Structure and metabolic potential of the prokaryotic communities from the hydrothermal system of Paleochori Bay, Milos, Greece.

Introduction: Shallow hydrothermal systems share many characteristics with their deep-sea counterparts, but their accessibility facilitates their study. One of the most studied shallow hydrothermal vent fields lies at Paleochori Bay off the coast of Milos in the Aegean Sea (Greece). It has been studied through extensive mapping and its physical and chemical processes have been characterized over the past decades.

Irrigation suitability, health risk assessment and source apportionment of heavy metals in surface water used for irrigation near marble industry in Malakand, Pakistan.

Water is a vital, finite resource whose quantity and quality are deteriorating as the world population increases. The current study aims to investigate the concentration of heavy metals (HM) in surface water for irrigation purposes with associated human health risks and pollution sources near the marble industry in Malakand, Pakistan. Twenty-seven water samples were randomly collected and analyzed for HM concentration by inductively coupled plasma‒optical emission spectrometry (ICP‒OES).

Principal microbial groups: compositional alternative to phylogenetic grouping of microbiome data.

Statistical and machine learning techniques based on relative abundances have been used to predict health conditions and to identify microbial biomarkers. However, high dimensionality, sparsity and the compositional nature of microbiome data represent statistical challenges. On the other hand, the taxon grouping allows summarizing microbiome abundance with a coarser resolution in a lower dimension, but it presents new challenges when correlating taxa with a disease.

Compositional baseline assessments to address soil pollution: An application in Langreo, Spain.

Potentially Toxic Elements (PTEs) are contaminants with high toxicity and complex geochemical behaviour and, therefore, high PTEs contents in soil may affect ecosystems and/or human health. However, before addressing the measurement of soil pollution, it is necessary to understand what is meant by pollution-free soil. Often, this background, or pollution baseline, is undefined or only partially known.

Some thoughts on counts in sequencing studies.

Measurements in sequencing studies are mostly based on counts. There is a lack of theoretical developments for the analysis and modelling of this type of data. Some thoughts in this direction are presented, which might serve as a seed.

Chronic kidney disease of unknown origin is associated with environmental urbanisation in Belfast, UK.

Chronic kidney disease (CKD), a collective term for many causes of progressive renal failure, is increasing worldwide due to ageing, obesity and diabetes. However, these factors cannot explain the many environmental clusters of renal disease that are known to occur globally. This study uses data from the UK Renal Registry (UKRR) including CKD of uncertain aetiology (CKDu) to investigate environmental factors in Belfast, UK.

Long-term impact of fecal transplantation in healthy volunteers.

Background: Fecal microbiota transplantation (FMT) has been recently approved by FDA for the treatment of refractory recurrent clostridial colitis (rCDI). Success of FTM in treatment of rCDI led to a number of studies investigating the effectiveness of its application in the other gastrointestinal diseases. However, in the majority of studies the effects of FMT were evaluated on the patients with initially altered microbiota.

Exploration of geochemical data with compositional canonical biplots.

The study of the relationships between two compositions is of paramount importance in geochemical data analysis. This paper develops a compositional version of canonical correlation analysis, called CoDA-CCO, for this purpose. We consider two approaches, using the centred log-ratio transformation and the calculation of all possible pairwise log-ratios within sets.

Balances: a New Perspective for Microbiome Analysis.

High-throughput sequencing technologies have revolutionized microbiome research by allowing the relative quantification of microbiome composition and function in different environments. In this work we focus on the identification of microbial signatures, groups of microbial taxa that are predictive of a phenotype of interest. We do this by acknowledging the compositional nature of the microbiome and the fact that it carries relative information.

Microbiome Datasets Are Compositional: And This Is Not Optional.

Datasets collected by high-throughput sequencing (HTS) of 16S rRNA gene amplimers, metagenomes or metatranscriptomes are commonplace and being used to study human disease states, ecological differences between sites, and the built environment. There is increasing awareness that microbiome datasets generated by HTS are compositional because they have an arbitrary total imposed by the instrument. However, many investigators are either unaware of this or assume specific properties of the compositional data.

It's all relative: analyzing microbiome data as compositions.

Purpose: The ability to properly analyze and interpret large microbiome data sets has lagged behind our ability to acquire such data sets from environmental or clinical samples. Sequencing instruments impose a structure on these data: the natural sample space of a 16S rRNA gene sequencing data set is a simplex, which is a part of real space that is restricted to nonnegative values with a constant sum. Such data are compositional and should be analyzed using compositionally appropriate tools and approaches.

Proportionality: a valid alternative to correlation for relative data.

In the life sciences, many measurement methods yield only the relative abundances of different components in a sample. With such relative-or compositional-data, differential expression needs careful interpretation, and correlation-a statistical workhorse for analyzing pairwise relationships-is an inappropriate measure of association. Using yeast gene expression data we show how correlation can be misleading and present proportionality as a valid alternative for relative data.

Differential effects of genetic vs. environmental quality in Drosophila melanogaster suggest multiple forms of condition dependence.

Condition is a central concept in evolutionary ecology, but the roles of genetic and environmental quality in condition-dependent trait expression remain poorly understood. Theory suggests that condition integrates genetic, epigenetic and somatic factors, and therefore predicts alignment between the phenotypic effects of genetic and environmental quality. To test this key prediction, we manipulated both genetic (mutational) and environmental (dietary) quality in Drosophila melanogaster and examined responses in morphological and chemical (cuticular hydrocarbon, CHC) traits in both sexes.

The plant ionome revisited by the nutrient balance concept.

Tissue analysis is commonly used in ecology and agronomy to portray plant nutrient signatures. Nutrient concentration data, or ionomes, belongs to the compositional data class, i.e.

Severe neutropenia in a renal transplant patient suggesting an interaction between mycophenolate and fenofibrate.

Objective: To describe a patient in whom initiation of micronized fenofibrate precipitated mycophenolate induced neutropenia.

Case Summary: A 57-year-old man was admitted to the hospital because of febrile neutropenia. He had undergone kidney transplantation seventeen years ago.

Chromatid segregation analysis in native human lymphocyte anaphases using sequential fluorescence in situ hybridization.

A sequential multiprobe fluorescence in situ hybridization technique was developed to study the 13, 18, 21, X and Y chromatid segregation in human lymphocytes anaphases cultures without antimitotic treatment. This method was used to know if exist any different chromosomes segregation in lymphocytes from Down syndrome patients and compared it with controls. The results show that the prevalent sequence of centromere separation was X, 13, 21, Y and 18 in Down syndrome patients and Y, 13, X, 21 and 18 in controls.

The use of foetal ovarian stromal cell culture for cytogenetic diagnosis. Stromal ovarian culture cytogenetic diagnosis.

Some studies have been carried out to analyze human female first meiotic prophase. Most of them use samples from foetuses collected after legal interruption of pregnancy. In some cases, a control population is needed and foetuses aborted for non-chromosomal reasons are used.

Genomic imbalances in urothelial cancer: intratumor heterogeneity versus multifocality.

Comparative genomic hybridization and fluorescence in situ hybridization were used to define genetic changes associated with multifocal bladder cancer and to investigate whether the genetic relationship between synchronous urothelial tumors is similar to that observed within different parts of the same tumor. We investigated 8 synchronous urothelial tumors from 3 patients and macroscopically different parts of the same tumor from 2 other patients. The most frequent imbalances were gains of 1q, 2p, and 17q, and losses in 4q.

Pairing and synapsis in oocytes from female fetuses with euploid and aneuploid chromosome complements.

Only little is known about the meiotic prophase events in human oocytes, although some of them are involved in the origin of aneuploidies. Here, a broad study of the pairing and synaptic processes in 3263 human euploid and 2613 aneuploid oocytes (47,XX, +21 and 47,XX, +13), using different techniques and methods, is presented in order to elucidate the characteristics of this essential meiotic process. Our results reaffirm the existence of a common high efficiency in the pairing process leading to the obtainment of a bivalent for all chromosomes studied in euploid and aneuploid cases.

The importance of aneuploidy screening in reciprocal translocation carriers.

The purpose of this study is to investigate the aneuploidy rate and the mosaicism of chromosomes not involved in reciprocal translocations. Aneuploidy screening (AS) (13, 16, 18, 21 and 22) was performed as a re-analysis on fixed blastomeres from 126 embryos already analysed in preimplantation genetic diagnosis (PGD) cycles of eight female and five male reciprocal translocation carriers who had not achieved a pregnancy. A successful diagnosis for AS was achieved in 91.

A human tetraploid pachytene spermatocyte as the possible origin of diploid sperm: a case report.

Diploid spermatozoa represent 0.2-0.3% of all spermatozoa in the normal population and cause 8.

Genetic reproductive risk in inversion carriers.

Objective: To evaluate the risk of four inversion carriers for producing unbalanced gametes.

Design: Prospective analysis of sperm nuclei by fluorescence in situ hybridization (FISH).

Setting: Universitat Autònoma de Barcelona.

Behaviour of human heterochromatic regions during the synapsis of homologous chromosomes.

Background: Alterations of synapsis can disturb or arrest meiosis and result in infertility. Synaptic abnormalities are frequently observed in infertile patients but also in fertile men.

Methods: The subtelomere-specific multiplex fluorescence in-situ hybridization (stM-FISH) has been applied in combination with immunofluorescence to identify all synaptonemal complexes (SCs) and to analyse those presenting synaptic anomalies in fertile and infertile men.

Human fetal ovarian culture permits meiotic progression and chromosome pairing process.

Background: The female meiotic process seems to be crucial for aneuploidy in humans. The first stages of mammalian female meiosis take place during the fetal period. Therefore, only little is known about female meiosis.

Crossover frequency and synaptonemal complex length: their variability and effects on human male meiosis.

In this study, immunocytogenetics has been used in combination with the subtelomere-specific multiplex-fluorescent in-situ hybridization (stM-FISH) assay to identify 4681 autosomal synaptonemal complexes (SCs) of two fertile men. Comparisons of crossover maps for each individual SC between two men with extremely different meiotic crossover frequencies show that a low crossover frequency results in (i) a higher frequency of XY pairs and of small SCs without MLH1 foci and (ii) lower frequency of crossovers in the proximity of centromeres. In both cases, the bivalents which most frequently lacked MLH1 foci were the XY pair and the SC21.