Rapid mapping of chromosomal breakpoints: from blood to BAC in 20 days

Structural chromosome aberrations and associated segmental or chromosomal aneusomies are major causes of reproductive failure in humans. Despite the fact that carriers of reciprocal balanced translocation often have no other clinical symptoms or disease, impaired chromosome homologue pairing in meiosis and karyokinesis errors lead to over-representation of translocations carriers in the infertile population and in recurrent pregnancy loss patients. At present, clinicians have no means to select healthy germ cells or balanced zygotes in vivo, but in vitro fertilization (IVF) followed by preimplantation genetic diagnosis (PGD) offers translocation carriers a chance to select balanced or normal embryos for transfer. Although a combination of telomeric and centromeric probes can differentiate embryos that are unbalanced from normal or unbalanced ones, a seemingly random position of breakpoints in these IVF-patients poses a serious obstacle to differentiating between normal and balanced embryos, which for most translocation couples, is desirable. Using a carrier with reciprocal translocation t(4;13) as an example, we describe our state-of-the-art approach to the preparation of patient-specific DNA probes that span or 'extent' the breakpoints. With the techniques and resources described here, most breakpoints can be accurately mapped in a matter of days using carrier lymphocytes, and a few extra days are allowed for PGD-probe optimization. The optimized probes will then be suitable for interphase cell analysis, a prerequisite for PGD since blastomeres are biopsied from normally growing day 3 – embryos regardless of their position in the mitotic cell cycle. Furthermore, routine application of these rapid methods should make PGD even more affordable for translocation carriers enrolled in IVF programs

Ensayo de una tipología de las cuencas mediterráneas del proyecto GUADALMED siguiendo las directrices de la Directiva Marco del Agua

RESUMEN Utilizando la propuesta de tipología de ríos de la Directiva Marco del Agua en su anexo 2 se realiza un ensayo tipológico de los puntos de muestreo del proyecto GUADALMED. Según el sistema A, se presentan 16 ecotipos, lo que se juzga poco adecuado para la gestión de los mismos y sin una base ecológica que lo justifique. De acuerdo con la selección previa hecha por los miembros del grupo GUADALMED para 5 de estos ecotipos no habría estaciones de referencia. Con algunas variables medidas en los puntos de muestreo y otras de tipo geológico e hidromorfológico, se realiza un ensayo tipológico usando el sistema B. El método implica un análisis de la correlación entre variables, un cluster de las estaciones utilizando el método K-means y un análisis discriminante de cuáles son las variables que distinguen estos grupos. El estudio da como resultado la caracterización de 6 ecotipos que sin embargo, a juicio de los miembros del proyecto GUADALMED, no recogen la variedad de tipos de ríos mediterráneos. Valorando cualitativamente parámetros no introducidos (por falta de datos) en el análisis K-means, se propone una tipología provisional en 9 grupos. Un análisis de las comunidades de macroinvertebrados (a nivel taxonómico de familia) revela un grado importante de coherencia entre las familias asociadas a cada tipo y sus preferencias ecológicas conocidas. ABSTRACT A preliminary analysis was conducted of the river types in the GUADALMED project using the river typology proposed in the Water Framework Directive (WFD) in its annex 2. Using System A, 16 different types were found, a number too high for water management purposes and such typology lacks a supportive ecological basis. For 5 of these 16 ecotypes, no reference stations exist. Reference stations were selected a priori in project GUADALMED for each of the 12 basins sampled. An ecotypological analysis was performed using System B of the WFD using several variables measured during the study, and other variables obtained from maps or data bases (e.g., geology). The method included the analysis of the calibration between variables, the clustering of stations by the K-means method and a discriminant analysis. The latter revealed which factors were distinctive of each group. Six ecotypes were established for the GUADALMED study sites. These, however, do not include all the mediterranean-type streams of the region. This is mainly due to the absence in the data base of some important features of streams in the data base such as temporality or the dependence of flow on the presence of karstic aquifers, attribute

Euploidy rates in donor egg cycles significantly differ between fertility centers

STUDY QUESTION: Do external factors affect euploidy in egg donor cycles? SUMMARY ANSWER: The study demonstrates that during human assisted reproduction, embryonic chromosome abnormalities may be partly iatrogenic. WHAT IS KNOWN ALREADY: Chromosome abnormalities have been linked in the past to culture conditions such as temperature and Ph variations, as well as hormonal stimulation. Those reports were performed with older screening techniques (FISH), or ART methods no longer in use, and the subjects studied were not a homogeneous group. STUDY DESIGN, SIZE, DURATION: A total of 1645 donor oocyte cycles and 13 282 blastocyst biopsies from 42 fertility clinics were included in this retrospective cohort study. Samples from donor cycles with PGS attempted between September 2011 and July 2015 were included. PARTICIPANTS/MATERIALS, SETTING, METHODS: PGS cycles from multiple fertility clinics referred to Reprogenetics (Livingston, NJ) that involved only oocyte donation were included in this study. Testing was performed by array comparative genomic hybridization (aCGH). Ploidy data were analyzed using Generalized Linear Mixed Models with logistic regression using a logit link function considering a number of variables that represent fixed and random effects. MAIN RESULTS AND THE ROLE OF CHANCE: Euploidy rate was associated with the referring center and independent of almost all the parameters examined except donor age and testing technology. Average euploidy rate per center ranged from 39.5 to 82.5%. The mean expected rate of euploidy was 68.4%, but there are variations in this rate associated with the center effect. LIMITATIONS, REASONS FOR CAUTION: Data set does not include details of the donor selection process, donor race or ethnic origin, ovarian reserve or ovarian responsiveness. Due to the retrospective nature of the study, associations are apparent, however, causality cannot be established. Discrepancies in regard to completeness and homogeneity of data exist due to data collection from over 40 different clinics. WIDER IMPLICATIONS OF THE FINDINGS: This is the first study to show a strong association between center-specific ART treatment practices and the incidence of chromosome abnormality in human embryos, although the meiotic or mitotic origin of these abnormalities could not be determined using these technologies. Given the widespread applications of ART in both subfertile and fertile populations, our findings should be of interest to the medical community in general as well as the ART community in particular. STUDY FUNDING/COMPETING INTEREST(S): No external funds were used for this study. S. Munne is a founding principle of Reprogenetics/current employee of Cooper Genomics. M Alikani’s spouse is a founding principle of Reprogenetics/current consultant for Cooper Genomics. The remaining authors have no conflicts to declare

Detailed investigation into the cytogenetic constitution and pregnancy outcome of replacing mosaic blastocysts detected with the use of high-resolution next-generation sequencing

Objective: To determine the pregnancy outcome potential of mosaic embryos, detected by means of preimplantation genetic screening (PGS) with the use of next-generation sequencing (NGS). Design: Retrospective study. Setting: Genetics laboratories. Patient(s): PGS cycles during which either mosaic or euploid embryos were replaced. Intervention(s): Blastocysts were biopsied and processed with the use of NGS, followed by frozen embryo transfer. Trophectoderm (TE) biopsies were classified as mosaic if they had 20%–80% abnormal cells. Main Outcome Measure(s): Implantation, miscarriage rates, and ongoing implantation rates (OIRs) were compared between euploid and types of mosaic blastocysts. Result(s): Complex mosaic embryos had a significantly lower OIR (10%) than aneuploidy mosaic (50%), double aneuploidy mosaic (45%), and segmental mosaic (41%). There was a tendency for mosaics with 40%–80% abnormal cells to have a lower OIR than those with 40% abnormal cells and those with multiple mosaic abnormalities (chaotic mosaics) are likely to have lower OIRs and should be given low transfer priority

Impacts of Use and Abuse of Nature in Catalonia with Proposals for Sustainable Management

This paper provides an overview of the last 40 years of use, and in many cases abuse, of the natural resources in Catalonia, a country that is representative of European countries in general, and especially those in the Mediterranean region. It analyses the use of natural resources made by mining, agriculture, livestock, logging, fishing, nature tourism, and energy production and consumption. This use results in an ecological footprint, i.e., the productive land and sea surface required to generate the consumed resources and absorb the resulting waste, which is about seven times the amount available, a very high number but very similar to other European countries. This overexploitation of natural resources has a huge impact on land and its different forms of cover, air, and water. For the last 25 years, forests and urban areas have each gained almost 3% more of the territory at the expense of agricultural land; those municipalities bordering the sea have increased their number of inhabitants and activity, and although they only occupy 6.7% of the total surface area, they account for 43.3% of the population; air quality has stabilized since the turn of the century, and there has been some improvement in the state of aquatic ecosystems, but still only 36% are in good condition, while the remainder have suffered morphological changes and different forms of nonpoint source pollution; meanwhile the biodiversity of flora and fauna remains still under threat. Environmental policies do not go far enough so there is a need for revision of the legislation related to environmental impact and the protection of natural areas, flora, and fauna. The promotion of environmental research must be accompanied by environmental education to foster a society which is Land 2021, 10, 144 3 of 53 more knowledgeable, has more control and influence over the decisions that deeply affect it. Indeed, nature conservation goes hand in hand with other social and economic challenges that require a more sustainable vision. Today’s problems with nature derive from the current economic model, which is environmentally unsustainable in that it does not take into account environmental impacts. Lastly, we propose a series of reasonable and feasible priority measures and actions related to each use made of the country’s natural resources, to the impacts they have had, and to their management, in the hope that these can contribute to improving the conservation and management of the environment and biodiversity and move towards sustainability.info:eu-repo/semantics/publishedVersio