Evaluation of Commercial Probiotic Products

Although there is a vast number of probiotic products commercially available due to their acceptability and increasing usage, their quality control has continuously been a major concern. This study aimed to assess some commercially available probiotics on the UK market for content in relation to their label claim. Seven products were used for the study. The bacteria content were isolated, identified and enumerated on selective media. The results revealed that all products evaluated contained viable probiotic bacteria but only three out of the seven products (43%) contained the claimed culture concentration or more. None of the multispecies product contained all the labelled probiotic bacteria. Misidentification of some species occurred. The results concurred with previous studies and showed that quality issues with commercial probiotics remain. Since probiotic activity is linked with probiotic concentration and is strain specific, the need exist for a global comprehensive legislation to control the quality of probiotics whose market is gaining huge momentum

Phenotypic Characterization of EIF2AK4 Mutation Carriers in a Large Cohort of Patients Diagnosed Clinically With Pulmonary Arterial Hypertension.

BACKGROUND: Pulmonary arterial hypertension (PAH) is a rare disease with an emerging genetic basis. Heterozygous mutations in the gene encoding the bone morphogenetic protein receptor type 2 (BMPR2) are the commonest genetic cause of PAH, whereas biallelic mutations in the eukaryotic translation initiation factor 2 alpha kinase 4 gene (EIF2AK4) are described in pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Here, we determine the frequency of these mutations and define the genotype-phenotype characteristics in a large cohort of patients diagnosed clinically with PAH. METHODS: Whole-genome sequencing was performed on DNA from patients with idiopathic and heritable PAH and with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis recruited to the National Institute of Health Research BioResource-Rare Diseases study. Heterozygous variants in BMPR2 and biallelic EIF2AK4 variants with a minor allele frequency of <1:10 000 in control data sets and predicted to be deleterious (by combined annotation-dependent depletion, PolyPhen-2, and sorting intolerant from tolerant predictions) were identified as potentially causal. Phenotype data from the time of diagnosis were also captured. RESULTS: Eight hundred sixty-four patients with idiopathic or heritable PAH and 16 with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis were recruited. Mutations in BMPR2 were identified in 130 patients (14.8%). Biallelic mutations in EIF2AK4 were identified in 5 patients with a clinical diagnosis of pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Furthermore, 9 patients with a clinical diagnosis of PAH carried biallelic EIF2AK4 mutations. These patients had a reduced transfer coefficient for carbon monoxide (Kco; 33% [interquartile range, 30%-35%] predicted) and younger age at diagnosis (29 years; interquartile range, 23-38 years) and more interlobular septal thickening and mediastinal lymphadenopathy on computed tomography of the chest compared with patients with PAH without EIF2AK4 mutations. However, radiological assessment alone could not accurately identify biallelic EIF2AK4 mutation carriers. Patients with PAH with biallelic EIF2AK4 mutations had a shorter survival. CONCLUSIONS: Biallelic EIF2AK4 mutations are found in patients classified clinically as having idiopathic and heritable PAH. These patients cannot be identified reliably by computed tomography, but a low Kco and a young age at diagnosis suggests the underlying molecular diagnosis. Genetic testing can identify these misclassified patients, allowing appropriate management and early referral for lung transplantation

Phenotypic Characterization of <i>EIF2AK4</i> Mutation Carriers in a Large Cohort of Patients Diagnosed Clinically With Pulmonary Arterial Hypertension

Background: Pulmonary arterial hypertension (PAH) is a rare disease with an emerging genetic basis. Heterozygous mutations in the gene encoding the bone morphogenetic protein receptor type 2 ( BMPR2 ) are the commonest genetic cause of PAH, whereas biallelic mutations in the eukaryotic translation initiation factor 2 alpha kinase 4 gene ( EIF2AK4 ) are described in pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Here, we determine the frequency of these mutations and define the genotype-phenotype characteristics in a large cohort of patients diagnosed clinically with PAH. Methods: Whole-genome sequencing was performed on DNA from patients with idiopathic and heritable PAH and with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis recruited to the National Institute of Health Research BioResource–Rare Diseases study. Heterozygous variants in BMPR2 and biallelic EIF2AK4 variants with a minor allele frequency of &lt;1:10 000 in control data sets and predicted to be deleterious (by combined annotation-dependent depletion, PolyPhen-2, and sorting intolerant from tolerant predictions) were identified as potentially causal. Phenotype data from the time of diagnosis were also captured. Results: Eight hundred sixty-four patients with idiopathic or heritable PAH and 16 with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis were recruited. Mutations in BMPR2 were identified in 130 patients (14.8%). Biallelic mutations in EIF2AK4 were identified in 5 patients with a clinical diagnosis of pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Furthermore, 9 patients with a clinical diagnosis of PAH carried biallelic EIF2AK4 mutations. These patients had a reduced transfer coefficient for carbon monoxide (K co ; 33% [interquartile range, 30%–35%] predicted) and younger age at diagnosis (29 years; interquartile range, 23–38 years) and more interlobular septal thickening and mediastinal lymphadenopathy on computed tomography of the chest compared with patients with PAH without EIF2AK4 mutations. However, radiological assessment alone could not accurately identify biallelic EIF2AK4 mutation carriers. Patients with PAH with biallelic EIF2AK4 mutations had a shorter survival. Conclusions: Biallelic EIF2AK4 mutations are found in patients classified clinically as having idiopathic and heritable PAH. These patients cannot be identified reliably by computed tomography, but a low K co and a young age at diagnosis suggests the underlying molecular diagnosis. Genetic testing can identify these misclassified patients, allowing appropriate management and early referral for lung transplantation. </jats:sec

Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

Telomere length is a risk factor in disease and the dynamics of telomere length are crucial to our understanding of cell replication and vitality. The proliferation of whole genome sequencing represents an unprecedented opportunity to glean new insights into telomere biology on a previously unimaginable scale. To this end, a number of approaches for estimating telomere length from whole-genome sequencing data have been proposed. Here we present Telomerecat, a novel approach to the estimation of telomere length. Previous methods have been dependent on the number of telomeres present in a cell being known, which may be problematic when analysing aneuploid cancer data and non-human samples. Telomerecat is designed to be agnostic to the number of telomeres present, making it suited for the purpose of estimating telomere length in cancer studies. Telomerecat also accounts for interstitial telomeric reads and presents a novel approach to dealing with sequencing errors. We show that Telomerecat performs well at telomere length estimation when compared to leading experimental and computational methods. Furthermore, we show that it detects expected patterns in longitudinal data, repeated measurements, and cross-species comparisons. We also apply the method to a cancer cell data, uncovering an interesting relationship with the underlying telomerase genotype

Biological heterogeneity in idiopathic pulmonary arterial hypertension identified through unsupervised transcriptomic profiling of whole blood

Idiopathic pulmonary arterial hypertension (IPAH) is a rare but fatal disease diagnosed by right heart catheterisation and the exclusion of other forms of pulmonary arterial hypertension, producing a heterogeneous population with varied treatment response. Here we show unsupervised machine learning identification of three major patient subgroups that account for 92% of the cohort, each with unique whole blood transcriptomic and clinical feature signatures. These subgroups are associated with poor, moderate, and good prognosis. The poor prognosis subgroup is associated with upregulation of the ALAS2 and downregulation of several immunoglobulin genes, while the good prognosis subgroup is defined by upregulation of the bone morphogenetic protein signalling regulator NOG, and the C/C variant of HLA-DPA1/DPB1 (independently associated with survival). These findings independently validated provide evidence for the existence of 3 major subgroups (endophenotypes) within the IPAH classification, could improve risk stratification and provide molecular insights into the pathogenesis of IPAH

Demographic and life-history variability across the range of a widespread herb: the role of environmental, geographical and genetic factors / Variabilidad demográfica y de historia vital en una planta de amplia distribución: el papel de los factores medioambientales, geográficos y genéticos

[spa] Las especies de amplia distribución han recibido tradicionalmente poca atención, a pesar de su importancia para la estructura y el funcionamiento de los ecosistemas. En esta tesis, se analiza la variabilidad demográfica, de historia vital y genética en una planta de amplia distribución en Europa y el norte de África (Plantago coronopus), en un total de 22 poblaciones a lo largo de gran parte del rango latitudinal de la especie (centro y periferia norte). Se pretende analizar la magnitud y las causas de esta variabilidad intraespecífica en relación con la posición de las poblaciones dentro del rango y con los principales factores medioambientales. Las poblaciones periféricas mostraron una menor diversidad genética, pero no mostraron en general un peor o más variable comportamiento demográfico en cuanto a densidad o tasa de crecimiento poblacional, contradiciendo así las hipótesis clásicas centro-periferia. Se encontró un mismo patrón de diferenciación demográfica dentro de las regiones tanto central como periférica, en relación con la variación en el régimen de precipitaciones. La tasa de reclutamiento de nuevos individuos fue el proceso del ciclo vital con mayor importancia para el funcionamiento de las poblaciones. Se encontró también una gran variación entre poblaciones en las características de las semillas (número, tamaño, mucílago y proporción de dos tipos de semilla dimórficos) en relación con el gradiente de estrés ambiental. Finalmente, la variación fenotípica dentro de las poblaciones se relacionó con la variabilidad ambiental, mientras que la diversidad genética se correlacionó con la posición central vs. periférica de las poblaciones y posiblemente con la historia demográfica de la especie. Globalmente, este estudio muestra la importancia de distinguir entre periferia geográfica y marginalidad ecológica, y sugiere que el éxito de las plantas de amplia distribución reside en una gran variabilidad demográfica y de historia vital a diferentes escalas espaciales.[eng] Widespread species have traditionally received much less attention than rare and endemic ones. However, they are crucial in macroecological patterns and in ecosystem structure and functioning. Thus, understanding the characteristics that allow widespread organisms to extend over large areas has a high interest from both theoretical and applied perspectives. One of the most frequent hypotheses to explain the success of widespread plants is that they show much wider ecological niches, and thus a high life-history and demographic variability. However, studies are often very specific and carried out over small spatio-temporal scales, which hinders a general understanding of intraspecific variation in widespread taxa. In this thesis, we span a large spatio-temporal scale and a large environmental gradient to analyze the magnitude and the possible causes of natural variation in the in the range centre and the northern periphery of the widespread herb Plantago coronopus. More precisely, we analyze variability in population dynamics, life-history traits, and genetic diversity in up to 22 populations in Europe and North Africa. We aim to explore the relation of such variability with the position of populations within the species’ range, since peripheral populations are traditionally expected to show a lower and more variable performance with respect to central populations. Additionally, we aim to analyze the effects of the most relevant environmental factors in population and individual performance at different spatial scales. In the first chapter, we found higher values in central populations in some vital rates, such as fecundity and growth, but recruitment and density were higher in northern peripheral populations, and there were no clear differences between regions in temporal variability of vital rates. Differences in population performance across the species’ range seemed to be correlated with local precipitation and intraspecific competition. In the second chapter, differences in mean values and variability of vital rates between central and peripheral areas led to no differences in stochastic population growth rates. In addition, recruitment was the most influential vital rate for population growth rates at different spatial scales, and we found the same pattern of differentiation in population dynamics in response to environmental conditions within central and peripheral regions. In the third chapter, we reported high variation among populations in seed traits along a steep environmental stress gradient. Moreover, patterns in seed production were opposite at the fruit and the individual scale, as a strategy of populations to maximize fitness in each set of local conditions. Finally, in the fourth chapter, we found no relationship within populations between phenotypic variability and genetic diversity. Phenotypic variation was mainly shaped by precipitation variability, suggesting adaptive variation, whereas genetic diversity was correlated with the central vs. peripheral position, probably in close relation with some random demographic processes experienced by populations in the past. Despite genetic diversity was higher in central populations, our results contradicted classical hypotheses predicting a lower demographic performance towards species’ range edges. In fact, environmental conditions seemed to have a higher influence on plant performance than the position of populations within the species’ range, which calls for the necessity of distinguishing between geographical periphery and ecological marginality in demographic studies. Overall, our study highlights the versatility of P. coronopus at different spatial scales in response to varying environmental conditions, complementing similar findings of previous research on the same taxon at smaller spatial scales. Such life-history variability seems to be a key factor for widespread plants to extend over large and heterogeneous ranges

On the surface topography of ultrashort laser pulse treated steel surfaces

This paper concentrates on observations of the surface topography by scanning electron microscopy (SEM) on alloyed and stainless steels samples treated by ultrashort laser pulses with duration of 210 fs and 6.7 ps. Globular-like and jet-like objects were found depending on the various levels of the fluence applied. It is shown that these features appear due to solid-liquid and liquid-gas transitions within surface layer irradiated by intense laser light. The observations are confronted to the theory of short-pulsed laser light-matter interactions, including interference, excitation of electrons, electron-phonon coupling as well as subsequent ablation. It is shown that the orientation of small ripples does not always depend on the direction of the polarization of laser light. (C) 2011 Elsevier B.V. All rights reserved