditions of genetic origin. While both coding and non-coding DNA variants contribute to a wide range of diseases, most patients who receive a WGS-based diagnosis today harbour a protein-coding mutation. Functional interpretation and prioritization of non-coding variants represents a persistent challenge, and disease-causing non-coding variants remain largely unidentified. Depending on the disease, WGS fails to identify a candidate variant in 20–80% of patients, severely limiting the usefulness of sequencing for personalised medicine. Here we present FINSURF, a machine-learning approach to predict the functional impact of non-coding variants in regulatory regions. FINSURF outperforms state-of-the-art methods, owing in particular to optimized control variants selection during training. In addition to ranking candidate variants, FINSURF breaks down the score for each variant into contributions from individual annotations, facilitating the evaluation of their functional relevance. We applied FINSURF to a diverse set of 30 diseases with described causative non-coding mutations, and correctly identified the disease-causative non-coding variant within the ten top hits in 22 cases. FINSURF is implemented as an online server to as well as custom browser tracks, and provides a quick and efficient solution to prioritize candidate non-coding variants in realistic clinical settings.     

Profiling substrate fluxes in the isolated working mouse heart using 13C-labeled substrates: focusing on the origin and fate of pyruvate and citrate carbons

The availability of genetically modified mice requires the development of methods to assess heart function and metabolism in the intact beating organ. With the use of radioactive substrates and ex vivo perfusion of the mouse heart in the working mode, previous studies have documented glucose and fatty acid oxidation pathways. This study was aimed at characterizing the metabolism of other potentially important exogenous carbohydrate sources, namely, lactate and pyruvate. This was achieved by using (13)C-labeling methods. The mouse heart perfusion setup and buffer composition were optimized to reproduce conditions close to the in vivo milieu in terms of workload, cardiac functions, and substrate-hormone supply to the heart (11 mM glucose, 0.8 nM insulin, 50 microM carnitine, 1.5 mM lactate, 0.2 mM pyruvate, 5 nM epinephrine, 0.7 mM oleate, and 3% albumin). The use of three differentially (13)C-labeled carbohydrates and a (13)C-labeled long-chain fatty acid allowed the quantitative assessment of the metabolic origin and fate of tissue pyruvate as well as the relative contribution of substrates feeding acetyl-CoA (pyruvate and fatty acids) and oxaloacetate (pyruvate) for mitochondrial citrate synthesis. Beyond concurring with the notion that the mouse heart preferentially uses fatty acids for energy production (63.5 +/- 3.9%) and regulates its fuel selection according to the Randle cycle, our study reports for the first time in the mouse heart the following findings. First, exogenous lactate is the major carbohydrate contributing to pyruvate formation (42.0 +/- 2.3%). Second, lactate and pyruvate are constantly being taken up and released by the heart, supporting the concept of compartmentation of lactate and glucose metabolism. Finally, mitochondrial anaplerotic pyruvate carboxylation and citrate efflux represent 4.9 +/- 1.8 and 0.8 +/- 0.1%, respectively, of the citric acid cycle flux and are modulated by substrate supply. The described (13)C-labeling strategy combined with an experimental setup that enables continuous monitoring of physiological parameters offers a unique model to clarify the link between metabolic alterations, cardiac dysfunction, and disease development.     

Bacterial endophytes from rice cut grass (<Emphasis Type="Italic">Leersia oryzoides</Emphasis> L.) increase growth,promote root gravitropic response,stimulate root hair formation,and protect rice seedlings from disease

Background and Aims

Leersia oryzoides, a wild relative of rice (Oryza sativa), may carry potential seed-borne bacterial endophytes which could be used to enhance growth of rice. We hypothesized that seed-associated bacteria from L. oryzoides would be compatible with rice and promote seedling growth, development, and survival.

Methods

We isolated bacteria from seed of L. oryzoides and checked compatibility with rice as well as Bermuda grass seeds for seedling growth promotion. Internal colonisation of bacteria into root cells was observed by ROS staining and microscopic observation. Growth promoting bacteria were evaluated for IAA production, phosphate solubilization and antifungal activities.

Results

Overall, ten bacteria were found to be growth promoting in rice seedlings with effects including restoration of root gravitropic response, increased root and shoot growth, and stimulation of root hair formation. All bacteria were identified by 16S rDNA sequencing. Six bacteria were found to become intracellular in root parenchyma and root hairs in rice and in Bermuda grass seedlings. Six bacteria were able to produce IAA in LB broth with highest (47.06 ± 1.99 μg ml^?1) by LTE3 (Pantoea hericii). Nine isolates solubilized phosphate and inhibited at least one soil borne fungal pathogen.

Conclusions

Seed bacteria of L. oryzoides are compatible with rice. Many of these bacteria become intracellular, induce root gravitropic response, increase root and shoot growth, and stimulate root hair formation in both rice and Bermuda grass seedlings. Presence of bacteria protects seedlings from soil pathogens during seedling establishment. This research suggests that bioprospecting microbes on near relatives of rice and other crop plants may be a viable strategy to obtain microbes to improve cultivation of crops.

     

Adapting the dynamic LakeMab model to simulate seasonal variations of phosphorus concentration in reservoirs: a case study of Lake Bultière (France)

Limnology - Controlling phosphorus is fundamental to limit the risk of eutrophication of continental aquatic ecosystems. Integrated modelling of its concentration in the aquatic continuum requires...     

Animal linguistics: a primer

The evolution of language has been investigated by several research communities, including biologists and linguists, striving to highlight similar linguistic capacities across species. To date, however, no consensus exists on the linguistic capacities of non-human species. Major controversies remain on the use of linguistic terminology, analysis methods and behavioural data collection. The field of ‘animal linguistics’ has emerged to overcome these difficulties and attempt to reach uniform methods and terminology. This primer is a tutorial review of ‘animal linguistics’. It describes the linguistic concepts of semantics, pragmatics and syntax, and proposes minimal criteria to be fulfilled to claim that a given species displays a particular linguistic capacity. Second, it reviews relevant methods successfully applied to the study of communication in animals and proposes a list of useful references to detect and overcome major pitfalls commonly observed in the collection of animal behaviour data. This primer represents a step towards mutual understanding and fruitful collaborations between linguists and biologists.     

Role of the antigenic loop of the hepatitis B virus envelope proteins in infectivity of hepatitis delta virus

The infectious particles of hepatitis B virus (HBV) and hepatitis delta virus (HDV) are coated with the large, middle, and small envelope proteins encoded by HBV. While it is clear that the N-terminal pre-S1 domain of the large protein, which is exposed at the virion surface, is implicated in binding to a cellular receptor at viral entry, the role in infectivity of the envelope protein antigenic loop, also exposed to the virion surface and accessible to neutralizing antibodies, remains to be established. In the present study, mutations were created in the antigenic loop of the three envelope proteins, and the resulting mutants were evaluated for their capacity to assist in the maturation and infectivity of HDV. We observed that short internal combined deletions and insertions, affecting residues 109 to 133 in the antigenic loop, were tolerated for secretion of both subviral HBV particles and HDV virions. However, when assayed for infectivity on primary cultures of human hepatocytes or on the recently described HepaRG cell line, virions carrying deletions between residues 118 and 129 were defective. Single amino acid substitutions in this region revealed that Gly-119, Pro-120, Cys-121, Arg-122, and Cys-124 were instrumental in viral entry. These results demonstrate that in addition to a receptor-binding site previously identified in the pre-S1 domain of the L protein, a determinant of infectivity resides in the antigenic loop of HBV envelope proteins.     

A Dietary Supplement Containing Cinnamon,Chromium and Carnosine Decreases Fasting Plasma Glucose and Increases Lean Mass in Overweight or Obese Pre-Diabetic Subjects: A Randomized,Placebo-Controlled Trial

Background

Preventing or slowing the progression of prediabetes to diabetes is a major therapeutic issue.

Objectives

Our aim was to evaluate the effects of 4-month treatment with a dietary supplement containing cinnamon, chromium and carnosine in moderately obese or overweight pre-diabetic subjects, the primary outcome being change in fasting plasma glucose (FPG) level. Other parameters of plasma glucose homeostasis, lipid profile, adiposity and inflammatory markers were also assessed.

Methods

In a randomized, double-blind, placebo-controlled study, 62 subjects with a FPG level ranging from 5.55 to 7 mmol/L and a body mass index ≥25 kg/m², unwilling to change their dietary and physical activity habits, were allocated to receive a 4-month treatment with either 1.2 g/day of the dietary supplement or placebo. Patients were followed up until 6 months post-randomization.

Results

Four-month treatment with the dietary supplement decreased FPG compared to placebo (-0.24±0.50 vs +0.12±0.59 mmol/L, respectively, p = 0.02), without detectable significant changes in HbA1c. Insulin sensitivity markers, plasma insulin, plasma lipids and inflammatory markers did not differ between the treatment groups. Although there were no significant differences in changes in body weight and energy or macronutrient intakes between the two groups, fat-free mass (%) increased with the dietary supplement compared to placebo (p = 0.02). Subjects with a higher FPG level and a milder inflammatory state at baseline benefited most from the dietary supplement.

Conclusions

Four-month treatment with a dietary supplement containing cinnamon, chromium and carnosine decreased FPG and increased fat-free mass in overweight or obese pre-diabetic subjects. These beneficial effects might open up new avenues in the prevention of diabetes.

Trial Registration

ClinicalTrials.gov NCT01530685     

The Evolution of Vocal Communication: Inertia and Divergence in Two Closely Related Primates

International Journal of Primatology - Primate vocal repertoires change slowly over evolutionary time, making them good indicators of phylogenetic relatedness. Occasionally, however,...     

Biotic composition and microfacies distribution of Upper Triassic build-ups: new insights from the Lower Carnian limestone of Lesno Brdo,central Slovenia

The architecture and composition of Middle to lower Upper Triassic platforms is often obscured by dolomitization. Hence, comparatively little is known about their architectures compared to their size and geographic extent. An active quarry near Lesno Brdo (central Slovenia) offers an excellent exposure of Lower Carnian (Julian) massive limestone, which is diagenetically little altered. A detailed microfacies analysis along a 15.5-m log revealed the presence of three facies types: fine-grained limestone as a groundmass, blocks and globular masses of sponge-microbialite boundstone, and lens-like aggregations of polychaete (terebellid) tubes. Sponge-microbialite boundstone contains a rather small number of cosmopolitan sponge taxa, solenoporacean red algae, microproblematica, bryozoans, and a small proportion of dwelling fauna. Instead, stromatolites represent the main constituent. While some blocks appear to have truncated margins, others show mammillary-like protrusions of microbialites into the surrounding sediment, suggesting active growth of microbialite-producing organisms. Aggregations of terebellid worm tubes show a highly irregular relief, with tubes placed sub-parallel to the ancient sea floor. The presence of fibrous rim cement, crystal silt, and in some cases fragmentation of the tubes, suggest at least moderately energetic waters. Aggregations are thus interpreted as preserved in situ, but not in toto. The entire complex was probably deposited at the margin or upper slope of a carbonate platform. Although the presence of a large number of terebellids associated with microbialites boundstone may indicate some sort of environmental stress, such a stress remains to be identified.