Thermal evolution of gene expression profiles in Drosophila subobscura

BACKGROUND: Despite its pervasiveness, the genetic basis of adaptation resulting in variation directly or indirectly related to temperature (climatic) gradients is poorly understood. By using 3-fold replicated laboratory thermal stocks covering much of the physiologically tolerable temperature range for the temperate (i.e., cold tolerant) species Drosophila subobscura we have assessed whole-genome transcriptional responses after three years of thermal adaptation, when the populations had already diverged for inversion frequencies, pre-adult life history components, and morphological traits. Total mRNA from each population was compared to a reference pool mRNA in a standard, highly replicated two-colour competitive hybridization experiment using cDNA microarrays. RESULTS: A total of 306 (6.6%) cDNA clones were identified as 'differentially expressed' (following a false discovery rate correction) after contrasting the two furthest apart thermal selection regimes (i.e., 13°C vs . 22°C), also including four previously reported candidate genes for thermotolerance in Drosophila (Hsp26, Hsp68, Fst, and Treh). On the other hand, correlated patterns of gene expression were similar in cold- and warm-adapted populations. Analysis of functional categories defined by the Gene Ontology project point to an overrepresentation of genes involved in carbohydrate metabolism, nucleic acids metabolism and regulation of transcription among other categories. Although the location of differently expressed genes was approximately at random with respect to chromosomes, a physical mapping of 88 probes to the polytene chromosomes of D. subobscura has shown that a larger than expected number mapped inside inverted chromosomal segments. CONCLUSION: Our data suggest that a sizeable number of genes appear to be involved in thermal adaptation in Drosophila, with a substantial fraction implicated in metabolism. This apparently illustrates the formidable challenge to understanding the adaptive evolution of complex trait variation. Furthermore, some clustering of genes within inverted chromosomal sections was detected. Disentangling the effects of inversions will be obviously required in any future approach if we want to identify the relevant candidate genes

Distribution of the transposable elements bilbo and gypsy in original and colonizing populations of Drosophila subobscura

Background: Transposable elements (TEs) constitute a substantial amount of all eukaryotic genomes. They induce an important proportion of deleterious mutations by insertion into genes or gene regulatory regions. However, their mutational capabilities are not always adverse but can contribute to the genetic diversity and evolution of organisms. Knowledge of their distribution and activity in the genomes of populations under different environmental and demographic regimes, is important to understand their role in species evolution. In this work we study the chromosomal distribution of two TEs, gypsy and bilbo, in original and colonizing populations of Drosophila subobscura to reveal the putative effect of colonization on their insertion profile. Results: Chromosomal frequency distribution of two TEs in one original and three colonizing populations of D. subobscura, is different. Whereas the original population shows a low insertion frequency in most TE sites, colonizing populations have a mixture of high (frequency ≥ 10%) and low insertion sites for both TEs. Most highly occupied sites are coincident among colonizing populations and some of them are correlated to chromosomal arrangements. Comparisons of TE copy number between the X chromosome and autosomes show that gypsy occupancy seems to be controlled by negative selection, but bilbo one does not. Conclusion: These results are in accordance that TEs in Drosophila subobscura colonizing populations are submitted to a founder effect followed by genetic drift as a consequence of colonization. This would explain the high insertion frequencies of bilbo and gypsy in coincident sites of colonizing populations. High occupancy sites would represent insertion events prior to colonization. Sites of low frequency would be insertions that occurred after colonization and/or copies from the original population whose frequency is decreasing in colonizing populations. This work is a pioneer attempt to explain the chromosomal distribution of TEs in a colonizing species with high inversion polymorphism to reveal the putative effect of arrangements in TE insertion profiles. In general no associations between arrangements and TE have been found, except in a few cases where the association is very strong. Alternatively, founder drift effects, seem to play a leading role in TE genome distribution in colonizing populations

Genotype–phenotype correlation in patients with Usher syndrome and pathogenic variants in MYO7A: implications for future clinical trials

Purpose: We aimed to establish correlations between the clinical features of a cohort of Usher syndrome (USH) patients with pathogenic variants in MYO7A, type of pathogenic variant, and location on the protein domain. Methods: Sixty-two USH patients from 46 families with biallelic variants in MYO7A were examined for visual and audiological features. Participants were evaluated based on self-reported ophthalmological history and ophthalmological investigations (computerized visual field testing, best-corrected visual acuity, and ophthalmoscopic and electrophysiological examination). Optical coherence tomography and fundus autofluorescence imaging were performed when possible. Auditory and vestibular functions were evaluated. Patients were classified according to the type of variant and the protein domain where the variants were located. Results: Most patients displayed a typical USH1 phenotype, that is, prelingual severe-profound sensorineural hearing loss, prepubertal retinitis pigmentosa (RP) and vestibular dysfunction. No statistically significant differences were observed for the variables analysed except for the onset of hearing loss due to the existence of two USH2 cases, defined as postlingual sensorineural hearing loss, postpubertal onset of RP, and absence of vestibular dysfunction, and one atypical case of USH. Conclusion: We were unable to find a correlation between genotype and phenotype for MYO7A. However, our findings could prove useful for the assessment of efficacy in clinical trials, since the type of MYO7A variant does not seem to change the onset, severity or course of visual disease.This project was financially supported by the Center for Biomedical Network Research on Rare Diseases (CIBERER), FIS (PI16/00425, PI16/00539 and IIS‐FJD Biobank PT13/0010/0012). LG‐M and IPR were supported by the Río Hortega and predoctoral Programs (CM16/00126 and FI17/00192, respectively) from Institute of Health Carlos III (ISCIII, Spanish Ministry of the Economy, Industry and Competitiveness), Regional Government of Madrid (CAM, B2017/BMD37), and Regional Government of the Valencian Community (PROMETEU/2018/135), with partial support from the European Regional Development Fund (ERDF). Additional support was received from the Ramon Areces Foundation, the University Chair UAM‐IIS‐FJD of Genomic Medicine, ONCE Foundation and the Spanish National Organization of the Blind (ONCE). Drafting of this manuscript was possible thanks to the UshTher project (Clinical trial of gene therapy with dual AAV vectors for retinitis pigmentosa in patients with Usher syndrome type IB), which has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 754848. The authors are grateful to the families that participated in this study and to the colleagues who referred patients to us. We also thank the Genetics and Ophthalmology Departments of Fundación Jimenez Diaz University Hospital (FJD, Madrid) and Asunción Giménez, Cristina Villaverde, and Ignacio Mahillo for their technical assistance

Clinical aspects of usher syndrome and the USH2A gene in a cohort of 433 patients

IMPORTANCE A new statistical approach is needed to describe the clinical differences between type I and type II Usher syndrome and between the 2 most frequent mutations in the USH2A gene. OBJECTIVES To describe the primary phenotypic characteristics and differences between type I and type II Usher syndrome and to establish a phenotype-genotype correlation for the 2 most frequent mutations in the USH2A gene. DESIGN, SETTING, AND PARTICIPANTS Cross-sectional study at a genetics department, in which clinical evaluations were performed for 433 patients (297 unrelated families) who were classified as having type I, II, III, atypical, or unclassified Usher syndrome according to their clinical history, pedigree data, results from ophthalmological studies, and audiological, neurophysiological, and vestibular test results. Molecular studies were performed for 304 patients (256 unrelated families). The Mann-Whitney U test or the χ2 test was used for calculating the differences between mean values for the analyzed parameters. MAIN OUTCOMES AND MEASURES Age at diagnosis; age at onset of night blindness, visual field loss, visual acuity loss, and cataracts; and severity and age at diagnosis of hearing loss. RESULTS The comparison between patients with type I Usher syndrome and those with type II Usher syndrome revealed P < .001 for most items analyzed. The most frequent mutations in the USH2A gene were the p.Glu767Serfs*21 and p.Cys759Phe mutations, with an allelic frequency of 23.2%(63 of 272 alleles) and 8.1% (22 of 272 alleles), respectively. The phenotypic analysis for patients carrying p.Cys759Phe showed P < .001 for most items analyzed when compared with patients carrying p.Glu767Serfs*21 and when compared with patients carrying other mutations in the USH2A gene. None of the p.Cys759Phe patients exhibited a severe hearing loss phenotype, and more than 60%had only mild hearing loss. Most patients carrying the p.Glu767Serfs*21 mutation (72.1%) were moderately deaf. CONCLUSIONS AND RELEVANCE Our study presents the clinical differences between type I and type II Usher syndrome and between the 2 most frequent mutations in the USH2A gene. Detailed genotype-phenotype correlations, as presented in our study, allow for a better correlation of clinical signs with a known genotype and can improve the clinical management, genetic counseling, and risk assessment of patients with Usher syndrome because an estimated prognosis of their disease can be madeThis work was supported by grant PI13/00226 (to Servicio de Genética, Instituto de Investigación–Fundación Jiménez Díaz, Madrid, Spain), by grant PI13/00638 (to Unidad de Genética y Diagnóstico Prenatal, Hospital Universitario y Politécnico La Fe, Valencia, Spain), and by grant 06/07/0036 (to Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain) from Fundaluce and Organización Nacional de Ciegos Españole

Carbon-encapsulated iron nanoparticles as reusable adsorbents for micropollutants removal from water

Adsorption represents the most plausible technology for micropollutants removal from water nowadays. Nevertheless, the regeneration of the saturated carbon materials is still an important challenge, being these solids in practice commonly disposed. This work aims at overcoming this issue by using innovative carbonencapsulated iron nanoparticles (CE-nFe). This material was synthesized by a low-cost and green method viz. hydrothermal carbonization (HTC), using olive mill wastewater as carbonaceous source. The solid was fully characterized by different techniques (magnetic properties, elemental analyses, N2-sorption isotherms, pHPZC, ICP, XRD and TEM). It showed a clear core-shell structure of around 40 nm in diameter. The core was mainly formed by zero-valent iron and the shell by graphitized carbon. Accordingly, it showed an essentially mesoporous structure, with a specific surface area of 169 m2 g−1 , and a clear hydrophobic character (pHPZC = 10). Its adsorption performance was investigated using three relevant micropollutants (diclofenac (DCF), sulfamethoxazole (SMX) and metronidazole (MNZ)). A very fast removal of the micropollutants was achieved (30 min at the most, with rate constants in the range of 0.11–0.41 g mg−1 min−1 ). The adsorption isotherms revealed the vertical packing of the adsorbate molecules onto the adsorbent active centers, being the data successfully described by the GAB model. The saturated adsorbents were effectively regenerated by heterogeneous Fenton oxidation, taking advantage of the iron core of CE-nFe and the opened mesoporous carbon shell. The regeneration efficiency increased with increasing the operating temperature (25–75 ◦C) and contact time (1–4 h), as well as the H2O2 dose up to 6 g L-1. The micropollutant nature affected the adsorbent regeneration yield in the order: SMX > DCF > MNZ, consistent with their reactivity towards Fenton oxidationThis research has been supported by the Spanish MINECO through the project CTM-2016-76454-R and by the CM through the project P2018/EMT-4341. M. Munoz and J. Nieto-Sandoval thank the Spanish MINECO for the Ramón y Cajal postdoctoral contract (RYC-2016-20648) and the FPI predoctoral grant (BES-2017-081346), respectivel

Proyecto de intervención paisajística en el Área Natural Protegida Ecoguardas

207 páginas. Especialización en Diseño.Ecoguardas es un Área Natural Protegida al sur de la Ciudad de México que precisa de un Plan Maestro de Conservación y Manejo integral de sus recursos, ya que cuenta con magníficos escenarios naturales que no son lo suficientemente aprovechados por la población aledaña, ya que presenta riesgos de invasiones y de contaminación por residuos sólidos de las construcciones colindantes. De tal manera que la intervención paisajística propuesta, permita que Ecoguardas pueda ser conocido y disfrutado por un usuario de diferentes edades, para garantizar su accesibilidad, pero de manera ordenada y sustentable, es decir, sin poner en riesgo el preciado equilibrio ambiental que posee por ser una reserva natural del Valle de México. Para poder llegar a hacer las propuestas espaciales pertinentes, y definir las distintas actividades que se realizarían en el lugar, el trabajo fue llevado a cabo en tres fases: en la Primera Fase, se llevó a cabo un estudio detallado del Sitio, en sus cualidades naturales, socioculturales y polisensoriales, no sólo del polígono que delimita el terreno de Ecoguardas, sino del entorno en el que está inmerso. En la segunda fase se concibió el Plan Maestro de intervención paisajística, donde se propusieron distintos escenarios para realizar diferentes actividades, privilegiando siempre la conservación de los recursos naturales, y respetando la vocación natural de cada espacio. Por último, en la tercera fase se realizó una propuesta específica para el escenario denominado Sendero principal, que es un espacio con un gran potencial para que el usuario pueda observar la riqueza natural del lugar, y pueda tener un acceso controlado a otros escenarios para realizar actividades específicas. Se propone un ordenamiento de las actividades que se realizan en el sendero, por edades, así como la creación de diferentes nodos de actividad recreativa, que permitan admirar el entorno, y establecer el necesario diálogo entre el hombre y el sitio

Estudio y caracterización de roca sedimentaria Lutita de la laguna de Metztitlán-Eloxochitlán Hidalgo

A study and characterization of sedimentary rock from the shores of the Metztitlán lagoon was carried out. Located in Eloxochitlán town of Hidalgo state, Mexico. The morphology of the crystals was determined by Scanning Electron Microscopy (SEM), with a pseudopolygonal shape and crystallite size of 100 μm. By Dispersive Energy Spectroscopy (EDS), microanalysis of chemical elements was performed. The average content of chemical elements in the sedimentary rock was C = 11.03%, O = 50.49%, Ca = 33.88%, Si = 3.63%, as the main ones. Which are present in the form of oxides, such as, CaO, SiO₂, MgO, Al₂O₃ and GaP. From these studies, it was possible to classify the sedimentary rock of an Impure Alloquímica composition, called dedrica, which is formed from sedimentation with an environmental alteration, characteristic of the land. By X-Ray Poweder Diffraction (XRD), the mineralogical phases of Alunite KAl₃ (SO⁴)(OH)₆, Cristobalite, Kaolinite Al₂Si₂O₅ and CaCO₃were determined.A study and characterization of sedimentary rock from the shores of the Metztitlán lagoon was carried out. Located in Eloxochitlán town of Hidalgo state, Mexico. The morphology of the crystals was determined by Scanning Electron Microscopy (SEM), with a pseudopolygonal shape and crystallite size of 100 μm. By Dispersive Energy Spectroscopy (EDS), microanalysis of chemical elements was performed. The average content of chemical elements in the sedimentary rock was C = 11.03%, O = 50.49%, Ca = 33.88%, Si = 3.63%, as the main ones. Which are present in the form of oxides, such as, CaO, SiO₂, MgO, Al₂O₃ and GaP. From these studies, it was possible to classify the sedimentary rock of an Impure Alloquímica composition, called dedrica, which is formed from sedimentation with an environmental alteration, characteristic of the land. By X-Ray Poweder Diffraction (XRD), the mineralogical phases of Alunite KAl₃ (SO⁴)(OH)₆, Cristobalite, Kaolinite Al₂Si₂O₅ and CaCO₃were determined

Whole-exome sequencing reveals ZNF408 as a new gene associated with autosomal recessive retinitis pigmentosa with vitreal alterations

Retinitis pigmentosa (RP) is a group of progressive inherited retinal dystrophies that cause visual impairment as a result of photoreceptor cell death. RP is heterogeneous, both clinically and genetically making difficult to establish precise genotype–phenotype correlations. In a Spanish family with autosomal recessive RP (arRP), homozygosity mapping and whole-exome sequencing led to the identification of a homozygous mutation (c.358_359delGT; p.Ala122Leufs*2) in the ZNF408 gene. A screening performed in 217 additional unrelated families revealed another homozygous mutation (c.1621C>T; p.Arg541Cys) in an isolated RP case. ZNF408 encodes a transcription factor that harbors 10 predicted C2H2-type fingers thought to be implicated in DNA binding. To elucidate the ZNF408 role in the retina and the pathogenesis of these mutations we have performed different functional studies. By immunohistochemical analysis in healthy human retina, we identified that ZNF408 is expressed in both cone and rod photoreceptors, in a specific type of amacrine and ganglion cells, and in retinal blood vessels. ZNF408 revealed a cytoplasmic localization and a nuclear distribution in areas corresponding with the euchromatin fraction. Immunolocalization studies showed a partial mislocalization of the p.Arg541Cys mutant protein retaining part of the WT protein in the cytoplasm. Our study demonstrates that ZNF408, previously associated with Familial Exudative Vitreoretinopathy (FEVR), is a new gene causing arRP with vitreous condensations supporting the evidence that this protein plays additional functions into the human retina.This work is supported by CIBERER (06/07/0036), FIS (PI013/00226), Ministry of Economy and Competitiveness-FEDER (BFU2012-36845), RETICS (RD12/0034/0010), Fundación ONCE, Fundaluce and grants BIO2011-27069 from the Spanish Ministry of Economy and Competitiveness, and PROMETEOII/2014/025 from the Conselleria de Educacio of the Valencia Community. PC is supported by Fundación Conchita Rábago (FCR), MC by Miguel Servet ISCIII (CP/03256) and dS by CAPES Foundation, Ministry of Education of Brazil

Allelic overload and its clinical modifier effect in Bardet-Biedl syndrome

Bardet–Biedl syndrome (BBS) is an autosomal recessive ciliopathy characterized by extensive inter- and intra-familial variability, in which oligogenic interactions have been also reported. Our main goal is to elucidate the role of mutational load in the clinical variability of BBS. A cohort of 99 patients from 77 different families with biallelic pathogenic variants in a BBS-associated gene was retrospectively recruited. Human Phenotype Ontology terms were used in the annotation of clinical symptoms. The mutational load in 39 BBS-related genes was studied in index cases using different molecular and next-generation sequencing (NGS) approaches. Candidate allele combinations were analysed using the in silico tools ORVAL and DiGePred. After clinical annotation, 76 out of the 99 cases a priori fulfilled established criteria for diagnosis of BBS or BBS-like. BBS1 alleles, found in 42% of families, were the most represented in our cohort. An increased mutational load was excluded in 41% of the index cases (22/54). Oligogenic inheritance was suspected in 52% of the screened families (23/45), being 40 tested by means of NGS data and 5 only by traditional methods. Together, ORVAL and DiGePred platforms predicted an oligogenic effect in 44% of the triallelic families (10/23). Intrafamilial variable severity could be clinically confirmed in six of the families. Our findings show that the presence of more than two alleles in BBSassociated genes correlated in six families with a more severe phenotype and associated with specific findings, highlighting the role of the mutational load in the management of BBS casesInstituto de Salud Carlos III | Ref. PI15/00049Instituto de Salud Carlos III | Ref. PI16/00425Instituto de Salud Carlos III | Ref. PI19/00321Instituto de Salud Carlos III | Ref. PI19/00332CIBERER | Ref. 07/06/0036IIS-FJD BioBank | Ref. PT13/0010/0012Comunidad de Madrid | Ref. B2017/BMD-3721Xunta de Galicia | Ref. ED431G-2019/06Xunta de Galicia | Ref. ED431C-2018/54ISCIII | Ref. FI17/00192Ministerio de Educación, Cultura y Deporte | Ref. FPU 19/00175ISCIII | Ref. CP16/0011