Structural variation on the human Y chromosome from population-scale resequencing.

AIM: To investigate the information about Y-structural variants (SVs) in the general population that could be obtained by low-coverage whole-genome sequencing. METHODS: We investigated SVs on the male-specific portion of the Y chromosome in the 70 individuals from Africa, Europe, or East Asia sequenced as part of the 1000 Genomes Pilot project, using data from this project and from additional studies on the same samples. We applied a combination of read-depth and read-pair methods to discover candidate Y-SVs, followed by validation using information from the literature, independent sequence and single nucleotide polymorphism-chip data sets, and polymerase chain reaction experiments. RESULTS: We validated 19 Y-SVs, 2 of which were novel. Non-reference allele counts ranged from 1 to 64. The regions richest in variation were the heterochromatic segments near the centromere or the DYZ19 locus, followed by the ampliconic regions, but some Y-SVs were also present in the X-transposed and X-degenerate regions. In all, 5 of the 27 protein-coding gene families on the Y chromosome varied in copy number. CONCLUSIONS: We confirmed that Y-SVs were readily detected from low-coverage sequence data and were abundant on the chromosome. We also reported both common and rare Y-SVs that are novel

Reduction of Total Harmonic Distortion (THD) on Multilevel Inverter with Modified PWM using Genetic Algorithm

In this research, modified PWM has been applied to the multilevel inverter (MLI) single-phase three-level diode clamp full bridge. Modified PWM is performed to produce minimum Total Harmonic Distortion (THD) the voltage because the quality of the good voltage is indicated by small THD. The THD indicates the quality of AC voltage source. The THD standard by the IEEE STD 519-1992 Harmonic Voltage Limits is 5% and the Pacific Corp standard is 8%, if the THD value is greater than the THD standard it can cause the electronic load to be damaged due to the damaged waveform. Modified PWM is applied by adding a 50 Hz sinusoidal reference signal with a sinusoidal signal which has a certain amplitude, frequency and phase shift angle. The frequency of the adder signal is the frequency at which the value of the individual harmonic voltage appears (n harmonic). To get maximum result, optimization using Genetic Algorithm (GA) method to determinate amplitude & phase shift angle done. The result of implementation hardware with modified PWM shows smaller THD voltage compared to the THD voltage with Sinusoidal Pulse Width Modulation (SPWM) switching up to 0.19 or decrease 65,51 % for modified PWM of harmonic injection n = 7 with GA optimization ma= 0.8 (A=0.0936 and ø = 0 rad) and up to 0.08 or decrease 12,30 % for modified PWM of harmonic injection n = 22 with GA optimization ma = 0.4 (A=0.1221 and ø = 0 rad)

Invariant Solutions for Nonhomogeneous Discrete Diffusion Equation

One-dimensional optimal systems for nonhomogeneous discrete heat equation with different source terms are calculated. By utilizing these optimal systems invariant solutions are found. Also generating solutions are calculated, using the elements of the symmetry algebra

Molecular Dynamics Simulations of Sound Wave Propagation in a Gas and Thermo-Acoustic Effects on a Carbon Nanotube

TesisLa educación sexual en el país, como responsabilidad asumida por el Estado, se remite a la década de 1980, con el Programa Nacional de Educación en Población 1980 - 1990, del Ministerio de Educación. Dicho programa desarrollaba acciones con enfoque demográfico y de lucha contra la pobreza. En ese período, se incorporaron en el diseño curricular de secundaria contenidos referentes a la familia y a la sexualidad humana, la paternidad responsable, los derechos del niño, la identidad sexual y la identidad de género, la planificación familiar y la prevención de enfermedades de transmisión sexual. De igual forma, entre 1985 y 1989, se incorporó un seminario de educación a la población en el currículo de formación magisterial. El Programa de Educación en Población apoyado por el Fondo de Población de Naciones Unidas UNFPA y UNESCO concluyó en 1991, quedando los contenidos de educación sexual insertos en las asignaturas de Educación Cívica, Educación Familiar, Familia y Civismo. En la actualidad, el Ministerio de Educación del Perú informó que viene desarrollando un programa intensivo de educación sexual integral en las Instituciones Educativas del país para contribuir a evitar embarazos precoces e infecciones de transmisión sexual en la población escolar. En el año 2008 se aprobó y publicó un documento denominado “Lineamientos Educativos y Orientaciones Pedagógicas para el Desarrollo de una Educación Sexual Integral”, que guía el trabajo sobre educación sexual integral en las instituciones educativas del país. Así mismo, el año 2011 el Ministerio de Salud, publicó la “Guía Técnica de Gestión de Promoción de la Salud en instituciones educativas para el desarrollo sostenible” con la finalidad de contribuir al desarrollo integral sostenible de los y las estudiantes y al óptimo desarrollo de sus capacidades, promoviendo una cultura de salud en el ámbito escolar. Estos lineamientos se vienen desarrollando en nuestro país a nivel de todas las Instituciones Educativas, a través del área de Tutoría y Orientación del Educando, lo que nos motivó a realizar la presente investigación titulada “Nivel de conocimiento y actitud frente a la educación sexual en adolescentes del quinto año de secundaria turno mañana de la Institución Educativa Estatal “Mariscal Cáceres”- Ayacucho. Setiembre - noviembre 2016”. La muestra estuvo conformada por 178 adolescentes del quinto año de educación secundaria-turno mañana, el tipo de investigación fue aplicada, relacional, prospectiva y de corte transversal. Los principales resultados hallados en esta investigación, fueron los siguientes: El 71.3% (127) de adolescentes tuvieron entre 15 a 16 años de edad y el 38.7% (51) entre 17 a 19 años de edad. El 91% de adolescentes, tuvieron nivel de conocimiento bueno y el 9% nivel de conocimientos regular; y las variables: sexo, edad, procedencia e información previa recibida, no están directamente relacionados con el nivel de conocimiento sobre el tema en estudio; mientras que los ingresos económicos familiares si está relacionado con el nivel de conocimiento. El 79% de los adolescentes presentaron una actitud de aceptación, el 19% presentaron una actitud de indiferencia y sólo el 2% una actitud de rechazo frente a la educación sexual. Las variables: edad, sexo y procedencia no están relacionados con la actitud hacia la educación sexual

Copy number variation arising from gene conversion on the human Y chromosome

We describe the variation in copy number of a ~ 10 kb region overlapping the long intergenic noncoding RNA (lincRNA) gene, TTTY22, within the IR3 inverted repeat on the short arm of the human Y chromosome, leading to individuals with 0–3 copies of this region in the general population. Variation of this CNV is common, with 266 individuals having 0 copies, 943 (including the reference sequence) having 1, 23 having 2 copies, and two having 3 copies, and was validated by breakpoint PCR, fbre-FISH, and 10× Genomics Chromium linked-read sequencing in subsets of 1234 individuals from the 1000 Genomes Project. Mapping the changes in copy number to the phylogeny of these Y chromosomes previously established by the Project identifed at least 20 mutational events, and investigation of fanking paralogous sequence variants showed that the mutations involved fanking sequences in 18 of these, and could extend over > 30 kb of DNA. While either gene conversion or double crossover between misaligned sister chromatids could formally explain the 0–2 copy events, gene conversion is the more likely mechanism, and these events include the longest non-allelic gene conversion reported thus far. Chromosomes with three copies of this CNV have arisen just once in our data set via another mechanism: duplication of 420 kb that places the third copy 230 kb proximal to the existing proximal copy. Our results establish gene conversion as a previously under-appreciated mechanism of generating copy number changes in humans and reveal the exceptionally large size of the conversion events that can occur

Positive selection in Europeans and East-Asians at the ABCA12 gene

Natural selection acts on genetic variants by increasing the frequency of alleles responsible for a cellular function that is favorable in a certain environment. In a previous genome-wide scan for positive selection in contemporary humans, we identified a signal of positive selection in European and Asians at the genetic variant rs10180970. The variant is located in the second intron of the ABCA12 gene, which is implicated in the lipid barrier formation and down-regulated by UVB radiation. We studied the signal of selection in the genomic region surrounding rs10180970 in a larger dataset that includes DNA sequences from ancient samples. We also investigated the functional consequences of gene expression of the alleles of rs10180970 and another genetic variant in its proximity in healthy volunteers exposed to similar UV radiation. We confirmed the selection signal and refine its location that extends over 35 kb and includes the first intron, the first two exons and the transcription starting site of ABCA12. We found no obvious effect of rs10180970 alleles on ABCA12 gene expression. We reconstructed the trajectory of the T allele over the last 80,000 years to discover that it was specific to H. sapiens and present in non-Africans 45,000 years ago

Deleterious- and Disease-Allele Prevalence in Healthy Individuals: Insights from Current Predictions, Mutation Databases, and Population-Scale Resequencing

We have assessed the numbers of potentially deleterious variants in the genomes of apparently healthy humans by using (1) low-coverage whole-genome sequence data from 179 individuals in the 1000 Genomes Pilot Project and (2) current predictions and databases of deleterious variants. Each individual carried 281–515 missense substitutions, 40–85 of which were homozygous, predicted to be highly damaging. They also carried 40–110 variants classified by the Human Gene Mutation Database (HGMD) as disease-causing mutations (DMs), 3–24 variants in the homozygous state, and many polymorphisms putatively associated with disease. Whereas many of these DMs are likely to represent disease-allele-annotation errors, between 0 and 8 DMs (0–1 homozygous) per individual are predicted to be highly damaging, and some of them provide information of medical relevance. These analyses emphasize the need for improved annotation of disease alleles both in mutation databases and in the primary literature; some HGMD mutation data have been recategorized on the basis of the present findings, an iterative process that is both necessary and ongoing. Our estimates of deleterious-allele numbers are likely to be subject to both overcounting and undercounting. However, our current best mean estimates of ∼400 damaging variants and ∼2 bona fide disease mutations per individual are likely to increase rather than decrease as sequencing studies ascertain rare variants more effectively and as additional disease alleles are discovered

A Worldwide Survey of Human Male Demographic History Based on Y-SNP and Y-STR Data from the HGDP–CEPH Populations

We have investigated human male demographic history using 590 males from 51 populations in the Human Genome Diversity Project - Centre d’Étude du Polymorphisme Humain worldwide panel, typed with 37 Y-chromosomal Single Nucleotide Polymorphisms and 65 Y-chromosomal Short Tandem Repeats and analyzed with the program Bayesian Analysis of Trees With Internal Node Generation. The general patterns we observe show a gradient from the oldest population time to the most recent common ancestors (TMRCAs) and expansion times together with the largest effective population sizes in Africa, to the youngest times and smallest effective population sizes in the Americas. These parameters are significantly negatively correlated with distance from East Africa, and the patterns are consistent with most other studies of human variation and history. In contrast, growth rate showed a weaker correlation in the opposite direction. Y-lineage diversity and TMRCA also decrease with distance from East Africa, supporting a model of expansion with serial founder events starting from this source. A number of individual populations diverge from these general patterns, including previously documented examples such as recent expansions of the Yoruba in Africa, Basques in Europe, and Yakut in Northern Asia. However, some unexpected demographic histories were also found, including low growth rates in the Hazara and Kalash from Pakistan and recent expansion of the Mozabites in North Africa