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. Urbanisation has been reported to have an increasing impact on soils. Using an urban soil geochemistry database of elemental concentrations of potentially toxic elements (PTEs), we investigated the association of the standardised incidence rates (SIRs) of both CKD and CKD of uncertain aetiology (CKDu) with environmental factors (PTEs), controlling for social deprivation. A compositional data analysis approach was used through balances (a special class of log contrasts) to identify elemental balances associated with CKDu. A statistically significant relationship was observed between CKD with the social deprivation measures of employment, income and education (significance levels of 0.001, 0.01 and 0.001, respectively), which have been used as a proxy for socio-economic factors such as smoking. Using three alternative regression methods (linear, generalised linear and Tweedie models), the elemental balances of Cr/Ni and As/Mo were found to produce the largest correlation with CKDu. Geogenic and atmospheric pollution deposition, traffic and brake wear emissions have been cited as sources for these PTEs which have been linked to kidney damage. This research, thus, sheds light on the increasing global burden of CKD and, in particular, the environmental and anthropogenic factors that may be linked to CKDu, particularly environmental PTEs linked to urbanisation.

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. Since the concentration of chemical elements is compositional, as the attributes vary together, here we present a novel approach to build compositional indicators based on Compositional Data (CoDa) principles. The steps of this new methodology are: 1) Exploratory data analysis through variation matrix, biplots or CoDa dendrograms; 2) Selection of geological background in terms of a trimmed subsample that can be assumed as non-pollutant; 3) Computing the spread Aitchison distance from each sample point to the trimmed sample; 4) Performing a compositional balance able to predict the Aitchison distance computed in step 3.Identifying a compositional balance, including pollutant and non-pollutant elements, with sparsity and simplicity as properties, is crucial for the construction of a Compositional Pollution Indicator (CI). Here we explored a database of 150 soil samples and 37 chemical elements from the contaminated region of Langreo, Northwestern Spain. There were obtained three Cis: the first two using elements obtained through CoDa analysis, and the third one selecting a list of pollutants and non-pollutants based on expert knowledge and previous studies. The three indicators went through a Stochastic Sequential Gaussian simulation. The results of the 100 computed simulations are summarized through mean image maps and probability maps of exceeding a given threshold, thus allowing characterization of the spatial distribution and variability of the CIs. A better understanding of the trends of relative enrichment and PTEs fate is discussed.

Chromosomal abnormalities in leukocytes from LSD-25 users.

A significant increase of chromosomal abnormalities was found in leukocytes from LSD-25 users (six out of eight) compared to nonuser controls (one out of nine). The two LSD-25 users showing no damage reported the lowest estimated average dose. The subjects whose cells showed damage were tested between 1 day and 6 months after their last LSD-25 dose.

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. Thus, instead of defining a microbial signature as a linear combination in real space corresponding to the abundances of a group of taxa, we consider microbial signatures given by the geometric means of data from two groups of taxa whose relative abundances, or balance, are associated with the response variable of interest. In this work we present selbal, a greedy stepwise algorithm for selection of balances or microbial signatures that preserves the principles of compositional data analysis. We illustrate the algorithm with 16S rRNA abundance data from a Crohn's microbiome study and an HIV microbiome study. IMPORTANCE We propose a new algorithm for the identification of microbial signatures. These microbial signatures can be used for diagnosis, prognosis, or prediction of therapeutic response based on an individual's specific microbiota.

Sperm studies in heterozygote inversion carriers: a review.

The risk of producing unbalanced gametes in heterozygous inversion carriers mostly depends on the occurrence of recombination events within the inverted segment. Recombination determines the possibility of producing chromosomes with duplications/deficiencies (pericentric inversions) or with duplications/deficiencies which furthermore appear as dicentric and acentric fragments (paracentric inversions). In this work, a general description of the close relationship between the occurrence of crossovers in pericentric and paracentric inversions and the final segregation outcome is presented. After this introduction, a compilation of inversion segregation data and interchromosomal effect results from previously published sperm studies have been reviewed. Segregation results indicate a great heterogeneity in the percentage of unbalanced gametes, from 0 to 37.38%. The size of the inverted segments and their proportion in the chromosome are two parameters closely related with the incidence of recombination (P < 0.0001; using a quadratic model and Pearson's correlation test). These results suggest that the production of a significant level of unbalanced gametes would require a minimum inversion size of 100 Mbp and the inversion of at least 50% of the chromosome. Interchromosomal effects are seldom observed in chromosomal inversions. Finally, implications of the meiotic behavior of the inversions in the progeny of the carriers and the incorporation of sperm FISH segregation analysis for reproductive genetic counseling are discussed.

Evolutionary conserved chromosomal segments in the human karyotype are bounded by unstable chromosome bands.

In this paper an ancestral karyotype for primates, defining for the first time the ancestral chromosome morphology and the banding patterns, is proposed, and the ancestral syntenic chromosomal segments are identified in the human karyotype. The chromosomal bands that are boundaries of ancestral segments are identified. We have analyzed from data published in the literature 35 different primate species from 19 genera, using the order Scandentia, as well as other published mammalian species as out-groups, and propose an ancestral chromosome number of 2n = 54 for primates, which includes the following chromosomal forms: 1(a+c(1)), 1(b+c(2)), 2a, 2b, 3/21, 4, 5, 6, 7a, 7b, 8, 9, 10a, 10b, 11, 12a/22a, 12b/22b, 13, 14/15, 16a, 16b, 17, 18, 19a, 19b, 20 and X and Y. From this analysis, we have been able to point out the human chromosome bands more "prone" to breakage during the evolutionary pathways and/or pathology processes. We have observed that 89.09% of the human chromosome bands, which are boundaries for ancestral chromosome segments, contain common fragile sites and/or intrachromosomal telomeric-like sequences. A more in depth analysis of twelve different human chromosomes has allowed us to determine that 62.16% of the chromosomal bands implicated in inversions and 100% involved in fusions/fissions correspond to fragile sites, intrachromosomal telomeric-like sequences and/or bands significantly affected by X irradiation. In addition, 73% of the bands affected in pathological processes are co-localized in bands where fragile sites, intrachromosomal telomeric-like sequences, bands significantly affected by X irradiation and/or evolutionary chromosomal bands have been described. Our data also support the hypothesis that chromosomal breakages detected in pathological processes are not randomly distributed along the chromosomes, but rather concentrate in those important evolutionary chromosome bands which correspond to fragile sites and/or intrachromosomal telomeric-like sequences.

Evolutionary breakpoints are co-localized with fragile sites and intrachromosomal telomeric sequences in primates.

The concentration of evolutionary breakpoints in primate karyotypes in some particular regions or chromosome bands suggests that these chromosome regions are more prone to breakage. This is the first extensive comparative study which investigates a possible relationship of two genetic markers (intrachromosomal telomeric sequences [TTAGGG]n, [ITSs] and fragile sites [FSs]), which are implicated in the evolutionary process as well as in chromosome rearrangements. For this purpose, we have analyzed: (a) the cytogenetic expression of aphidicolin-induced FSs in Cebus apella and Cebus nigrivittatus (F. Cebidae, Platyrrhini) and Mandrillus sphinx (F. Cercopithecidae, Catarrhini), and (b) the intrachromosomal position of telomeric-like sequences by FISH with a synthetic (TTAGGG)n probe in C. apella chromosomes. The multinomial FSM statistical model allowed us to determinate 53 FSs in C. apella, 16 FSs in C. nigrivittatus and 50 FSs in M. sphinx. As expected, all telomeres hybridized with the probe, and 55 intrachromosomal loci were also detected in the Cebus apella karyotype. The chi(2) test indicates that the coincidence of the location of Cebus and Mandrillus FSs with the location of human FSs is significant (P < 0.005). Based on a comparative cytogenetic study among different primate species we have identified (or described) the chromosome bands in the karyotypes of Papionini and Cebus species implicated in evolutionary reorganizations. More than 80% of these evolutionary breakpoints are located in chromosome bands that express FSs and/or contain ITSs.

Meiotic abnormalities in infertile males.

Meiotic anomalies, as reviewed here, are synaptic chromosome abnormalities, limited to germ cells that cannot be detected through the study of the karyotype. Although the importance of synaptic errors has been underestimated for many years, their presence is related to many cases of human male infertility. Synaptic anomalies can be studied by immunostaining of synaptonemal complexes (SCs), but in this case their frequency is probably underestimated due to the phenomenon of synaptic adjustment. They can also be studied in classic meiotic preparations, which, from a clinical point of view, is still the best approach, especially if multiplex fluorescence in situ hybridization is at hand to solve difficult cases. Sperm chromosome FISH studies also provide indirect evidence of their presence. Synaptic anomalies can affect the rate of recombination of all bivalents, produce achiasmate small univalents, partially achiasmate medium-sized or large bivalents, or affect all bivalents in the cell. The frequency is variable, interindividually and intraindividually. The baseline incidence of synaptic anomalies is 6-8%, which may be increased to 17.6% in males with a severe oligozoospermia, and to 27% in normozoospermic males with one or more previous IVF failures. The clinical consequences are the production of abnormal spermatozoa that will produce a higher number of chromosomally abnormal embryos. The indications for a meiotic study in testicular biopsy are provided.

Linear increase of diploidy in human sperm with age: a four-colour FISH study.

The aim of this study was to determine if donor age is associated with an increased incidence of diploidy and of disomy for the sex chromosomes and for chromosomes 6 and 21. We used simultaneous fluorescence in situ hybridisation (FISH) for chromosomes 6, 21, X and Y in sperm from 18 healthy donors, aged 24-74 years (mean 48.8 years). A total of 194 024 sperm were analysed, with a minimum of 10 000 sperm scored for each donor. Our results indicate a significant increase of the level of diploidy (P=0.002), and a marginal significance of total sex chromosome disomy (P=0.055) with age. No increase was observed for disomies XX, YY, XY, 21 or 6. The percentages of increase for disomy and for diploidy ranged from 0.3 to 17% for each 10-year period. Chromosomes 6 and 21 did not segregate preferentially with the X or Y chromosomes. Our findings show a linear trend association between age and diploidy in human males.

Meiotic segregation analysis in a t(4;8) carrier: comparison of FISH methods on sperm chromosome metaphases and interphase sperm nuclei.

Meiotic segregation of a t(4;8)(q28;p23) translocation carrier was determined by two different methods to compare the final results. A total of 352 sperm chromosome complements, obtained after human-hamster in vitro fertilisation, were analysed by whole chromosome painting, and 6590 sperm heads were studied by fluorescence in situ hybridisation (FISH). Frequencies of alternate, adjacent I, adjacent II and 3 : 1 segregations were, for sperm chromosomes, 35.5, 33.2, 19.9 and 11.3% respectively. For sperm head analysis, results were 30.5, 28.5, 20.5 and 19.5% respectively. There were no statistically significant differences between the two methods with respect to the observed frequencies of sperm with balanced and unbalanced chromosome constitutions. Among unbalanced gametes, the methods differed only in the frequency of 3 : 1 segregation (chi(2), P<0.0001). Different factors that could explain this result are discussed. To determine possible interchromosomal effects, multicolour FISH was used on sperm heads. Disomy rates of sex and 18 chromosomes were higher in the translocation carrier than in the control. The differences observed were statistically significant (P<0.0001 for chromosomes X and 18, and P=0.0091 for chromosome Y).

Cytogenetic analysis of sperm chromosomes and sperm nuclei in a male heterozygous for a reciprocal translocation t(5;7)(q21;q32) by in situ hybridisation.

We have studied the meiotic segregation of a reciprocal translocation t(5;7)(q21;q32) in a male carrier, using the human sperm-hamster oocyte fusion technique and the whole chromosome painting. A total of 296 sperm complements were analysed by dual chromosome painting. The frequencies of alternate, adjacent-1, adjacent-2 and 3:1 segregation were 49.7%, 32.4%, 16.2% and 1.7% respectively. Aneuploidy frequencies for chromosomes not involved in the translocation were determined by FISH on decondensed sperm heads using probes from chromosomes X, Y, 6, 18 and 21. A total of 20,118 spermatozoa was analysed, 10,201 by two-colour FISH (probes for chromosomes 6 and 21) and 9917 by three-colour FISH (probes for chromosomes X, Y, and 18). There was no evidence of an interchromosomal effect, since disomy frequencies were within the range of normal controls.

Cytogenetic effects of radiotherapy: frequency and types of chromosome aberrations.

The frequency and types of chromosome aberrations induced by ionizing radiation in cancer patients were evaluated in 24 cases studied just before and immediately after radiotherapy. The incidence of aberrant metaphases prior to treatment was 9.98% and increased significantly after treatment to 32.8%. The frequency of chromosome aberrations before radiotherapy was, with the exception of the cases of breast cancer and seminoma, significantly higher than that in our laboratory controls. A comparison of chromosome abnormalities observed before and after treatment indicated that dicentric translocations, rings, and reciprocal translocations increased by a factor of 23, 13, and 11, respectively, after radiotherapy. Ionizing radiation produces more asymmetrical than symmetrical chromosome aberrations and more two-break than one-break anomalies.

Human supernumeraries: are they B chromosomes?

In humans, the presence of supernumerary chromosomes is an unusual phenomenon, which is often associated with developmental abnormalities and malformations. In contrast to most animal and plant species, the extensive knowledge of the human genome and the ample set of molecular and cytogenetic tools available have permitted to ascertain not only that most human supernumerary chromosomes (HSCs) derive from the A chromosome set, but also the specific A chromosome from which most of them arose. These extra chromosomes are classified into six types on the basis of morphology and size. There are both heterochromatic and euchromatic HSCs, the latter being more detrimental. Most are mitotically stable, except some producing individual mosaicism. No information is available on the HSC transmission rate since extensive familial studies are not usually performed generally because of death of the relatives or lack of cooperation. The main B chromosome property failing in HSCs seems to be their population spread as polymorphisms, since most HSCs seem to correspond to extra A chromosomes or centric fragments spontaneously arisen in the analysed individual or one of his/her parents. However, we cannot rule out at this moment, that more intensive studies on population distribution and frequency of those HSCs most closely resembling B chromosomes (i.e. those heterochromatic and thus less detrimental) would reveal possible HSCs polymorphisms. Although HSCs cannot be considered B chromosomes, some of them might be a source for future B chromosomes. The best candidates would be heterochromatic HSCs, which might manage to drive in either sex. To ascertain this possibility, research on inheritance and population studies would be very helpful in combination with the powerful cytogenetic and molecular tools available for our species.

The use of a cell-cycle phase-marker may decrease the percentage of errors when using FISH in PGD.

Fluorescent DNA probes are used to characterise the chromosome constitution of preimplantation embryos. FISH is used to select normal or balanced embryos in carriers of balanced chromosomal rearrangements, for embryo sexing or for aneuploidy screening in women of advanced age, who have had recurrent abortions or IVF failures. In most cases, FISH is performed on interphase blastomeres which are asynchronously dividing cells, that can be in G1, S or G2. However, a correct interpretation of a double FISH signal, which may correspond to a split signal, to a replicated chromosome region or to the presence of an extra chromosome is essential to establish an accurate diagnosis. To determine if the cell stage could influence the interpretation of FISH results, we compared the signal characteristics of one locus-specific probe, two different subtelomere region probes, and a centromere region probe in non-dividing Sertoli cells and in proliferating lymphocytes. Most cells had two signals per chromosome pair (i.e., a situation corresponding to G0 in Sertoli cells and to G1 or to a prereplication stage in lymphocytes). Nevertheless, in proliferating cells the percentage of nuclei with a number of signals different from the expected (two unreplicated chromosomes per pair) was different from that found in non-dividing cells (P < 0.05). It was estimated that 10.8% of double dots in dividing cells resulted from DNA replication. The sequence of replication was first the locus-specific region, second a telomere region, and third the centromere. In conclusion, the DNA replication process could result in errors of interpretation (misdiagnosis) in 7% of proliferating cells. Thus, the use of a cell cycle phase-specific marker could avoid errors by indicating the cell stage in which the nucleus analysed is found.

Characterization of all human male synaptonemal complexes by subtelomere multiplex-FISH.

During meiotic prophase I, homologous chromosomes synapse and recombine. Both events are of vital importance for the success of meiosis. When homologous chromosomes synapse, a proteinaceous structure called synaptonemal complex (SC) appears along the pairing axis and meiotic recombination takes place. The existence of immunolabeling techniques for SC proteins (SCP1, SCP2 and SCP3) and for DNA mismatch repair proteins present in late recombination nodules (MLH1) allow analyses of both synapsis and meiotic recombination in the gametocyte I. In situ hybridization methods can be applied afterwards because chromatin is preserved during cell fixation for immunoanalysis. The combination of both methodologies allows the analysis of synapsis and the creation of recombination maps for each bivalent. In this work we apply the seven-fluorochrome subtelomere-specific multiplex FISH assay (stM-FISH) to human male meiotic cells previously labeled by immunofluorescence (SCP1, SCP3, MLH1, CENP) to assess its utility for human SC karyotyping. This FISH method consists of microdissected subtelomeric probes labeled combinatorially with seven different fluorochromes. Results prove its usefulness for the identification of all human SCs. Furthermore, by labeling subtelomeric regions this one-single-step method enables the characterization of interstitial and terminal SC fragments and SC delineation even if superposition is present in pachytene spreads.

Genetic analysis of sperm and implications of severe male infertility--a review.

The use of fluorescence in situ hybridization (FISH) on decondensed sperm heads has allowed to analyse the chromosome constitution of spermatozoa in different populations. In controls, the mean incidence of disomy (including all chromosomes) is about 6.7 per cent; diploidy increases with age, and some individuals may show a special tendency to nondisjunction. Carriers of numerical sex chromosome anomalies show a low incidence of sex chromosome disomies (2.54-7.69 per cent), and the need to screen ICSI candidates for these conditions has to be reconsidered. Carriers of inversions produce from 0 to 54.3 per cent abnormal sperm. Carriers of Robertsonian translocations produce from 3.4 to 36.0 per cent abnormal sperm, and carriers of reciprocal translocations produce from 47.5 to 81.0 per cent abnormal spermatozoa. However, carriers of translocations usually produce more abnormal embryos than expected from these figures. This may be partly related to interchromosomal effects induced by some structural reorganizations. Males with oligoasthenozoospermia, low motility and/or high FSH concentrations show frequent synaptic anomalies, resulting in the production of aneuploid and diploid sperm. Testicular sperm show extremely high rates of chromosomal abnormalities. The risk of recurrent abortion is increased by the presence of chromosome abnormalities in sperm.

Chromosomal abnormalities in sperm.

The use of FISH (fluorescent in situ hybridization) in decondensed sperm nuclei has allowed, during the last decade, to indirectly study the chromosome constitution of human spermatozoa. Studies in control populations have been used to set up the basal level of aneuploidy for all human chromosomes and, based on conservative estimates, the percentage of chromosomally abnormal sperm in the general population could be considered to be at least 6.7%. In carriers of sex chromosome numerical anomalies and in severe oligozoospermic males (both frequent candidates for intracytoplasmic sperm injection), in structural chromosome carriers (enrolled in preimplantation genetic diagnosis programs) and in couples with recurrent miscarriage, sperm chromosome analyses by FISH could help to better establish a reproductive prognosis.

Preimplantation genetic diagnosis.

Preimplantation genetic diagnosis (PGD) includes a variety of techniques that have been developed to detect the transmission to the offspring of genetic diseases or of chromosome abnormalities by couples at risk before a pregnancy is established, to avoid these couples the risk of recurrent abortions and/or of repeated terminations of pregnancy. Candidate couples are carriers of gene mutations or of structural chromosome rearrangements, or with recurrent spontaneous abortions of unknown origin. Diagnostic procedures include different modalities of gene amplification using the polymerase chain reaction (PCR) or of fluorescent in situ hybridization (FISH). Embryo biopsies are carried out at the 6-8 cell stage. Healthy embryos are transferred on day 4 or at the blastocyst stage. By now, several hundred healthy children have been born using PGD, and only one diagnostic error has been reported.

Characterization of a heritable partial monosomy 18p by molecular and cytogenetic analysis.

This report describes the fourth case of heritable 18p monosomy, which was ascertained by prenatal diagnosis. Cytogenetic analysis of amniotic fluid cells by G-banding showed an apparently distal 18p chromosome deletion and a derivative X chromosome resulting from a translocation between the X and Y chromosomes. Analysis of peripheral blood lymphocytes from the parents by G-banding revealed the same chromosome 18 deletion in the mother, who did not have the X/Y translocation. Comparative genomic hybridization (CGH) studies confirmed the loss of chromosome region 18p11.3-pter previously detected, and eliminated the presence of unbalanced reorganizations of other chromosome regions. No subtle translocation was detected by fluorescence in situ hybridization (FISH) studies using whole chromosome specific painting probes. This is a new report of a heritable 18p monosomy. Although in our case the mother had several minor congenital malformations, the loss of 18p11.3 band was not associated with any obvious phenotypic alteration in the fetus.

Bends in human mitotic metaphase chromosomes revisited: 15q11-13 is the most frequent non-random autosomal bend in blood cultures.

We have investigated the preferential bending of some chromosome sites in blood cultures from normal and chromosomally abnormal subjects. A total of 2,262 centromeric and 2,718 non-centromeric bends were recorded, and 69 non-centromeric sites were found not to bend at random. 15q11-13 bending was found to be the most frequent non-random autosomal bend. Bends on chromosomes may be remnants of a folded chromosome state in the nucleus, and may facilitate the preferential involvement of some chromosomal bands in structural reorganizations such as the isoacentric fragments, or contribute to the high frequency of interstitial deletions and isodicentric inversion duplications involving the 15q11-13 region.