Sample records for multigenerational human pedigree
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Directory of Open Access Journals (Sweden)
Anouk Georges
Full Text Available A genome-wide linkage scan was conducted in a Northern-European multigenerational pedigree with nine of 40 related members affected with concomitant strabismus. Twenty-seven members of the pedigree including all affected individuals were genotyped using a SNP array interrogating > 300,000 common SNPs. We conducted parametric and non-parametric linkage analyses assuming segregation of an autosomal dominant mutation, yet allowing for incomplete penetrance and phenocopies. We detected two chromosome regions with near-suggestive evidence for linkage, respectively on chromosomes 8 and 18. The chromosome 8 linkage implied a penetrance of 0.80 and a rate of phenocopy of 0.11, while the chromosome 18 linkage implied a penetrance of 0.64 and a rate of phenocopy of 0. Our analysis excludes a simple genetic determinism of strabismus in this pedigree.
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Georges, Anouk; Cambisano, Nadine; Ahariz, Naïma; Karim, Latifa; Georges, Michel
2013-01-01
A genome-wide linkage scan was conducted in a Northern-European multigenerational pedigree with nine of 40 related members affected with concomitant strabismus. Twenty-seven members of the pedigree including all affected individuals were genotyped using a SNP array interrogating > 300,000 common SNPs. We conducted parametric and non-parametric linkage analyses assuming segregation of an autosomal dominant mutation, yet allowing for incomplete penetrance and phenocopies. We detected two chromosome regions with near-suggestive evidence for linkage, respectively on chromosomes 8 and 18. The chromosome 8 linkage implied a penetrance of 0.80 and a rate of phenocopy of 0.11, while the chromosome 18 linkage implied a penetrance of 0.64 and a rate of phenocopy of 0. Our analysis excludes a simple genetic determinism of strabismus in this pedigree.
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Exome sequencing of a multigenerational human pedigree.
Directory of Open Access Journals (Sweden)
Dale J Hedges
2009-12-01
Full Text Available Over the next few years, the efficient use of next-generation sequencing (NGS in human genetics research will depend heavily upon the effective mechanisms for the selective enrichment of genomic regions of interest. Recently, comprehensive exome capture arrays have become available for targeting approximately 33 Mb or approximately 180,000 coding exons across the human genome. Selective genomic enrichment of the human exome offers an attractive option for new experimental designs aiming to quickly identify potential disease-associated genetic variants, especially in family-based studies. We have evaluated a 2.1 M feature human exome capture array on eight individuals from a three-generation family pedigree. We were able to cover up to 98% of the targeted bases at a long-read sequence read depth of > or = 3, 86% at a read depth of > or = 10, and over 50% of all targets were covered with > or = 20 reads. We identified up to 14,284 SNPs and small indels per individual exome, with up to 1,679 of these representing putative novel polymorphisms. Applying the conservative genotype calling approach HCDiff, the average rate of detection of a variant allele based on Illumina 1 M BeadChips genotypes was 95.2% at > or = 10x sequence. Further, we propose an advantageous genotype calling strategy for low covered targets that empirically determines cut-off thresholds at a given coverage depth based on existing genotype data. Application of this method was able to detect >99% of SNPs covered > or = 8x. Our results offer guidance for "real-world" applications in human genetics and provide further evidence that microarray-based exome capture is an efficient and reliable method to enrich for chromosomal regions of interest in next-generation sequencing experiments.
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First genealogy for a wild marine fish population reveals multigenerational philopatry
Salles, Océ ane C.; Pujol, Benoit; Maynard, Jeffrey A.; Almany, Glenn R.; Berumen, Michael L.; Jones, Geoffrey P.; Saenz-Agudelo, Pablo; Srinivasan, Maya; Thorrold, Simon R.; Planes, Serge
2016-01-01
Natal philopatry, the return of individuals to their natal area for reproduction, has advantages and disadvantages for animal populations. Natal philopatry may generate local genetic adaptation, but it may also increase the probability of inbreeding that can compromise persistence. Although natal philopatry is well documented in anadromous fishes, marine fish may also return to their birth site to spawn. How philopatry shapes wild fish populations is, however, unclear because it requires constructing multigenerational pedigrees that are currently lacking for marine fishes. Here we present the first multigenerational pedigree for a marine fish population by repeatedly genotyping all individuals in a population of the orange clownfish (Amphiprion percula) at Kimbe Island (Papua New Guinea) during a 10-y period. Based on 2927 individuals, our pedigree analysis revealed that longitudinal philopatry was recurrent over five generations. Progeny tended to settle close to their parents, with related individuals often sharing the same colony. However, successful inbreeding was rare, and genetic diversity remained high, suggesting occasional inbreeding does not impair local population persistence. Local reproductive success was dependent on the habitat larvae settled into, rather than the habitat they came from. Our study suggests that longitudinal philopatry can influence both population replenishment and local adaptation of marine fishes. Resolving multigenerational pedigrees during a relatively short period, as we present here, provides a framework for assessing the ability of marine populations to persist and adapt to accelerating climate change.
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First genealogy for a wild marine fish population reveals multigenerational philopatry
Salles, Océane C.
2016-11-01
Natal philopatry, the return of individuals to their natal area for reproduction, has advantages and disadvantages for animal populations. Natal philopatry may generate local genetic adaptation, but it may also increase the probability of inbreeding that can compromise persistence. Although natal philopatry is well documented in anadromous fishes, marine fish may also return to their birth site to spawn. How philopatry shapes wild fish populations is, however, unclear because it requires constructing multigenerational pedigrees that are currently lacking for marine fishes. Here we present the first multigenerational pedigree for a marine fish population by repeatedly genotyping all individuals in a population of the orange clownfish (Amphiprion percula) at Kimbe Island (Papua New Guinea) during a 10-y period. Based on 2927 individuals, our pedigree analysis revealed that longitudinal philopatry was recurrent over five generations. Progeny tended to settle close to their parents, with related individuals often sharing the same colony. However, successful inbreeding was rare, and genetic diversity remained high, suggesting occasional inbreeding does not impair local population persistence. Local reproductive success was dependent on the habitat larvae settled into, rather than the habitat they came from. Our study suggests that longitudinal philopatry can influence both population replenishment and local adaptation of marine fishes. Resolving multigenerational pedigrees during a relatively short period, as we present here, provides a framework for assessing the ability of marine populations to persist and adapt to accelerating climate change.
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Vinson, Amanda; Prongay, Kamm; Ferguson, Betsy
2013-01-01
Complex diseases (e.g., cardiovascular disease and type 2 diabetes, among many others) pose the biggest threat to human health worldwide and are among the most challenging to investigate. Susceptibility to complex disease may be caused by multiple genetic variants (GVs) and their interaction, by environmental factors, and by interaction between GVs and environment, and large study cohorts with substantial analytical power are typically required to elucidate these individual contributions. Here, we discuss the advantages of both power and feasibility afforded by the use of extended pedigrees of rhesus macaques (Macaca mulatta) for genetic studies of complex human disease based on next-generation sequence data. We present these advantages in the context of previous research conducted in rhesus macaques for several representative complex diseases. We also describe a single, multigeneration pedigree of Indian-origin rhesus macaques and a sample biobank we have developed for genetic analysis of complex disease, including power of this pedigree to detect causal GVs using either genetic linkage or association methods in a variance decomposition approach. Finally, we summarize findings of significant heritability for a number of quantitative traits that demonstrate that genetic contributions to risk factors for complex disease can be detected and measured in this pedigree. We conclude that the development and application of an extended pedigree to analysis of complex disease traits in the rhesus macaque have shown promising early success and that genome-wide genetic and higher order -omics studies in this pedigree are likely to yield useful insights into the architecture of complex human disease.
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Two Search Techniques within a Human Pedigree Database
Gersting, J. M.; Conneally, P. M.; Rogers, K.
1982-01-01
This paper presents the basic features of two search techniques from MEGADATS-2 (MEdical Genetics Acquisition and DAta Transfer System), a system for collecting, storing, retrieving and plotting human family pedigrees. The individual search provides a quick method for locating an individual in the pedigree database. This search uses a modified soundex coding and an inverted file structure based on a composite key. The navigational search uses a set of pedigree traversal operations (individual...
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KinLinks: Software Toolkit for Kinship Analysis and Pedigree Generation from NGS Datasets
2015-04-21
combined into multi-generation 2 pedigrees via a set of heuristics to resolve relationship type (half siblings vs avuncular vs grandparent...this metric is able to differentiate parent- child relationships from siblings . • Kinship Coefficient as calculated by the KING algorithm [22]. The...second classifier predicts the exact relationship among a pair of samples (i.e. parent/ child , sibling , grandparent, avuncular, cousin, unrelated). Both
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Anderson, Eric C; Ng, Thomas C
2016-02-01
We develop a computational framework for addressing pedigree inference problems using small numbers (80-400) of single nucleotide polymorphisms (SNPs). Our approach relaxes the assumptions, which are commonly made, that sampling is complete with respect to the pedigree and that there is no genotyping error. It relies on representing the inferred pedigree as a factor graph and invoking the Sum-Product algorithm to compute and store quantities that allow the joint probability of the data to be rapidly computed under a large class of rearrangements of the pedigree structure. This allows efficient MCMC sampling over the space of pedigrees, and, hence, Bayesian inference of pedigree structure. In this paper we restrict ourselves to inference of pedigrees without loops using SNPs assumed to be unlinked. We present the methodology in general for multigenerational inference, and we illustrate the method by applying it to the inference of full sibling groups in a large sample (n=1157) of Chinook salmon typed at 95 SNPs. The results show that our method provides a better point estimate and estimate of uncertainty than the currently best-available maximum-likelihood sibling reconstruction method. Extensions of this work to more complex scenarios are briefly discussed. Published by Elsevier Inc.
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Strategies for Managing a Multigenerational Workforce
Iden, Ronald
The multigenerational workforce presents a critical challenge for business managers, and each generation has different expectations. A human resource management study of organizations with more than 500 employees reported 58% of the managers experiencing conflict between younger and older workers. The purpose of this single case study was to explore the multigenerational strategies used by 3 managers from a Franklin County, Ohio manufacturing facility with a population size of 6 participants. The conceptual framework for this study was built upon generational theory and cohort group theory. The data were collected through face-to-face semistructured interviews, company documents, and a reflexive journal. Member checking was completed to strengthen the credibility and trustworthiness of the interpretation of participants' responses. A modified van Kaam method enabled separation of themes following the coding of data. Four themes emerged from the data: (a) required multigenerational managerial skills, (b) generational cohort differences, (c) most effective multigenerational management strategies, and (d) least effective multigenerational management strategies. Findings from this study may contribute to social change through better understanding, acceptance, and appreciation of the primary generations in the workforce, and, in turn, improve community relationships.
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Cervera-Juanes, Rita; Vinson, Amanda; Ferguson, Betsy; Carbone, Lucia; Spindel, Eliot; Mccouch, Susan; Spindel, Jennifer; Nevonen, Kimberly; Letaw, John; Raboin, Michael; Bimber, Ben
2016-01-01
Background: Rhesus macaques are widely used in biomedical research, but the application of genomic information in this species to better understand human disease is still undeveloped. Whole-genome sequence (WGS) data in pedigreed macaque colonies could provide substantial experimental power, but the collection of WGS data in large cohorts remains a formidable expense. Here, we describe a cost-effective approach that selects the most informative macaques in a pedigree for whole-genome sequenci...
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Strategies for Managing a Multigenerational Workforce
Iden, Ronald
2016-01-01
The multigenerational workforce presents a critical challenge for business managers, and each generation has different expectations. A human resource management study of organizations with more than 500 employees reported 58% of the managers experiencing conflict between younger and older workers. The purpose of this single case study was to…
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Family Issues in Multigenerational Households.
Feinauer, Leslie L; And Others
1987-01-01
Studied issues faced by multigenerational families and their implications for family therapy. Major factors in multigenerational households included dependency, sibling relationships, depression, and demanding and egocentric behavior. Factors to consider during family therapy include respite care, age, interdependence, dignity, provision of care,…
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Partitioning of copy-number genotypes in pedigrees
Directory of Open Access Journals (Sweden)
Andelfinger Gregor U
2010-05-01
Full Text Available Abstract Background Copy number variations (CNVs and polymorphisms (CNPs have only recently gained the genetic community's attention. Conservative estimates have shown that CNVs and CNPs might affect more than 10% of the genome and that they may be at least as important as single nucleotide polymorphisms in assessing human variability. Widely used tools for CNP analysis have been implemented in Birdsuite and PLINK for the purpose of conducting genetic association studies based on the unpartitioned total number of CNP copies provided by the intensities from Affymetrix's Genome-Wide Human SNP Array. Here, we are interested in partitioning copy number variations and polymorphisms in extended pedigrees for the purpose of linkage analysis on familial data. Results We have developed CNGen, a new software for the partitioning of copy number polymorphism using the integrated genotypes from Birdsuite with the Affymetrix platform. The algorithm applied to familial trios or extended pedigrees can produce partitioned copy number genotypes with distinct parental alleles. We have validated the algorithm using simulations on a complex pedigree structure using frequencies calculated from a real dataset of 300 genotyped samples from 42 pedigrees segregating a congenital heart defect phenotype. Conclusions CNGen is the first published software for the partitioning of copy number genotypes in pedigrees, making possible the use CNPs and CNVs for linkage analysis. It was implemented with the Python interpreter version 2.5.2. It was successfully tested on current Linux, Windows and Mac OS workstations.
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Leadership Styles of a Multigenerational Leader
Welsh, Raymond John, Jr.
2010-01-01
The purpose of this concurrent, nested, mixed-methods case study was to trace the evolution of the multigenerational success of the winningest college football coach of all time, John Gagliardi, to identify potential leadership styles, characteristics, and coaching effectiveness methods that others in a multigenerational leadership role may use.…
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ON PEDIGREE POLYTOPE AND ITS PROPERTIES
Directory of Open Access Journals (Sweden)
Tiru S. Arthanari
2013-07-01
Full Text Available The fact that linear optimization over a polytope can be done in polynomial time in the input size of the instance, has created renewed interest in studying 0-1 polytopes corresponding to combinatorial optimization problems. Studying their polyhedral structure has resulted in new algorithms to solve very large instances of some difficult problems like the symmetric traveling salesman problem. The multistage insertion formulation (MI given by the author, in 1982, for the symmetric traveling salesman problem (STSP, gives rise to a combinatorial object called the pedigree. The pedigrees are in one-to-one correspondence with Hamiltonian cycles. Given n, the convex hull of all the pedigrees is called the corresponding pedigree polytope. In this article we bring together the research done a little over a decade by the author and his doctoral students, on the pedigree polytope, its structure, membership problem and properties of the MI formulation for the STSP. In addition we summarise some of the computational and other peripheral results relating to pedigree approach to solve the STSP. The pedigree polytope possesses properties not shared by the STSP (tour polytope, which makes it interesting to study the pedigrees, both from theoretical and algorithmic perspectives.
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In Silico Genome Mismatch Scanning to Map Breast Cancer Genes in Extended Pedigrees
2008-07-01
University College London Annals of Human Genetics (2008) 72,279–287 279 A. Thomas et al. Methods IBD sharing in pedigrees There is considerable literature...is sufficient to maintain interest in the region. 282 Annals of Human Genetics (2008) 72,279–287 C© 2007 The Authors Journal compilation C© 2007...for observed IBS instead of IBD, and for sporadic cases reducing the number of meioses, pedigrees with meiosis count d in the 25 to 30 range are
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pedigreejs: a web-based graphical pedigree editor.
Carver, Tim; Cunningham, Alex P; Babb de Villiers, Chantal; Lee, Andrew; Hartley, Simon; Tischkowitz, Marc; Walter, Fiona M; Easton, Douglas F; Antoniou, Antonis C
2018-03-15
The collection, management and visualization of clinical pedigree (family history) data is a core activity in clinical genetics centres. However, clinical pedigree datasets can be difficult to manage, as they are time consuming to capture, and can be difficult to build, manipulate and visualize graphically. Several standalone graphical pedigree editors and drawing applications exist but there are no freely available lightweight graphical pedigree editors that can be easily configured and incorporated into web applications. We developed 'pedigreejs', an interactive graphical pedigree editor written in JavaScript, which uses standard pedigree nomenclature. Pedigreejs provides an easily configurable, extensible and lightweight pedigree editor. It makes use of an open-source Javascript library to define a hierarchical layout and to produce images in scalable vector graphics (SVG) format that can be viewed and edited in web browsers. The software is freely available under GPL licence (https://ccge-boadicea.github.io/pedigreejs/). tjc29@cam.ac.uk. Supplementary data are available at Bioinformatics online.
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Multigenerational challenges in academic medicine: UCDavis's responses.
Howell, Lydia Pleotis; Servis, Gregg; Bonham, Ann
2005-06-01
Academic medicine is a unique work environment, one of the few where members of four different generations regularly interact and where multigenerational teams are key to fulfilling its missions, particularly education. This can lead to increased creativity, but also to intergenerational conflict, since each generation has different values and expectations. The authors describe multigenerational challenges confronted at the University of California, Davis, School of Medicine, and that school's responses to them. These challenges include issues related to work hours, workload, compensation, evaluation for advancement, recruitment and retention, and attendance at required meetings. Awareness of the different generational qualities and values allowed the school of medicine to identify the multigenerational origin of many of these ongoing issues and challenges and to plan appropriate solutions within the Office of Academic Affairs. These include policy changes related to work-life balance, utilizing multiple faculty tracks with different roles, allowing part-time faculty appointments, creating a variety of faculty development programs geared toward different generational needs (which utilize flexible modules, menus of options, and alternative technologies for presentation), defining appropriate reward and incentives through compensations plans, and creating peer-reviewed awards. The authors conclude that these efforts mitigate conflict, promote diversity, and allow multigenerational teams to function more effectively and creatively in education, research, and clinical care. Ongoing evaluation will further refine this approach.
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Using Python for Pedigree Analysis
A pedigree is a way of describing a population of people or animals in terms of genetic relationships among individuals. Pedigrees are of interest to many people, including scientists, animal and plant breeders, and genealogists. They are used to assess the diversity of populations, in combination ...
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MULTIGENERATIONAL ASPECTS OF SOCIAL STRATIFICATION: ISSUES FOR FURTHER RESEARCH.
Mare, Robert D
2014-03-01
The articles in this special issue show the vitality and progress of research on multigenerational aspects of social mobility, stratification, and inequality. The effects of the characteristics and behavior of grandparents and other kin on the statuses, resources, and positions of their descendants are best viewed in a demographic context. Intergenerational effects work through both the intergenerational associations of socioeconomic characteristics and also differential fertility and mortality. A combined socioeconomic and demographic framework informs a research agenda which addresses the following issues: how generational effects combine with variation in age, period, and cohort within each generation; distinguishing causal relationships across generations from statistical associations; how multigenerational effects vary across socioeconomic hierarchies, including the possibility of stronger effects at the extreme top and bottom; distinguishing between endowments and investments in intergenerational effects; multigenerational effects on associated demographic behaviors and outcomes (especially fertility and mortality); optimal tradeoffs among diverse types of data on multigenerational processes; and the variability across time and place in how kin, education, and other institutions affect stratification.
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Maximum likelihood pedigree reconstruction using integer linear programming.
Cussens, James; Bartlett, Mark; Jones, Elinor M; Sheehan, Nuala A
2013-01-01
Large population biobanks of unrelated individuals have been highly successful in detecting common genetic variants affecting diseases of public health concern. However, they lack the statistical power to detect more modest gene-gene and gene-environment interaction effects or the effects of rare variants for which related individuals are ideally required. In reality, most large population studies will undoubtedly contain sets of undeclared relatives, or pedigrees. Although a crude measure of relatedness might sometimes suffice, having a good estimate of the true pedigree would be much more informative if this could be obtained efficiently. Relatives are more likely to share longer haplotypes around disease susceptibility loci and are hence biologically more informative for rare variants than unrelated cases and controls. Distant relatives are arguably more useful for detecting variants with small effects because they are less likely to share masking environmental effects. Moreover, the identification of relatives enables appropriate adjustments of statistical analyses that typically assume unrelatedness. We propose to exploit an integer linear programming optimisation approach to pedigree learning, which is adapted to find valid pedigrees by imposing appropriate constraints. Our method is not restricted to small pedigrees and is guaranteed to return a maximum likelihood pedigree. With additional constraints, we can also search for multiple high-probability pedigrees and thus account for the inherent uncertainty in any particular pedigree reconstruction. The true pedigree is found very quickly by comparison with other methods when all individuals are observed. Extensions to more complex problems seem feasible. © 2012 Wiley Periodicals, Inc.
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Directory of Open Access Journals (Sweden)
Loy Clement T
2008-08-01
Full Text Available Abstract Background Frontotemporal lobar degeneration (FTLD represents a clinically, pathologically and genetically heterogenous neurodegenerative disorder, often complicated by neurological signs such as motor neuron-related limb weakness, spasticity and paralysis, parkinsonism and gait disturbances. Linkage to chromosome 9p had been reported for pedigrees with the neurodegenerative disorder, frontotemporal lobar degeneration (FTLD and motor neuron disease (MND. The objective in this study is to identify the genetic locus in a multi-generational Australian family with FTLD-MND. Methods Clinical review and standard neuropathological analysis of brain sections from affected pedigree members. Genome-wide scan using microsatellite markers and single nucleotide polymorphism fine mapping. Examination of candidate genes by direct DNA sequencing. Results Neuropathological examination revealed cytoplasmic deposition of the TDP-43 protein in three affected individuals. Moreover, we identify a family member with clinical Alzheimer's disease, and FTLD-Ubiquitin neuropathology. Genetic linkage and haplotype analyses, defined a critical region between markers D9S169 and D9S1845 on chromosome 9p21. Screening of all candidate genes within this region did not reveal any novel genetic alterations that co-segregate with disease haplotype, suggesting that one individual carrying a meiotic recombination may represent a phenocopy. Re-analysis of linkage data using the new affection status revealed a maximal two-point LOD score of 3.24 and a multipoint LOD score of 3.41 at marker D9S1817. This provides the highest reported LOD scores from a single FTLD-MND pedigree. Conclusion Our reported increase in the minimal disease region should inform other researchers that the chromosome 9 locus may be more telomeric than predicted by published recombination boundaries. Moreover, the existence of a family member with clinical Alzheimer's disease, and who shares the disease
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Multigenerational effects of maternal undernutrition
Einstein, Francine H.
2014-01-01
Intrauterine exposure to reduced nutrient availability can have major effects in determining susceptibility to chronic disease later in life. Martínez et al. (2014) demonstrate multigenerational effects of poor maternal nutrition and evidence of germ-line transmission through alterations in DNA methylation. PMID:24896533
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Multigenerational Perspectives on Family Formation Behaviour
DEFF Research Database (Denmark)
Loft, Lisbeth Trille Gylling
2014-01-01
The transformed opportunity structure individuals have experienced over the course of the 20th century has not only changed family life, but also led to increased educational requirements, higher expectations of social mobility in the labor market, and overall perceived prospects of a healthier...... life. Moreover, presence of generational transmission of family formation behavior such as cohabitation, age at first marriage and childbearing has been widely documented. Thus, it has become more appropriate to approach family life events in a non-linear manner by emphasizing the existence of various...... family formation pathways, and to study these pathways from a generational point of view. Drawing on a life course perspective and by means of rich multigenerational longitudinal data combined with data from the Danish central population registers, this study examines multigenerational transmission...
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Design and optimization of flexible multi-generation systems
DEFF Research Database (Denmark)
Lythcke-Jørgensen, Christoffer Ernst
variations and dynamics, and energy system analysis, which fails to consider process integration synergies in local systems. The primary objective of the thesis is to derive a methodology for linking process design practices with energy system analysis for enabling coherent and holistic design optimization...... of flexible multi-generation system. In addition, the case study results emphasize the importance of considering flexible operation, systematic process integration, and systematic assessment of uncertainties in the design optimization. It is recommended that future research focus on assessing system impacts...... from flexible multi-generation systems and performance improvements from storage options....
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Pedigrees or markers: Which are better in estimating relatedness and inbreeding coefficient?
Wang, Jinliang
2016-02-01
Individual inbreeding coefficient (F) and pairwise relatedness (r) are fundamental parameters in population genetics and have important applications in diverse fields such as human medicine, forensics, plant and animal breeding, conservation and evolutionary biology. Traditionally, both parameters are calculated from pedigrees, but are now increasingly estimated from genetic marker data. Conceptually, a pedigree gives the expected F and r values, FP and rP, with the expectations being taken (hypothetically) over an infinite number of individuals with the same pedigree. In contrast, markers give the realised (actual) F and r values at the particular marker loci of the particular individuals, FM and rM. Both pedigree (FP, rP) and marker (FM, rM) estimates can be used as inferences of genomic inbreeding coefficients FG and genomic relatedness rG, which are the underlying quantities relevant to most applications (such as estimating inbreeding depression and heritability) of F and r. In the pre-genomic era, it was widely accepted that pedigrees are much better than markers in delineating FG and rG, and markers should better be used to validate, amend and construct pedigrees rather than to replace them. Is this still true in the genomic era when genome-wide dense SNPs are available? In this simulation study, I showed that genomic markers can yield much better estimates of FG and rG than pedigrees when they are numerous (say, 10(4) SNPs) under realistic situations (e.g. genome and population sizes). Pedigree estimates are especially poor for species with a small genome, where FG and rG are determined to a large extent by Mendelian segregations and may thus deviate substantially from their expectations (FP and rP). Simulations also confirmed that FM, when estimated from many SNPs, can be much more powerful than FP for detecting inbreeding depression in viability. However, I argue that pedigrees cannot be replaced completely by genomic SNPs, because the former allows for
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Thermodynamic analysis of a solar-based multi-generation system with hydrogen production
International Nuclear Information System (INIS)
Ozturk, Murat; Dincer, Ibrahim
2013-01-01
Thermodynamic analysis of a renewable-based multi-generation energy production system which produces a number of outputs, such as power, heating, cooling, hot water, hydrogen and oxygen is conducted. This solar-based multi-generation system consists of four main sub-systems: Rankine cycle, organic Rankine cycle, absorption cooling and heating, and hydrogen production and utilization. Exergy destruction ratios and rates, power or heat transfer rates, energy and exergy efficiencies of the system components are carried out. Some parametric studies are performed in order to examine the effects of varying operating conditions (e.g., reference temperature, direct solar radiation and receiver temperature) on the exergy efficiencies of the sub-systems as well as the whole system. The solar-based multi-generation system which has an exergy efficiency of 57.35%, is obtained to be higher than using these sub-systems separately. The evaluation of the exergy efficiency and exergy destruction for the sub-systems and the overall system show that the parabolic dish collectors have the highest exergy destruction rate among constituent parts of the solar-based multi-generation system, due to high temperature difference between the working fluid and collector receivers. -- Highlights: ► Development of a new multi-generation system for solar-based hydrogen production. ► Investigation of exergy efficiencies and destructions in each process of the system. ► Evaluation of varying operating conditions on the exergy destruction and efficiency
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Wang, H; Misztal, I; Legarra, A
2014-12-01
This work studied differences between expected (calculated from pedigree) and realized (genomic, from markers) relationships in a real population, the influence of quality control on these differences, and their fit to current theory. Data included 4940 pure line chickens across five generations genotyped for 57,636 SNP. Pedigrees (5762 animals) were available for the five generations, pedigree starting on the first one. Three levels of quality control were used. With no quality control, mean difference between realized and expected relationships for different type of relationships was ≤ 0.04 with standard deviation ≤ 0.10. With strong quality control (call rate ≥ 0.9, parent-progeny conflicts, minor allele frequency and use of only autosomal chromosomes), these numbers reduced to ≤ 0.02 and ≤ 0.04, respectively. While the maximum difference was 1.02 with the complete data, it was only 0.18 with the latest three generations of genotypes (but including all pedigrees). Variation of expected minus realized relationships agreed with theoretical developments and suggests an effective number of loci of 70 for this population. When the pedigree is complete and as deep as the genotypes, the standard deviation of difference between the expected and realized relationships is around 0.04, all categories confounded. Standard deviation of differences larger than 0.10 suggests bad quality control, mistakes in pedigree recording or genotype labelling, or insufficient depth of pedigree. © 2014 Blackwell Verlag GmbH.
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PRIMAL: Fast and accurate pedigree-based imputation from sequence data in a founder population.
Directory of Open Access Journals (Sweden)
Oren E Livne
2015-03-01
Full Text Available Founder populations and large pedigrees offer many well-known advantages for genetic mapping studies, including cost-efficient study designs. Here, we describe PRIMAL (PedigRee IMputation ALgorithm, a fast and accurate pedigree-based phasing and imputation algorithm for founder populations. PRIMAL incorporates both existing and original ideas, such as a novel indexing strategy of Identity-By-Descent (IBD segments based on clique graphs. We were able to impute the genomes of 1,317 South Dakota Hutterites, who had genome-wide genotypes for ~300,000 common single nucleotide variants (SNVs, from 98 whole genome sequences. Using a combination of pedigree-based and LD-based imputation, we were able to assign 87% of genotypes with >99% accuracy over the full range of allele frequencies. Using the IBD cliques we were also able to infer the parental origin of 83% of alleles, and genotypes of deceased recent ancestors for whom no genotype information was available. This imputed data set will enable us to better study the relative contribution of rare and common variants on human phenotypes, as well as parental origin effect of disease risk alleles in >1,000 individuals at minimal cost.
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Being part of a multi-generational medical practice team.
Hills, Laura
2010-01-01
What happens when you find yourself working in your medical practice every day with co-workers who are the ages of your parents or children? Do you find yourself reverting to age-related roles? Do you become exasperated with or bewildered by the values and behaviors of older or younger colleagues? This article explores the challenges and opportunities the medical practice staff member faces when he or she is part of a multi-generational medical practice team. It describes the tensions that often occur when a medical practice staff runs the gamut from those who remember using a library card catalog and those who can't remember the days before Google. It describes the core values, career goals, key formative events, and attitudes that may have shaped the thinking and behavior of the four generations that may work in the medical practice today: Traditionalists, Baby Boomers, Generation X, and Generation Y. It suggests preferred communication and learning methods for staff members of different generations. Finally, this article offers 10 best practices for working in a multi-generational staff and for creating a supportive multi-generational medical practice culture.
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Completeness of pedigree and family cancer history for ovarian cancer patients.
Son, Yedong; Lim, Myong Cheol; Seo, Sang Soo; Kang, Sokbom; Park, Sang Yoon
2014-10-01
To investigate the completeness of pedigree and of number of pedigree analysis to know the acceptable familial history in Korean women with ovarian cancer. Interview was conducted in 50 ovarian cancer patients for obtaining familial history three times over the 6 weeks. The completeness of pedigree is estimated in terms of familial history of disease (cancer), health status (health living, disease and death), and onset age of disease and death. The completion of pedigree was 79.3, 85.1, and 85.6% at the 1st, 2nd, and 3rd time of interview and the time for pedigree analysis was 34.3, 10.8, and 3.1 minutes, respectively. The factors limiting pedigree analysis were as follows: out of contact with their relatives (38%), no living ancestors who know the family history (34%), dispersed family member because of the Korean War (16%), unknown cause of death (12%), reluctance to ask medical history of relatives (10%), and concealing their ovarian cancer (10%). The percentage of cancers revealed in 1st (2%) and 2nd degree (8%) relatives were increasing through surveys, especially colorectal cancer related with Lynch syndrome (4%). Analysis of pedigree at least two times is acceptable in Korean woman with ovarian cancer from the first study. The completion of pedigree is increasing, while time to take family history is decreasing during three time survey.
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Comparison of association mapping methods in a complex pedigreed population
DEFF Research Database (Denmark)
Sahana, Goutam; Guldbrandtsen, Bernt; Janss, Luc
2010-01-01
to collect SNP signals in intervals, to avoid the scattering of a QTL signal over multiple neighboring SNPs. Methods not accounting for genetic background (full pedigree information) performed worse, and methods using haplotypes were considerably worse with a high false-positive rate, probably due...... to the presence of low-frequency haplotypes. It was necessary to account for full relationships among individuals to avoid excess false discovery. Although the methods were tested on a cattle pedigree, the results are applicable to any population with a complex pedigree structure...
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VIPER:a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees
Paterson, Trevor; Graham, Martin; Kennedy, Jessie; Law, Andy
2012-01-01
Background Pedigree genotype datasets are used for analysing genetic inheritance and to map genetic markers and traits. Such datasets consist of hundreds of related animals genotyped for thousands of genetic markers and invariably contain multiple errors in both the pedigree structure and in the associated individual genotype data. These errors manifest as apparent inheritance inconsistencies in the pedigree, and invalidate analyses of marker inheritance patterns across the dataset. Cleaning ...
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Two-level mixed modeling of longitudinal pedigree data for genetic association analysis
DEFF Research Database (Denmark)
Tan, Q.
2013-01-01
of follow-up. Approaches have been proposed to integrate kinship correlation into the mixed effect models to explicitly model the genetic relationship which have been proven as an efficient way for dealing with sample clustering in pedigree data. Although useful for adjusting relatedness in the mixed...... assess the genetic associations with the mean level and the rate of change in a phenotype both with kinship correlation integrated in the mixed effect models. We apply our method to longitudinal pedigree data to estimate the genetic effects on systolic blood pressure measured over time in large pedigrees......Genetic association analysis on complex phenotypes under a longitudinal design involving pedigrees encounters the problem of correlation within pedigrees which could affect statistical assessment of the genetic effects on both the mean level of the phenotype and its rate of change over the time...
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Hierarchical linear modeling of longitudinal pedigree data for genetic association analysis
DEFF Research Database (Denmark)
Tan, Qihua; B Hjelmborg, Jacob V; Thomassen, Mads
2014-01-01
-effect models to explicitly model the genetic relationship. These have proved to be an efficient way of dealing with sample clustering in pedigree data. Although current algorithms implemented in popular statistical packages are useful for adjusting relatedness in the mixed modeling of genetic effects...... associated with blood pressure with estimated inflation factors of 0.99, suggesting that our modeling of random effects efficiently handles the genetic relatedness in pedigrees. Application to simulated data captures important variants specified in the simulation. Our results show that the method is useful......Genetic association analysis on complex phenotypes under a longitudinal design involving pedigrees encounters the problem of correlation within pedigrees, which could affect statistical assessment of the genetic effects. Approaches have been proposed to integrate kinship correlation into the mixed...
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Multigenerational organisations: a challenge for technology and social change
Millar-Schijf, Carla C.J.M.; Lockett, Martin
2014-01-01
This paper analyses demographic and organisational trends associated with an ageing workforce and introduces the articles in the special issue of Technological Forecasting and Social Change on Ageing2Agility: Multi-stakeholder Technological Forecasting for the Multi-generational Challenges in the
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Effects of phytosterols on zebrafish reproduction in multigeneration test
International Nuclear Information System (INIS)
Nakari, Tarja; Erkomaa, Kirsti
2003-01-01
A multigeneration test is used to show disruption of the reproductive system by phytosterols. - Zebrafish from mixed sex populations were exposed continuously across three generations to two phytosterol preparations both containing β-sitosterol. The phytosterols were isolated from wood and soy beans. Blood vitellogenin levels and sex ratio changes were used as intermediate indicators of the reproduction failures. Both sterol preparations caused vitellogenin induction in the exposed fish. The wood sterol changed the sex ratio of the exposed fish. In generation F1, the predominant sex was male, and in generation F2 it was female. The soy sterol in the used test concentration was lethal to the exposed fish in generation F1. This multigeneration test evidenced that phytosterols containing β-sitosterol disrupt the reproduction system of zebrafish by changing the sex ratios and by inducing the vitellogenin production in the exposed fish
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Effects of phytosterols on zebrafish reproduction in multigeneration test
Energy Technology Data Exchange (ETDEWEB)
Nakari, Tarja; Erkomaa, Kirsti
2003-05-01
A multigeneration test is used to show disruption of the reproductive system by phytosterols. - Zebrafish from mixed sex populations were exposed continuously across three generations to two phytosterol preparations both containing {beta}-sitosterol. The phytosterols were isolated from wood and soy beans. Blood vitellogenin levels and sex ratio changes were used as intermediate indicators of the reproduction failures. Both sterol preparations caused vitellogenin induction in the exposed fish. The wood sterol changed the sex ratio of the exposed fish. In generation F1, the predominant sex was male, and in generation F2 it was female. The soy sterol in the used test concentration was lethal to the exposed fish in generation F1. This multigeneration test evidenced that phytosterols containing {beta}-sitosterol disrupt the reproduction system of zebrafish by changing the sex ratios and by inducing the vitellogenin production in the exposed fish.
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Multigenerational cadmium acclimation and biokinetics in Daphnia magna
International Nuclear Information System (INIS)
Guan Rui; Wang Wenxiong
2006-01-01
A Cd exposure (3 μg L -1 ) experiment was conducted for six successive generations to investigate the responses to chronic Cd stress in Daphnia magna. We observed a biphasic accumulation of Cd in the six generations and suggested a similar pattern with respect to daphnids' tolerance. Cd assimilation efficiencies, daphnid growth, and reproduction corresponded to the changes of tolerance, which was partially accounted for by metallothionein induction. When maternally exposed neonates grew in Cd-free water for one or two generations, their growth, MT concentration and biokinetic parameters partially or totally recovered. The rapid recovery suggests the high potential for ecological restoration from Cd pollution. Our results indicate that the tolerance of sensitive D. magna clones to Cd was dependent on long-term or multigenerational exposure. The tolerance developed within the first several generations might not be maintained, and the animals may become even more sensitive to Cd stress in subsequent generations. - Tolerance of sensitive Daphnia magna clones to cadmium was dependent on long-term or multigenerational exposure
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Martin, Michael D; Jay, Flora; Castellano, Sergi; Slatkin, Montgomery
2017-08-01
We develop and evaluate methods for inferring relatedness among individuals from low-coverage DNA sequences of their genomes, with particular emphasis on sequences obtained from fossil remains. We suggest the major factors complicating the determination of relatedness among ancient individuals are sequencing depth, the number of overlapping sites, the sequencing error rate and the presence of contamination from present-day genetic sources. We develop a theoretical model that facilitates the exploration of these factors and their relative effects, via measurement of pairwise genetic distances, without calling genotypes, and determine the power to infer relatedness under various scenarios of varying sequencing depth, present-day contamination and sequencing error. The model is validated by a simulation study as well as the analysis of aligned sequences from present-day human genomes. We then apply the method to the recently published genome sequences of ancient Europeans, developing a statistical treatment to determine confidence in assigned relatedness that is, in some cases, more precise than previously reported. As the majority of ancient specimens are from animals, this method would be applicable to investigate kinship in nonhuman remains. The developed software grups (Genetic Relatedness Using Pedigree Simulations) is implemented in Python and freely available. © 2017 John Wiley & Sons Ltd.
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Burholt, Vanessa; Dobbs, Christine
2014-08-01
This paper considers the support networks of older people in populations with a preponderance of multigenerational households and examines the most vulnerable network types in terms of loneliness and isolation. Current common typologies of support networks may not be sensitive to differences within and between different cultures. This paper uses cross-sectional data drawn from 590 elders (Gujaratis, Punjabis and Sylhetis) living in the United Kingdom and South Asia. Six variables were used in K-means cluster analysis to establish a new network typology. Two logistic regression models using loneliness and isolation as dependent variables assessed the contribution of the new network type to wellbeing. Four support networks were identified: 'Multigenerational Households: Older Integrated Networks', 'Multigenerational Households: Younger Family Networks', 'Family and Friends Integrated Networks' and 'Non-kin Restricted Networks'. Older South Asians with 'Non-kin Restricted Networks' were more likely to be lonely and isolated compared to others. Using network typologies developed with individualistically oriented cultures, distributions are skewed towards more robust network types and could underestimate the support needs of older people from familistic cultures, who may be isolated and lonely and with limited informal sources of help. The new typology identifies different network types within multigenerational households, identifies a greater proportion of older people with vulnerable networks and could positively contribute to service planning.
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Acar, Tulin; Voltan-Acar, Nilufer
2013-01-01
The aim of this study was to evaluate the basic concepts of multigenerational Family Therapy and to evaluate the scenes of the film ''My Father and My Son'' according to these concepts. For these purposes firstly basic concepts of Multigenerational Family Therapy such as differentiation of self, triangles/triangulation, nuclear family emotional…
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Next Generation Sequencing Plus (NGS+) with Y-chromosomal Markers for Forensic Pedigree Searches.
Qian, Xiaoqin; Hou, Jiayi; Wang, Zheng; Ye, Yi; Lang, Min; Gao, Tianzhen; Liu, Jing; Hou, Yiping
2017-09-12
There is high demand for forensic pedigree searches with Y-chromosome short tandem repeat (Y-STR) profiling in large-scale crime investigations. However, when two Y-STR haplotypes have a few mismatched loci, it is difficult to determine if they are from the same male lineage because of the high mutation rate of Y-STRs. Here we design a new strategy to handle cases in which none of pedigree samples shares identical Y-STR haplotype. We combine next generation sequencing (NGS), capillary electrophoresis and pyrosequencing under the term 'NGS+' for typing Y-STRs and Y-chromosomal single nucleotide polymorphisms (Y-SNPs). The high-resolution Y-SNP haplogroup and Y-STR haplotype can be obtained with NGS+. We further developed a new data-driven decision rule, FSindex, for estimating the likelihood for each retrieved pedigree. Our approach enables positive identification of pedigree from mismatched Y-STR haplotypes. It is envisaged that NGS+ will revolutionize forensic pedigree searches, especially when the person of interest was not recorded in forensic DNA database.
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Identification of Mendelian inconsistencies between SNP and pedigree information of sibs
Directory of Open Access Journals (Sweden)
Calus Mario PL
2011-10-01
Full Text Available Abstract Background Using SNP genotypes to apply genomic selection in breeding programs is becoming common practice. Tools to edit and check the quality of genotype data are required. Checking for Mendelian inconsistencies makes it possible to identify animals for which pedigree information and genotype information are not in agreement. Methods Straightforward tests to detect Mendelian inconsistencies exist that count the number of opposing homozygous marker (e.g. SNP genotypes between parent and offspring (PAR-OFF. Here, we develop two tests to identify Mendelian inconsistencies between sibs. The first test counts SNP with opposing homozygous genotypes between sib pairs (SIBCOUNT. The second test compares pedigree and SNP-based relationships (SIBREL. All tests iteratively remove animals based on decreasing numbers of inconsistent parents and offspring or sibs. The PAR-OFF test, followed by either SIB test, was applied to a dataset comprising 2,078 genotyped cows and 211 genotyped sires. Theoretical expectations for distributions of test statistics of all three tests were calculated and compared to empirically derived values. Type I and II error rates were calculated after applying the tests to the edited data, while Mendelian inconsistencies were introduced by permuting pedigree against genotype data for various proportions of animals. Results Both SIB tests identified animal pairs for which pedigree and genomic relationships could be considered as inconsistent by visual inspection of a scatter plot of pairwise pedigree and SNP-based relationships. After removal of 235 animals with the PAR-OFF test, SIBCOUNT (SIBREL identified 18 (22 additional inconsistent animals. Seventeen animals were identified by both methods. The numbers of incorrectly deleted animals (Type I error, were equally low for both methods, while the numbers of incorrectly non-deleted animals (Type II error, were considerably higher for SIBREL compared to SIBCOUNT. Conclusions
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International Nuclear Information System (INIS)
Kimberly, David A.; Salice, Christopher J.
2015-01-01
Generally, ecotoxicologists rely on short-term tests that assume populations to be static. Conversely, natural populations may be exposed to the same stressors for many generations, which can alter tolerance to the same (or other) stressors. The objective of this study was to improve our understanding of how multigenerational stressors alter life history traits and stressor tolerance. After continuously exposing Daphnia magna to cadmium for 120 days, we assessed life history traits and conducted a challenge at higher temperature and cadmium concentrations. Predictably, individuals exposed to cadmium showed an overall decrease in reproductive output compared to controls. Interestingly, control D. magna were the most cadmium tolerant to novel cadmium, followed by those exposed to high cadmium. Our data suggest that long-term exposure to cadmium alter tolerance traits in a non-monotonic way. Because we observed effects after one-generation removal from cadmium, transgenerational effects may be possible as a result of multigenerational exposure. - Highlights: • Daphnia magna exposed to cadmium for 120 days. • D. magna exposed to cadmium had decreased reproductive output. • Control D. magna were most cadmium tolerant to novel cadmium stress. • Long-term exposure to cadmium alter tolerance traits in a non-monotonic way. • Transgenerational effects observed as a result of multigenerational exposure. - Adverse effects of long-term cadmium exposure persist into cadmium free conditions, as seen by non-monotonic responses when exposed to novel stress one generation removed.
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The Influence of Multigenerational Workforce in Effective Informal Team Learning
Directory of Open Access Journals (Sweden)
Roza Marsaulina Sibarani
2015-01-01
Full Text Available The urgency of this research arises from the convergence of two dynamics that are transforming the workplace and impacting organization performance. The first is multigenerational workforce work side by side in the same organization even in the same team. The second is informal learning, a major mode of learning in an organization. Therefore, this paper aims to explore the influence of generational background of Baby Boomers, Generation X and Generation Y in relation to informal team learning in the Indonesian business environment. Both, qualitative and quantitative studies were conducted with 21 interviewees and 184 survey respondents representing a total of 191 multigenerational teams participating in this research. The findings suggest that generational background influence informal learner and effective informal team learning, but have no direct impact on team climate. Understanding generational differences will enable individuals to learn informally and create a conducive team climate that will lead to effective informal team learning.
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Experiences of Adult Students in Multi-Generational Community College Classrooms
Clemente, Kathleen Ann
2010-01-01
This qualitative study is a basic interpretative inquiry studying the experiences of fourteen adult students 45 years of age or older in a multi-generational community college classroom. The study is informed by social constructivism, social constructionism and andragogy. It focused on how students viewed their experiences in the…
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Barbosa, Miguel; Inocentes, Núrya; Soares, Amadeu M V M; Oliveira, Miguel
2017-12-01
Increased variability in water temperature is predicted to impose disproportionally greater fitness costs than mean increase in temperature. Additionally, water contaminants are currently a major source of human-induced stress likely to produce fitness costs. Global change models forecast an increase in these two human-induced stressors. Yet, in spite the growing interest in understanding how organisms respond to global change, the joint fitness effects of water pollution and increased variability in temperature remain unclear. Here, using a multigenerational design, we test the hypothesis that exposure to high concentrations of fluoxetine, a human medicine commonly found in freshwater systems, causes increased lifetime fitness costs, when associated with increased variability in temperature. Although fluoxetine and variability in temperature elicited some fitness cost when tested alone, when both stressors acted together the costs were disproportionally greater. The combined effect of fluoxetine and variability in temperature led to a reduction of 37% in lifetime reproductive success and a 17.9% decrease in population growth rate. Interestingly, fluoxetine and variability in temperature had no effect on the probability of survival. Freshwater systems are among the most imperilled ecosystems, often exposed to multiple human-induced stressors. Our results indicate that organisms face greater fitness risk when exposed to multiple stressors at the same time than when each stress acts alone. Our study highlights the importance of using a multi-generational approach to fully understand individual environmental tolerance and its responses to a global change scenario in aquatic systems. Copyright © 2017 Elsevier B.V. All rights reserved.
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Breed-Predispositions to Cancer in Pedigree Dogs
Dobson, Jane M.
2013-01-01
Cancer is a common problem in dogs and although all breeds of dog and crossbred dogs may be affected, it is notable that some breeds of pedigree dogs appear to be at increased risk of certain types of cancer suggesting underlying genetic predisposition to cancer susceptibility. Although the aetiology of most cancers is likely to be multifactorial, the limited genetic diversity seen in purebred dogs facilitates genetic linkage or association studies on relatively small populations as compared to humans, and by using newly developed resources, genome-wide association studies in dog breeds are proving to be a powerful tool for unravelling complex disorders. This paper will review the literature on canine breed susceptibility to histiocytic sarcoma, osteosarcoma, haemangiosarcoma, mast cell tumours, lymphoma, melanoma, and mammary tumours including the recent advances in knowledge through molecular genetic, cytogenetic, and genome wide association studies. PMID:23738139
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Multigenerational Head Start Participation: An Unexpected Marker of Progress
Chor, Elise
2018-01-01
One-quarter of the Head Start population has a mother who participated in the program as a child. This study uses experimental Head Start Impact Study (HSIS) data on 3- and 4-year-olds (N = 2,849) to describe multigenerational Head Start families and their program experiences. In sharp contrast to full-sample HSIS findings, Head Start has large,…
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Nuclear Pedigree Criteria of Suspected HNPCC
Directory of Open Access Journals (Sweden)
Kładny Józef
2003-01-01
Full Text Available Abstract The criteria for the diagnosis of HNPCC established by the ICG-HNPCC are very restrictive as they do not allow for the diagnosis of a large number of "suspected HNPCC" cases - these are families which do no fulfill the strict diagnostic "Amsterdam criteria", but do present with several pedigree and clinical features characteristic for HNPCC. Several series of families suspected of harboring germline mutations in DNA mismatch repair genes have been studied for germline changes in DNA mismatch repair genes and a mutation rate of somewhere between 8-60% was found. Therefore a subgroup of members of the ICG-HNPCC has been working on pedigree/clinical diagnostic criteria for suspected HNPCC. Materials and methods Part I The study was based on two series of colorectal cancer (CRC cases: 1 HNPCC - this group comprised 190 patients affected by CRC from randomly selected families which fulfilled the Amsterdam II criteria registered in Düsseldorf, Germany (102 cases of CRC, Denmark (18 CRCs, Leiden, Holland (23 CRCs and Szczecin, Poland (47 CRCs. 2 Consecutive CRCs - this group comprised 629 (78.0% of 806 individuals with CRC diagnosed in 1991-1997 in the city of Szczecin (ca. 400,000 of inhabitants, Poland. Nuclear pedigrees in both groups were compared for frequency of occurrence of clinical features, that have been shown to be associated with HNPCC. Part II 52 consecutive CRC cases from Szczecin, matching the criteria recognized in part I as appropriate for diagnosis of cases "suspected of HNPCC" were studied for the occurrence of germline hMSH2/hMLH1 constitutional mutations using "exon by exon" sequencing. Results The combination of features - i.e. the occurrence of an HNPCC associated cancer (CRC or cancer of the endometrium, small bowel or urinary tract in a 1st degree relative of a CRC patient; at least one of the patients being diagnosed under age of 50 - appeared to be strongly associated to HNPCC with an OR - 161. Constitutional
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Parker, Lisa S
2002-02-01
Focusing on bipolar disorders research, this article considers ethical issues of informed consent and privacy arising in genetic pedigree research at two stages: the construction of tentative pedigrees to determine family eligibility for study and, subsequently, the enrollment of subjects in and conduct of the family study. Increasing concern to protect the privacy of family members of primary subjects or probands, following ethical controversy over a survey study at Virginia Commonwealth University, has led some researchers and Institutional Review Boards (IRBs) to apply informed consent requirements to those represented on a tentative pedigree at the initial stage of research. This article analyzes the possible benefits, risks, and burdens to prospective subjects of seeking prospective consent for pedigree construction at this initial stage. It argues that the likely risk-benefit ratio favors granting a waiver of consent requirements for this stage of pedigree research and presents grounds for IRBs to grant such a waiver. The article closes by considering particular ethical concerns that should be addressed in the informed consent discussion when enrolling subjects in pedigree studies of bipolar disorder, including concerns about subjects' competence to consent, management of interim and incidental findings, and issues particular to psychiatric research.
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Family genome browser: visualizing genomes with pedigree information.
Juan, Liran; Liu, Yongzhuang; Wang, Yongtian; Teng, Mingxiang; Zang, Tianyi; Wang, Yadong
2015-07-15
Families with inherited diseases are widely used in Mendelian/complex disease studies. Owing to the advances in high-throughput sequencing technologies, family genome sequencing becomes more and more prevalent. Visualizing family genomes can greatly facilitate human genetics studies and personalized medicine. However, due to the complex genetic relationships and high similarities among genomes of consanguineous family members, family genomes are difficult to be visualized in traditional genome visualization framework. How to visualize the family genome variants and their functions with integrated pedigree information remains a critical challenge. We developed the Family Genome Browser (FGB) to provide comprehensive analysis and visualization for family genomes. The FGB can visualize family genomes in both individual level and variant level effectively, through integrating genome data with pedigree information. Family genome analysis, including determination of parental origin of the variants, detection of de novo mutations, identification of potential recombination events and identical-by-decent segments, etc., can be performed flexibly. Diverse annotations for the family genome variants, such as dbSNP memberships, linkage disequilibriums, genes, variant effects, potential phenotypes, etc., are illustrated as well. Moreover, the FGB can automatically search de novo mutations and compound heterozygous variants for a selected individual, and guide investigators to find high-risk genes with flexible navigation options. These features enable users to investigate and understand family genomes intuitively and systematically. The FGB is available at http://mlg.hit.edu.cn/FGB/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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Multigeneration reproduction and male developmental toxicity studies on atrazine in rats.
DeSesso, John M; Scialli, Anthony R; White, Tacey E K; Breckenridge, Charles B
2014-06-01
Reproductive toxicity of Atrazine (ATR) was evaluated in two rat multigenerational studies. Development of male reproductive parameters was evaluated in separate studies after prenatal or postnatal exposure. In multigenerational studies, rats received dietary concentrations of 0, 10, 50, 100 or 500 ppm ATR. In separate studies in female rats, ATR was administered by gavage at 0, 1, 5, 25 or 125 mg/kg/day during pregnancy (GD6-21) or lactation (LD2-21). Plasma testosterone concentration, testicular and epididymal weights, and sperm counts were measured in male offspring on PND70 and 170. In the multigenerational studies, parental systemic toxicity occurred at 500 ppm (38.7 mg/kg/day), but reproductive endpoints were unaffected. In the prenatal study, maternal toxicity and embryo-fetal mortality occurred at 125 mg/kg/day. In male offspring, testosterone levels and sperm counts were unaffected, although the percentage of abnormal sperm increased at 125 mg/kg/day (PND 70) and 25 mg/kg/day (PND170). In the postnatal study, maternal toxicity and reduced body weights of male offspring occurred at 125 mg/kg/day. Additionally, reduced testicular (PND70, PND170) and epididymal (PND70) weights and increased numbers of abnormal sperm (PND70, PND170) were seen, but no changes in plasma testosterone or sperm counts. Dietary administration of ATR did not affect rat reproduction up to a parentally toxic dose of 38.7 mg/kg/day. Some effects on male reproductive system development occurred after high dose, bolus administration to dams, but doses were much higher than expected under normal use conditions. Thus, oral RfDs for ATR would be protective for reproductive effects. © 2014 Wiley Periodicals, Inc.
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Multilocus lod scores in large pedigrees: combination of exact and approximate calculations.
Tong, Liping; Thompson, Elizabeth
2008-01-01
To detect the positions of disease loci, lod scores are calculated at multiple chromosomal positions given trait and marker data on members of pedigrees. Exact lod score calculations are often impossible when the size of the pedigree and the number of markers are both large. In this case, a Markov Chain Monte Carlo (MCMC) approach provides an approximation. However, to provide accurate results, mixing performance is always a key issue in these MCMC methods. In this paper, we propose two methods to improve MCMC sampling and hence obtain more accurate lod score estimates in shorter computation time. The first improvement generalizes the block-Gibbs meiosis (M) sampler to multiple meiosis (MM) sampler in which multiple meioses are updated jointly, across all loci. The second one divides the computations on a large pedigree into several parts by conditioning on the haplotypes of some 'key' individuals. We perform exact calculations for the descendant parts where more data are often available, and combine this information with sampling of the hidden variables in the ancestral parts. Our approaches are expected to be most useful for data on a large pedigree with a lot of missing data. (c) 2007 S. Karger AG, Basel
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Leveraging multi-generational workforce values in interactive information societies
Sophie van der Walt; Tanya du Plessis
2010-01-01
Background: The success of organisations relies on various factors including the ability of its multi-generational workforce to collaborate within the interactive information society. By developing an awareness of the different values of a diverse workforce, organisations may benefit from diversity. Various diversity factors, such as ethnicity, age and gender, impact on the way people interact, especially in the interactive information society.Objectives: This article advocates the need for g...
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Chronic effects of clofibric acid in zebrafish (Danio rerio): A multigenerational study
Energy Technology Data Exchange (ETDEWEB)
Coimbra, Ana M., E-mail: acoimbra@utad.pt [Centre for The Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes e Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real (Portugal); Department of Biology and Environment, Life Sciences and Environment School (ECVA), University of Trás-os-Montes e Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real (Portugal); Peixoto, Maria João [CIMAR/CIIMAR, Interdisciplinary Centre for Marine and Environmental Research, University of Porto, Rua dos Bragas 177, 4050-123 Porto (Portugal); Department of Biology and Environment, Life Sciences and Environment School (ECVA), University of Trás-os-Montes e Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real (Portugal); Coelho, Inês; Lacerda, Ricardo [CIMAR/CIIMAR, Interdisciplinary Centre for Marine and Environmental Research, University of Porto, Rua dos Bragas 177, 4050-123 Porto (Portugal); Carvalho, António Paulo [CIMAR/CIIMAR, Interdisciplinary Centre for Marine and Environmental Research, University of Porto, Rua dos Bragas 177, 4050-123 Porto (Portugal); FCUP, Faculty of Sciences University of Porto, Department of Biology, Rua do Campo Alegre, 4169-007 Porto (Portugal); Gesto, Manuel [CIMAR/CIIMAR, Interdisciplinary Centre for Marine and Environmental Research, University of Porto, Rua dos Bragas 177, 4050-123 Porto (Portugal); Department of Functional Biology and Health Sciences, Faculty of Biology, University of Vigo, As Lagoas-Marcosende s/n, 36310, Vigo (Spain); Lyssimachou, Angeliki; Lima, Daniela; Soares, Joana; André, Ana; Capitão, Ana [CIMAR/CIIMAR, Interdisciplinary Centre for Marine and Environmental Research, University of Porto, Rua dos Bragas 177, 4050-123 Porto (Portugal); and others
2015-03-15
Highlights: • Clofibric acid (CA) induces multigenerational effects in zebrafish (Danio rerio). • CA impacts fish lipid metabolism, with similarities to those reported in mammals. • Weight is impacted in F1 and F2 generations, thought with opposite patterns. - Abstract: Clofibric acid (CA) is an active metabolite of the blood lipid lowering agent clofibrate, a pharmaceutical designed to work as agonist of peroxisome proliferator-activated receptor alpha (PPARa). It is the most commonly reported fibrate in aquatic environments with low degradation rate and potential environmental persistence. Previous fish exposures showed that CA may impact spermatogenesis, growth and the expression of fat binding protein genes. However, there are limited data on the effects of chronic multigenerational CA exposures. Here, we assessed chronic multigenerational effects of CA exposure using zebrafish (Danio rerio) as a teleost model. Zebrafish were exposed through the diet to CA (1 and 10 mg/g) during their whole lifetime. Growth, reproduction-related parameters and embryonic development were assessed in the exposed fish (F1 generation) and their offspring (F2 generation), together with muscle triglyceride content and gonad histology. In order to study the potential underlying mechanisms, the transcription levels of genes coding for enzymes involved in lipid metabolism pathways were determined. The results show that chronic life-cycle exposure to CA induced a significant reduction in growth of F1 generation and lowered triglyceride muscle content (10 mg/g group). Also, an impact in male gonad development was observed together with a decrease in the fecundity (10 mg/g group) and higher frequency of embryo abnormalities in the offspring of fish exposed to the lowest CA dose. The profile of the target genes was sex- and tissue-dependent. In F1 an up-regulation of male hepatic pparaa, pparb and acox transcript levels was observed, suggesting an activation of the fatty acid
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Chronic effects of clofibric acid in zebrafish (Danio rerio): A multigenerational study
International Nuclear Information System (INIS)
Coimbra, Ana M.; Peixoto, Maria João; Coelho, Inês; Lacerda, Ricardo; Carvalho, António Paulo; Gesto, Manuel; Lyssimachou, Angeliki; Lima, Daniela; Soares, Joana; André, Ana; Capitão, Ana
2015-01-01
Highlights: • Clofibric acid (CA) induces multigenerational effects in zebrafish (Danio rerio). • CA impacts fish lipid metabolism, with similarities to those reported in mammals. • Weight is impacted in F1 and F2 generations, thought with opposite patterns. - Abstract: Clofibric acid (CA) is an active metabolite of the blood lipid lowering agent clofibrate, a pharmaceutical designed to work as agonist of peroxisome proliferator-activated receptor alpha (PPARa). It is the most commonly reported fibrate in aquatic environments with low degradation rate and potential environmental persistence. Previous fish exposures showed that CA may impact spermatogenesis, growth and the expression of fat binding protein genes. However, there are limited data on the effects of chronic multigenerational CA exposures. Here, we assessed chronic multigenerational effects of CA exposure using zebrafish (Danio rerio) as a teleost model. Zebrafish were exposed through the diet to CA (1 and 10 mg/g) during their whole lifetime. Growth, reproduction-related parameters and embryonic development were assessed in the exposed fish (F1 generation) and their offspring (F2 generation), together with muscle triglyceride content and gonad histology. In order to study the potential underlying mechanisms, the transcription levels of genes coding for enzymes involved in lipid metabolism pathways were determined. The results show that chronic life-cycle exposure to CA induced a significant reduction in growth of F1 generation and lowered triglyceride muscle content (10 mg/g group). Also, an impact in male gonad development was observed together with a decrease in the fecundity (10 mg/g group) and higher frequency of embryo abnormalities in the offspring of fish exposed to the lowest CA dose. The profile of the target genes was sex- and tissue-dependent. In F1 an up-regulation of male hepatic pparaa, pparb and acox transcript levels was observed, suggesting an activation of the fatty acid
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Pedigree analysis of the Hungarian Thoroughbred population
Bokor, A.; Jonas, D.; Ducro, B.J.; Nagy, I.; Bokor, J.; Szabari, M.
2013-01-01
The aim of the study was to analyse the pedigree information of Thoroughbred horses which were participating in gallop races between 1998 and 2010 in Hungary. Among the 3043 individuals of the reference population there were imported animals from foreign countries (e.g. Germany, England or Ireland)
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High mitochondrial mutation rates estimated from deep-rooting Costa Rican pedigrees
Madrigal, Lorena; Melendez-Obando, Mauricio; Villegas-Palma, Ramon; Barrantes, Ramiro; Raventos, Henrieta; Pereira, Reynaldo; Luiselli, Donata; Pettener, Davide; Barbujani, Guido
2012-01-01
Estimates of mutation rates for the noncoding hypervariable Region I (HVR-I) of mitochondrial DNA (mtDNA) vary widely, depending on whether they are inferred from phylogenies (assuming that molecular evolution is clock-like) or directly from pedigrees. All pedigree-based studies so far were conducted on populations of European origin. In this paper we analyzed 19 deep-rooting pedigrees in a population of mixed origin in Costa Rica. We calculated two estimates of the HVR-I mutation rate, one considering all apparent mutations, and one disregarding changes at sites known to be mutational hot spots and eliminating genealogy branches which might be suspected to include errors, or unrecognized adoptions along the female lines. At the end of this procedure, we still observed a mutation rate equal to 1.24 × 10−6, per site per year, i.e., at least three-fold as high as estimates derived from phylogenies. Our results confirm that mutation rates observed in pedigrees are much higher than estimated assuming a neutral model of long-term HVRI evolution. We argue that, until the cause of these discrepancies will be fully understood, both lower estimates (i.e., those derived from phylogenetic comparisons) and higher, direct estimates such as those obtained in this study, should be considered when modeling evolutionary and demographic processes. PMID:22460349
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Identification of kin structure among Guam rail founders: a comparison of pedigrees and DNA profiles
Haig, Susan M.; Ballou, J.D.; Casna, N.J.
1994-01-01
Kin structure among founders can have a significant effect on subsequent population structure. Here we use the correlation between DNA profile similarity and relatedness calculated from pedigrees to test hypotheses regarding kin structure among founders to the captive Guam rail (Rallus owstoni) population. Five different pedigrees were generated under the following hypotheses: (i) founders are unrelated; (ii) founders are unrelated except for same-nest chicks; (iii) founders from the same major site are siblings; (iv) founders from the same local site are siblings; and (v) founders are related as defined by a UPGMA cluster analysis of DNA similarity data. Relatedness values from pedigrees 1, 2 and 5 had the highest correlation with DNA similarity but the correlation between relatedness and similarity were not significantly different among pedigrees. Pedigree 5 resulted in the highest correlation overall when using only relatedness values that changed as a result of different founder hypotheses. Thus, founders were assigned relatedness based on pedigree 5 because it had the highest correlations with DNA similarity, was the most conservative approach, and incorporated all field data. The analyses indicated that estimating relatedness using DNA profiles remains problematic, therefore we compared mean kinship, a measure of genetic importance, with mean DNA profile similarity to determine if genetic importance among individuals could be determined via use of DNA profiles alone. The significant correlation suggests this method may provide more information about population structure than was previously thought. Thus, DNA profiles can provide a reasonable explanation for founder relatedness and mean DNA profile similarity may be helpful in determining relative genetic importance of individuals when detailed pedigrees are absent.
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Multi-generational effects of propranolol on Daphnia magna at different environmental concentrations
International Nuclear Information System (INIS)
Jeong, Tae-Yong; Kim, Hyun Young; Kim, Sang Don
2015-01-01
To evaluate the effects of propranolol on Daphnia magna (D. magna), we employed a multi-generational exposure period for eight generations and an environmentally relevant low concentration with 1.5 ng/L, 0.2 μg/L and 26 μg/L to reflect a realistic exposure scenario. Physiological endpoints were checked, including growth, number of neonates, heart rate, frequency of abdominal appendage movement and malformation rate of neonates. In the results, growth and abdominal appendage movement were affected by environmental concentration during several generations, and the responses showed consistent tendencies of response increase with concentration increase. Heart rate was the only endpoint affected throughout all exposure generations. Inhibitory and acceleratory effects on heart rate, growth and abdominal appendage movement suggest that it is necessary to cover sub-lethal endpoints of non-targeted organisms in eco-toxicity study because the physiological responses were detected at much lower concentrations than the results of traditional toxicity tests, including environmental concentration. - Highlights: • Multi-generational exposure was conducted to evaluate the effect of propranolol on Daphnia magna. • Heart rate was the only endpoint affected throughout all exposure generations. • Growth and abdominal appendage movement were affected at environmental concentrations. • Time series fluctuations in responses appeared with no tendencies throughout all generations. • It is necessary to cover sub-organismal endpoints and long-term exposure in ecotoxicity test. - Heart rate, growth and abdominal appendage movement of D. magna were affected by the multigenerational exposure of propranolol at environmental levels.
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Clinical features and genetic analysis of tuberous sclerosis pedigrees
Directory of Open Access Journals (Sweden)
LI Ya-qin
2012-06-01
Full Text Available Objective In order to understand tuberous sclerosis complex better, the clinical manifestation, imaging characteristics, and genetic characteristics of tuberous sclerosis complex from 3 pedigrees were investigated. Methods The clinical data of patients from 3 tuberous sclerosis families were collected. The gene mutation type of TSC2 of proband in pedigree one was determined by PCR and direct gene sequencing. Results All of the 3 probands went to our clinic for the reason of epilepsy. Brain imaging examination noted intracranial nodular calcification. EEG showed comprehensive spines and slow waves, sharp waves. The pedigree 1 has family history, two male patients and 3 female patients, all had facial angiofibromas and epilepsy. Gene mutation analysis of TSC2 demonstrated the c.1444-2A > C mutation in index patient. All the 3 index patients had mental retardation, autism and hypopigmented macule. Conclusion For infants and young children with epilepsy as the first symptom, accompanied by mental retardation, autism, facial angiofibromas or hypopigmented macule and other skin abnormalities, brain imaging examination noted intracranial nodular calcification are highly suggestive of tuberous sclerosis complex. TSC1 and TSC2 gene analysis contribute to the diagnosis of this disease, genentic counseling and prenatal diagnosis.
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International Nuclear Information System (INIS)
Zhou, Dong; Yang, Jie; Li, Hui; Lu, Qiang; Liu, Yong-di; Lin, Kuang-fei
2016-01-01
In order to understand how bisphenol A (BPA) exposure acts on the evolutionary dynamics of populations and changes of stress response across generations, the model animal Caenorhabditis elegans was used to conduct the multigenerational testing. Multiple endpoints at the physiological (growth, reproduction, and locomotion behaviors) and molecular (stress-related gene expressions) levels were examined by multigenerational exposure to low-concentration BPA (0.001–10 μM) across four generations. The results showed that changes of physiological-level effects across four generations varied in magnitude and direction, depending on the exposure concentrations. C. elegans individuals in the first generation grew smaller, moved slower, and produced less offsprings than the controls by BPA exposure. As for each trait tested, the first generation response could be commonly mirrored in the subsequent generations at the highest concentration of 10 μM. However, at lower concentrations, response of parental generation was a relatively poor predictor of the effects on progeny, as acclimation or cumulative damage could occur in the subsequent generations. The integrated gene expression profiles visually illustrated that the tested gene expressions at low concentrations (0.001–0.01 μM) were more obviously changed in both G_1 and G_4 generations, and the G_1 generation showed a much greater degree of increase in stress-related gene expressions than the G_4 generation. The multigenerational toxicity data emphasize the need of considering biological effects over multiple generations to conduct accurate assessment of environmental risks of toxicants on population dynamics. - Highlights: • Multigenerational exposure was conducted to evaluate effects of BPA on C. elegans. • Changes of biological effects varied in magnitude and direction across generations. • A more significant induction in stress-related gene expressions was found in G_1. • Multigenerational tests have
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Directory of Open Access Journals (Sweden)
Ornella Ludovico
Full Text Available Some patients diagnosed as having type 2 diabetes mellitus (T2DM are, instead, affected by multigenerational diabetes whose clinical characteristics are mostly undefined.1. To identify among patients who had been previously defined as affected by T2DM those, in fact, affected by multigenerational diabetes; 2. After excluding patients carrying the most common MODY genes and mitochondrial mutations, we compared clinical features of remaining patients with those of patients with T2DM.Among 2,583 consecutive adult patients who had been defined as affected by T2DM, we looked for those with diabetes in ≥3 consecutive generations. All probands were screened for mutations in six MODY genes (HNF4A, GCK, HNF1A, PDX1, HNF1B and NeuroD1 and for the A3243G mitochondrial mutation. After excluding patients with mutations in one of such genes, we compared clinical features of the remaining 67 patients (2.6% of the whole initial sample affected by multigenerational "familial diabetes of the adulthood" (FDA and of their diabetic relatives (n = 63 to those with T2DM (n = 1,028 by generalized hierarchical linear models followed by pairwise comparisons.Age, age at diagnosis, proportion of hypertension (all p<0.001, and waist circumference (p<0.05 were lower in FDA than T2DM. Nonetheless, the two groups had similar age-adjusted incidence rate of all-cause mortality.Beside younger age at diagnosis, FDA patients show lower waist circumference and reduced proportion of hypertension as compared to those with T2DM; despite such reduced potential cardiovascular risk factors, FDA patients did not show a reduced mortality risk than patients with T2DM.
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Distribution of volatile composition in 'marion' ( rubus species hyb) blackberry pedigree.
Du, Xiaofen; Finn, Chad; Qian, Michael C
2010-02-10
The distribution of volatile constituents in ancestral genotypes of 'Marion' blackberry's pedigree was investigated over two growing seasons. Each genotype in the pedigree had a specific volatile composition. Red raspberry was dominated by norisoprenoids, lactones, and acids. 'Logan' and 'Olallie' also had a norisoprenoid dominance but at much lower concentrations. The concentration of norisoprenoids in other blackberry genotypes was significantly lower. Terpenes and furanones were predominant in wild 'Himalaya' blackberry, whereas terpenes were the major volatiles in 'Santiam'. 'Marion', a selection from 'Chehalem' and 'Olallie', contained almost all of the volatile compounds in its pedigree at moderate amount. The chiral isomeric ratios of 11 pairs of compounds were also studied. Strong chiral isomeric preference was observed for most of the chiral compounds, and each cultivar had its unique chiral isomeric distribution. An inherent pattern was observed for some volatile compounds in the 'Marion' pedigree. Raspberry and 'Logan' had a very high concentration of beta-ionone, but was reduced by half in 'Olallie' and by another half in 'Marion' as the crossing proceeded. A high content of linalool in 'Olallie' and a low content in 'Chehalem' resulted in a moderate content of linalool in their progeny 'Marion'. However, the concentration of furaneol in 'Marion' was higher than in its parents. A high content of (S)-linalool in 'Olallie' and a racemic content of (S)-,(R)-linalool in 'Chehalem' resulted in a preference for the (S)-form in 'Marion'.
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Li, Pang; Cui, Kai; Zhang, Bo; Wang, Zhendan; Shen, Yangyang; Wang, Xiangyu; Zhang, Jianbo; Tong, Feng; Li, Sheng
2015-04-01
The regeneration of muscle tissue has been achieved using multipotent mesenchymal stem cells in mouse models of injured skeletal muscle. In the present study, the utility of multipotent human umbilical cord-derived mesenchymal stem cells (hUC-MSCs) in the treatment of Becker muscular dystrophy (BMD), a genetic disease where muscle tissue fails to regenerate, was examined in members from a pedigree affected by BMD. The disease status was evaluated in 4 affected pedigree members (II1, II2, II3 and III2; aged 50, 46, 42 and 6 years, respectively). The transplantation of the hUC‑MSCs (performed on 3 patients, I2, II3 and III2) was performed by infusion with an intravenous drip over a 30‑min period, and the patients were evaluated at 1, 3, 4 and 12 weeks following the procedure. The evaluation was based on physical characteristics, as well as on molecular testing for serum creatine kinase (CK) and lactate dehydrogenase (LDH) levels and a histological examination of muscle biopsies. The patients suffered no adverse reactions in response to the transplantation of the hUC‑MSCs. At 1 week following transplantation all 3 patients showed improvement in the muscle force of the limbs, muscle size and daily activity. The walking gait of patient III2 had improved by 1 week post-transplantation and reached a normal status by 12 weeks. Serum CK and LDH levels were decreased relative to the baseline levels. A histological examination of muscle biopsies displayed no obvious tissue regeneration. In conclusion, the treatment of patients with BMD using hUC-MSCs was safe and of therapeutic benefit that lasted for up to 12 weeks. hUC-MSCs are, therefore, a potential cell therapy-based treatment option for patients with muscular dystrophies.
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Human factors issues for interstellar spacecraft
Cohen, Marc M.; Brody, Adam R.
1991-01-01
Developments in research on space human factors are reviewed in the context of a self-sustaining interstellar spacecraft based on the notion of traveling space settlements. Assumptions about interstellar travel are set forth addressing costs, mission durations, and the need for multigenerational space colonies. The model of human motivation by Maslow (1970) is examined and directly related to the design of space habitat architecture. Human-factors technology issues encompass the human-machine interface, crew selection and training, and the development of spaceship infrastructure during transtellar flight. A scenario for feasible instellar travel is based on a speed of 0.5c, a timeframe of about 100 yr, and an expandable multigenerational crew of about 100 members. Crew training is identified as a critical human-factors issue requiring the development of perceptual and cognitive aids such as expert systems and virtual reality.
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Zou, Qi-Lei; You, Xiao-Ping; Li, Jian-Long; Fung, Wing Kam; Zhou, Ji-Yuan
2018-01-05
Genomic imprinting is one of the well-known epigenetic factors causing the association between traits and genes, and has generally been examined by detecting parent-of-origin effects of alleles. A lot of methods have been proposed to test for parent-of-origin effects on autosomes based on nuclear families and general pedigrees. Although these parent-of-origin effects tests on autosomes have been available for more than 15 years, there has been no statistical test developed to test for parent-of-origin effects on X chromosome, until the parental-asymmetry test on X chromosome (XPAT) and its extensions were recently proposed. However, these methods on X chromosome are only applicable to nuclear families and thus are not suitable for general pedigrees. In this article, we propose the pedigree parental-asymmetry test on X chromosome (XPPAT) statistic to test for parent-of-origin effects in the presence of association, which can accommodate general pedigrees. When there are missing genotypes in some pedigrees, we further develop the Monte Carlo pedigree parental-asymmetry test on X chromosome (XMCPPAT) to test for parent-of-origin effects, by inferring the missing genotypes given the observed genotypes based on a Monte Carlo estimation. An extensive simulation study has been carried out to investigate the type I error rates and the powers of the proposed tests. Our simulation results show that the proposed methods control the size well under the null hypothesis of no parent-of-origin effects. Moreover, XMCPPAT substantially outperforms the existing tests and has a much higher power than XPPAT which only uses complete nuclear families (with both parents) from pedigrees. We also apply the proposed methods to analyze rheumatoid arthritis data for their practical use. The proposed XPPAT and XMCPPAT test statistics are valid and powerful in detecting parent-of-origin effects on X chromosome for qualitative traits based on general pedigrees and thus are recommended.
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This study examined the etiology of typical replant disease symptom development, including growth reduction and leaf chlorosis, that was limited to specific foci within three multi-generation apple orchards that overall demonstrated optimal growth and good quality standard production. In bioassays c...
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Elemental marking of arthropod pests in agricultural systems: single and multigenerational marking
Jane Leslie Hayes
1991-01-01
Use of elemental markers to study movement of arthropod pests of field crops is reviewed. Trace elements, rubidium (Rb) and cesium (Cs), have provided a nondisruptive method of marking natural adult populations via developmental stage consumption of treated host plants. Multigenerational marking occurs with the transfer of elemental markers from marked adults to...
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Checking Consistency of Pedigree Information is NP-complete
DEFF Research Database (Denmark)
Aceto, Luca; Hansen, Jens A.; Ingolfsdottir, Anna
Consistency checking is a fundamental computational problem in genetics. Given a pedigree and information on the genotypes of some of the individuals in it, the aim of consistency checking is to determine whether these data are consistent with the classic Mendelian laws of inheritance. This probl...
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Zeng, Li-ping; Hu, Zheng-mao; Mu, Li-li; Mei, Gui-sen; Lu, Xiu-ling; Zheng, Yong-jun; Li, Pei-jian; Zhang, Ying-xue; Pan, Qian; Long, Zhi-gao; Dai, He-ping; Zhang, Zhuo-hua; Xia, Jia-hui; Zhao, Jing-ping; Xia, Kun
2011-06-01
To investigate the relationship of susceptibility loci in chromosomes 1q21-25 and 6p21-25 and schizophrenia subtypes in Chinese population. A genomic scan and parametric and non-parametric analyses were performed on 242 individuals from 36 schizophrenia pedigrees, including 19 paranoid schizophrenia and 17 undifferentiated schizophrenia pedigrees, from Henan province of China using 5 microsatellite markers in the chromosome region 1q21-25 and 8 microsatellite markers in the chromosome region 6p21-25, which were the candidates of previous studies. All affected subjects were diagnosed and typed according to the criteria of the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, Text Revised (DSM-IV-TR; American Psychiatric Association, 2000). All subjects signed informed consent. In chromosome 1, parametric analysis under the dominant inheritance mode of all 36 pedigrees showed that the maximum multi-point heterogeneity Log of odds score method (HLOD) score was 1.33 (α = 0.38). The non-parametric analysis and the single point and multi-point nonparametric linkage (NPL) scores suggested linkage at D1S484, D1S2878, and D1S196. In the 19 paranoid schizophrenias pedigrees, linkage was not observed for any of the 5 markers. In the 17 undifferentiated schizophrenia pedigrees, the multi-point NPL score was 1.60 (P= 0.0367) at D1S484. The single point NPL score was 1.95(P= 0.0145) and the multi-point NPL score was 2.39 (P= 0.0041) at D1S2878. Additionally, the multi-point NPL score was 1.74 (P= 0.0255) at D1S196. These same three loci showed suggestive linkage during the integrative analysis of all 36 pedigrees. In chromosome 6, parametric linkage analysis under the dominant and recessive inheritance and the non-parametric linkage analysis of all 36 pedigrees and the 17 undifferentiated schizophrenia pedigrees, linkage was not observed for any of the 8 markers. In the 19 paranoid schizophrenias pedigrees, parametric analysis showed that under recessive
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Machado-Joseph Disease in Pedigrees of Azorean descent is Linked to Chromosome 14
George-Hyslop, P. St; Rogaeva, E.; Huterer, J.; Tsuda, T.; Santos, J.; Haines, J. L.; Schlumpf, K.; Rogaev, E. I.; Liang, Y.; McLachlan, D. R. Crapper; Kennedy, J.; Weissenbach, J.; Billingsley, G. D.; Cox, D. W.; Lang, A. E.
1994-01-01
A locus for Machado-Joseph disease (MJD) has recently been mapped to a 30-cM region of chromosome 14q in five pedigrees of Japanese descent. MJD is a clinically pleomorphic neurodegenerative disease that was originally described in subjects of Azorean descent. In light of the nonallelic heterogeneity in other inherited spinocere-bellar ataxias, we were interested to determine if the MJD phenotype in Japanese and Azorean pedigrees arose from mutations at the same locus. We provide evidence tha...
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Jathar, S. H.; Cappa, C. D.; Wexler, A. S.; Seinfeld, J. H.; Kleeman, M. J.
2016-02-01
Multi-generational oxidation of volatile organic compound (VOC) oxidation products can significantly alter the mass, chemical composition and properties of secondary organic aerosol (SOA) compared to calculations that consider only the first few generations of oxidation reactions. However, the most commonly used state-of-the-science schemes in 3-D regional or global models that account for multi-generational oxidation (1) consider only functionalization reactions but do not consider fragmentation reactions, (2) have not been constrained to experimental data and (3) are added on top of existing parameterizations. The incomplete description of multi-generational oxidation in these models has the potential to bias source apportionment and control calculations for SOA. In this work, we used the statistical oxidation model (SOM) of Cappa and Wilson (2012), constrained by experimental laboratory chamber data, to evaluate the regional implications of multi-generational oxidation considering both functionalization and fragmentation reactions. SOM was implemented into the regional University of California at Davis / California Institute of Technology (UCD/CIT) air quality model and applied to air quality episodes in California and the eastern USA. The mass, composition and properties of SOA predicted using SOM were compared to SOA predictions generated by a traditional two-product model to fully investigate the impact of explicit and self-consistent accounting of multi-generational oxidation.Results show that SOA mass concentrations predicted by the UCD/CIT-SOM model are very similar to those predicted by a two-product model when both models use parameters that are derived from the same chamber data. Since the two-product model does not explicitly resolve multi-generational oxidation reactions, this finding suggests that the chamber data used to parameterize the models captures the majority of the SOA mass formation from multi-generational oxidation under the conditions
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Protecting the privacy of family members in survey and pedigree research.
Botkin, J
2001-01-10
The recent controversy at Virginia Commonwealth University involving research ethics raises important and complex issues in survey and pedigree research. The primary questions are whether family members of survey respondents themselves become subjects of the project and if they are subjects whether informed consent must be obtained for investigators to retain private information on these individuals. This article provides an analysis of the ethical issues and regulatory standards involved in this debate for consideration by investigators and institutional review boards. The analysis suggests that strong protections for the rights and welfare of subjects and their family members can be incorporated into survey and pedigree research protocols without hindering projects with extensive consent requirements.
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Siddiqui, Osamah; Dincer, Ibrahim
2017-12-01
In the present study, a new solar-based multigeneration system integrated with an ammonia fuel cell and solid oxide fuel cell-gas turbine combined cycle to produce electricity, hydrogen, cooling and hot water is developed for analysis and performance assessment. In this regard, thermodynamic analyses and modeling through both energy and exergy approaches are employed to assess and evaluate the overall system performance. Various parametric studies are conducted to study the effects of varying system parameters and operating conditions on the energy and exergy efficiencies. The results of this study show that the overall multigeneration system energy efficiency is obtained as 39.1% while the overall system exergy efficiency is calculated as 38.7%, respectively. The performance of this multigeneration system results in an increase of 19.3% in energy efficiency as compared to single generation system. Furthermore, the exergy efficiency of the multigeneration system is 17.8% higher than the single generation system. Moreover, both energy and exergy efficiencies of the solid oxide fuel cell-gas turbine combined cycle are determined as 68.5% and 55.9% respectively.
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Multi-Generation Concentrating Solar-Hydrogen Power System for Sustainable Rural Development
Energy Technology Data Exchange (ETDEWEB)
Krothapalli, A.; Greska, B.
2007-07-01
This paper describes an energy system that is designed to meet the demands of rural populations that currently have no access to grid-connected electricity. Besides electricity, it is well recognized that rural populations need at least a centralized refrigeration system for storage of medicines and other emergency supplies, as well as safe drinking water. Here we propose a district system that will employ a multi-generation concentrated solar power (CSP) system that will generate electricity and supply the heat needed for both absorption refrigeration and membrane distillation (MD) water purification. The electricity will be used to generate hydrogen through highly efficient water electrolysis and individual households can use the hydrogen for generating electricity, via affordable proton exchange membrane (PEM) fuel cells, and as a fuel for cooking. The multi-generation system is being developed such that its components will be easy to manufacture and maintain. As a result, these components will be less efficient than their typical counterparts but their low cost-to-efficiency ratio will allow for us to meet our installation cost goal of $1/Watt for the entire system. The objective of this paper is to introduce the system concept and discuss the system components that are currently under development. (auth)
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Curwen, Margie Sauceda
2011-01-01
This study explored how multi-generational, middle-class, fifth-graders from Latino families responded to classroom discussions of social issues--particularly discrimination--and draws upon sociocultural views of culture, educational theory, and sociological perspectives of immigration to provide insight into the learning experiences of one group…
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Modeling and Assessment of a Biomass Gasification Integrated System for Multigeneration Purpose
Directory of Open Access Journals (Sweden)
Shoaib Khanmohammadi
2016-01-01
Full Text Available The use of biomass due to the reduction in greenhouse gas emissions and environmental impacts has attracted many researchers’ attention in the recent years. Access to an energy conversion system which is able to have the optimum performance for applying valuable low heating value fuels has been considered by many practitioners and scholars. This paper focuses on the accurate modeling of biomass gasification process and the optimal design of a multigeneration system (heating, cooling, electrical power, and hydrogen as energy carrier to take the advantage of this clean energy. In the process of gasification modeling, a thermodynamic equilibrium model based on Gibbs energy minimization is used. Also, in the present study, a detailed parametric analysis of multigeneration system for undersigning the behavior of objective functions with changing design parameters and obtaining the optimal design parameters of the system is done as well. The results show that with exergy efficiency as an objective function this parameter can increase from 19.6% in base case to 21.89% in the optimized case. Also, for the total cost rate of system as an objective function it can decrease from 154.4 $/h to 145.1 $/h.
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Rodgers, Erica M.; Simon, Matthew A.; Antol, Jeffrey; Chai, Patrick R.; Jones, Christopher A.; Klovstad, Jordan J.; Neilan, James H.; Stillwagen, Frederic H.; Williams, Phillip A.; Bednara, Michael;
2015-01-01
The path from Earth to Mars requires exploration missions to be increasingly Earth-independent as the foundation is laid for a sustained human presence in the following decades. NASA pioneering of Mars will expand the boundaries of human exploration, as a sustainable presence on the surface requires humans to successfully reproduce in a partial gravity environment independent from Earth intervention. Before significant investment is made in capabilities leading to such pioneering efforts, the challenges of multigenerational mammalian reproduction in a partial gravity environment need be investigated. The Multi-generational Independent Colony for Extraterrestrial Habitation, Autonomy, and Behavior health is designed to study these challenges. The proposed concept is a conceptual, long duration, autonomous habitat designed to house rodents in a partial gravity environment with the goal of understanding the effects of partial gravity on mammalian reproduction over multiple generations and how to effectively design such a facility to operate autonomously while keeping the rodents healthy in order to achieve multiple generations. All systems are designed to feed forward directly to full-scale human missions to Mars. This paper presents the baseline design concept formulated after considering challenges in the mission and vehicle architectures such as: vehicle automation, automated crew health management/medical care, unique automated waste disposal and hygiene, handling of deceased crew members, reliable long-duration crew support systems, and radiation protection. This concept was selected from an architectural trade space considering the balance between mission science return and robotic and autonomy capabilities. The baseline design is described in detail including: transportation and facility operation constraints, artificial gravity system design, habitat design, and a full-scale mock-up demonstration of autonomous rodent care facilities. The proposed concept has
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Parent and Child Cigarette Use: A Longitudinal, Multigenerational Study
Staff, Jeremy
2013-01-01
OBJECTIVES: Using longitudinal data from the multigenerational Youth Development Study (YDS), this article documents how parents’ long-term smoking trajectories are associated with adolescent children’s likelihood of smoking. Prospective data from the parents (from age 14–38 years) enable unique comparisons of the parents’ and children’s smoking behavior, as well as that of siblings. METHODS: Smoking trajectories are constructed using latent class analysis for the original YDS cohort (n = 1010). Multigenerational longitudinal data from 214 parents and 314 offspring ages 11 years and older are then analyzed by using logistic regression with cluster-corrected SEs. RESULTS: Four latent smoking trajectories emerged among the original cohort: stable nonsmokers (54%), early-onset light smokers who quit/reduce (16%), late-onset persistent smokers (14%), and early-onset persistent heavy smokers (16%). Although 8% of children of stable nonsmokers smoked in the last year, the other groups’ children had much higher percentages, ranging from 23% to 29%. Multivariate logistic regression models confirm that these significant differences were robust to the inclusion of myriad child- and parent-level measures (for which child age and grade point average [GPA] are significant predictors). Older sibling smoking, however, mediated the link between parental heavy smoking and child smoking. CONCLUSIONS: Even in an era of declining rates of teenage cigarette use in the United States, children of current and former smokers face an elevated risk of smoking. Prevention efforts to weaken intergenerational associations should consider parents’ long-term cigarette use, as well as the smoking behavior of older siblings in the household. PMID:23918887
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Leveraging multi-generational workforce values in interactive information societies
Directory of Open Access Journals (Sweden)
Sophie van der Walt
2010-08-01
Full Text Available Background: The success of organisations relies on various factors including the ability of its multi-generational workforce to collaborate within the interactive information society. By developing an awareness of the different values of a diverse workforce, organisations may benefit from diversity. Various diversity factors, such as ethnicity, age and gender, impact on the way people interact, especially in the interactive information society.Objectives: This article advocates the need for generational awareness and addresses how this awareness presents benefits to companies, such as, increased productivity, improved succession planning policies and strategies to recruit and retain a diverse workforce. The research problem is directed at how diversity management influences Traditionalists, Baby Boomers, Generation X and Generation Y in terms of their work performance and co-worker relationships.Method: The research design combines Critical Theory and Generational Theory within the mixed-method paradigm. The sequential exploratory design was decided upon as it studies the unknown relationships between different generations of employees. The literature review was followed by a quantitative empirical research component and data was collected by means of a questionnaire. Results: The findings highlight specific differences between generations regarding their perspectives on work values and co-worker relationships, rewards, work-life balance and retirement.Conclusion: The article concludes with recommendations on the role diversity management plays in terms of work performance and co-worker relationships. By leveraging generational awareness in the interactive information society organizations with a multi-generational workforce will succeed in the competitive business environment.
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Chronic effects of clofibric acid in zebrafish (Danio rerio): a multigenerational study.
Coimbra, Ana M; Peixoto, Maria João; Coelho, Inês; Lacerda, Ricardo; Carvalho, António Paulo; Gesto, Manuel; Lyssimachou, Angeliki; Lima, Daniela; Soares, Joana; André, Ana; Capitão, Ana; Castro, Luís Filipe C; Santos, Miguel M
2015-03-01
Clofibric acid (CA) is an active metabolite of the blood lipid lowering agent clofibrate, a pharmaceutical designed to work as agonist of peroxisome proliferator-activated receptor alpha (PPARa). It is the most commonly reported fibrate in aquatic environments with low degradation rate and potential environmental persistence. Previous fish exposures showed that CA may impact spermatogenesis, growth and the expression of fat binding protein genes. However, there are limited data on the effects of chronic multigenerational CA exposures. Here, we assessed chronic multigenerational effects of CA exposure using zebrafish (Danio rerio) as a teleost model. Zebrafish were exposed through the diet to CA (1 and 10mg/g) during their whole lifetime. Growth, reproduction-related parameters and embryonic development were assessed in the exposed fish (F1 generation) and their offspring (F2 generation), together with muscle triglyceride content and gonad histology. In order to study the potential underlying mechanisms, the transcription levels of genes coding for enzymes involved in lipid metabolism pathways were determined. The results show that chronic life-cycle exposure to CA induced a significant reduction in growth of F1 generation and lowered triglyceride muscle content (10mg/g group). Also, an impact in male gonad development was observed together with a decrease in the fecundity (10mg/g group) and higher frequency of embryo abnormalities in the offspring of fish exposed to the lowest CA dose. The profile of the target genes was sex- and tissue-dependent. In F1 an up-regulation of male hepatic pparaa, pparb and acox transcript levels was observed, suggesting an activation of the fatty acid metabolism (provided that transcript level change indicates also a protein level change). Interestingly, the F2 generation, raised with control diet, displayed a response pattern different from that observed in F1, showing an increase in weight in the descendants of CA exposed fish, in
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Motivation in a multigenerational radiologic science workplace.
Kalar, Traci
2008-01-01
For the first time in history, radiologic science (RS) workplaces consist of 4 generational cohorts. As each cohort possess their own attitudes, values, work habits, and expectations, motivating a generational diverse workplace is challenging. Through the understanding of generational differences, managers are better able to accommodate individual as well as generational needs and help create a more productive and higher performing workplace. The purpose of this paper is to assist managers in the understanding and utilization of generational differences to effectively motivate staff in an RS workplace. Generational cohorts will be defined and discussed along with an in-depth discussion on each of the generations performing in today's RS workplace. Motivators and how they impact the different generational cohorts will be addressed along with how to best motivate a multigenerational RS workplace.
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Hemmer, R.L., G.M. Cripe and L.R. Goodman. In press. Maximizing Growth and Sexual Maturation of Sheepshead Minnows (Cyprinodon variegatus) in Support of Multi-Generation Test Development (Abstract). To be presented at the SETAC Fourth World Congress, 14-18 November 2004, Portland...
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International Nuclear Information System (INIS)
Akrami, Ehsan; Chitsaz, Ata; Nami, Hossein; Mahmoudi, S.M.S.
2017-01-01
In this paper, a geothermal based multi-generation energy system, including organic Rankine cycle, domestic water heater, absorption refrigeration cycle and proton exchange membrane electrolyzer, is developed to generate electricity, heating, cooling and hydrogen. For this purpose, energetic, exergetic and exergoeconomic analysis are undertaken upon proposed system. Also, the effects of some important variables, i.e. geothermal water temperature, turbine inlet temperature and pressure, generator temperature, geothermal water mass flow rate and electrolyzer current density on the several parameters such as energy and exergy efficiencies of the proposed system, heating and cooling load, net electrical output power, hydrogen production, unit cost of each system products and total unit cost of the products are investigated. For specified conditions, the results show that energy and exergy efficiencies of the proposed multi-generation system are calculated about 34.98% and 49.17%, respectively. The highest and lowest total unit cost of the products estimated approximately 23.18 and 22.73 $/GJ, respectively, by considering that geothermal water temperature increases from 185 °C to 215 °C. - Highlights: • A multigeneration energy system based on geothermal energy is developed. • The energetic, exergetic and exergoeconomic analysis are undertaken upon proposed system. • The influences of several significant parameters are investigated. • The energy and exergy efficiencies of the entire system are calculated around 34.98% and 49.17%.
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Ding, Qiu-lan; Wang, Hong-li; Wang, Xue-feng; Wang, Ming-shan; Fu, Qi-hua; Wu, Wen-man; Hu, Yi-qun; Wang, Zhen-yi
2003-10-01
To identify the genetic mutations of a severe inherited coagulation factor VII (FVII) deficiency pedigree. The diagnosis was validated by coagulant and haemostatic parameters. FVII gene mutations were screened in the propositus and his family members by DNA direct sequencing and confirmed by digestions of the restriction enzymes of the PCR production. Two heterozygous missense mutations were found in the propositus of the pedigree: a G to T transversion at position 9482 in exon 6 and a C to T mutation at position 11348 in exon 8 resulting in the amino acid substitution of Arg152 with Leu and Arg304 with Trp, respectively. A heterozygous single nucleotide deletion (C) at position 11487-11489(CCC) within exon 8 was identified, which predicted the frameshift mutation at position His351 followed by the changes of six corresponding amino acids and appearance of a premature protein caused by stop codon. The heterozygous mutations identified in the proband were derived from his father (Arg152 to Leu) and his mother (Arg304 to Trp mutation) and a heterozygous deletion (C) at position 11487-9(CCC). By tracing the other pedigree members, it was found that his grandmother had a heterozygous mutation of Arg304Trp and a heterozygous polymorphism of Arg353Gln and his grandfather had a heterozygous Arg152Leu mutation. Three heterozygous mutations were found in a pedigree with hereditary coagulation factor VII deficiency. Arg152Leu and deletion C at position 11487-9(CCC) were novel mutations.
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Directory of Open Access Journals (Sweden)
S. H. Jathar
2016-02-01
Full Text Available Multi-generational oxidation of volatile organic compound (VOC oxidation products can significantly alter the mass, chemical composition and properties of secondary organic aerosol (SOA compared to calculations that consider only the first few generations of oxidation reactions. However, the most commonly used state-of-the-science schemes in 3-D regional or global models that account for multi-generational oxidation (1 consider only functionalization reactions but do not consider fragmentation reactions, (2 have not been constrained to experimental data and (3 are added on top of existing parameterizations. The incomplete description of multi-generational oxidation in these models has the potential to bias source apportionment and control calculations for SOA. In this work, we used the statistical oxidation model (SOM of Cappa and Wilson (2012, constrained by experimental laboratory chamber data, to evaluate the regional implications of multi-generational oxidation considering both functionalization and fragmentation reactions. SOM was implemented into the regional University of California at Davis / California Institute of Technology (UCD/CIT air quality model and applied to air quality episodes in California and the eastern USA. The mass, composition and properties of SOA predicted using SOM were compared to SOA predictions generated by a traditional two-product model to fully investigate the impact of explicit and self-consistent accounting of multi-generational oxidation.Results show that SOA mass concentrations predicted by the UCD/CIT-SOM model are very similar to those predicted by a two-product model when both models use parameters that are derived from the same chamber data. Since the two-product model does not explicitly resolve multi-generational oxidation reactions, this finding suggests that the chamber data used to parameterize the models captures the majority of the SOA mass formation from multi-generational oxidation under
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Exome sequencing of a pedigree with Tourette syndrome or chronic tic disorder.
Sundaram, Senthil K; Huq, Ahm M; Sun, Zhen; Yu, Wu; Bennett, Lindsey; Wilson, Benjamin J; Behen, Michael E; Chugani, Harry T
2011-05-01
Ten members of a 3-generation pedigree with 7 showing Tourette syndrome/chronic tic phenotype (TS-CTD) were evaluated with whole exome sequencing. We identified 3 novel, nonsynonymous single nucleotide variants in the MRPL3, DNAJC13, and OFCC1 genes that segregated with chronic tic phenotype. These variants were not present in 100 control subjects or in dbSNP/1000 Genomes databases. A novel variant in the 5' untranslated region of the OFCC1 gene was found in 2 TS-CTD patients from a different pedigree. Further studies will clarify the importance of variants in MRPL3, DNAJC13, and OFCC1 genes in TS. Copyright © 2011 American Neurological Association.
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Validation of DNA-based identification software by computation of pedigree likelihood ratios.
Slooten, K
2011-08-01
Disaster victim identification (DVI) can be aided by DNA-evidence, by comparing the DNA-profiles of unidentified individuals with those of surviving relatives. The DNA-evidence is used optimally when such a comparison is done by calculating the appropriate likelihood ratios. Though conceptually simple, the calculations can be quite involved, especially with large pedigrees, precise mutation models etc. In this article we describe a series of test cases designed to check if software designed to calculate such likelihood ratios computes them correctly. The cases include both simple and more complicated pedigrees, among which inbred ones. We show how to calculate the likelihood ratio numerically and algebraically, including a general mutation model and possibility of allelic dropout. In Appendix A we show how to derive such algebraic expressions mathematically. We have set up these cases to validate new software, called Bonaparte, which performs pedigree likelihood ratio calculations in a DVI context. Bonaparte has been developed by SNN Nijmegen (The Netherlands) for the Netherlands Forensic Institute (NFI). It is available free of charge for non-commercial purposes (see www.dnadvi.nl for details). Commercial licenses can also be obtained. The software uses Bayesian networks and the junction tree algorithm to perform its calculations. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.
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Sinclair, Maureen
2010-01-01
Purpose: The purpose of the study was to determine to what extent multigenerational teachers: (a) perceive that their secondary school principal demonstrates the following dimensions of authentic leadership: heart, values, purpose, relationship building, and self-discipline; (b) reveal a difference by generation in the importance they assign to…
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A methodology for designing flexible multi-generation systems
DEFF Research Database (Denmark)
Lythcke-Jørgensen, Christoffer Ernst; Viana Ensinas, Adriano; Münster, Marie
2016-01-01
An FMG (flexible multi-generation system) consists of integrated and flexibly operated facilities that provide multiple links between the various layers of the energy system. FMGs may facilitate integration and balancing of fluctuating renewable energy sources in the energy system in a cost...... is based on consideration of the following points: Selection, location and dimensioning of processes; systematic heat and mass integration; flexible operation optimization with respect to both short-term market fluctuations and long-term energy system development; global sensitivity and uncertainty...... analysis; biomass supply chains; variable part-load performance; and multi-objective optimization considering economic and environmental performance. Tested in a case study, the methodology is proved effective in screening the solution space for efficient FMG designs, in assessing the importance...
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Machado-Joseph disease in pedigrees of Azorean descent is linked to chromosome 14.
St George-Hyslop, P; Rogaeva, E; Huterer, J; Tsuda, T; Santos, J; Haines, J L; Schlumpf, K; Rogaev, E I; Liang, Y; McLachlan, D R
1994-07-01
A locus for Machado-Joseph disease (MJD) has recently been mapped to a 30-cM region of chromosome 14q in five pedigrees of Japanese descent. MJD is a clinically pleomorphic neurodegenerative disease that was originally described in subjects of Azorean descent. In light of the nonallelic heterogeneity in other inherited spinocerebellar ataxias, we were interested to determine if the MJD phenotype in Japanese and Azorean pedigrees arose from mutations at the same locus. We provide evidence that MJD in five pedigrees of Azorean descent is also linked to chromosome 14q in an 18-cM region between the markers D14S67 and AACT (multipoint lod score +7.00 near D14S81). We also report molecular evidence for homozygosity at the MJD locus in an MJD-affected subject with severe, early-onset symptoms. These observations confirm the initial report of linkage of MJD to chromosome 14; suggest that MJD in Japanese and Azorean subjects may represent allelic or identical mutations at the same locus; and provide one possible explanation (MJD gene dosage) for the observed phenotypic heterogeneity in this disease.
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Multi-generation cadmium acclimation and tolerance in Daphnia magna Straus
International Nuclear Information System (INIS)
Muyssen, Brita T.A.; Janssen, Colin R.
2004-01-01
The cladoceran Daphnia magna was acclimated for seven generations to cadmium concentrations ranging from 0 (control) to 250 μg/l Cd (corresponding to a free ion activity of 4.60 nM Cd 2+ ). Acute and chronic cadmium tolerance as well as cadmium accumulation were monitored as a function of acclimation time. After two to three generations of acclimation to concentrations ranging from 0.23 to 1.11 nM Cd 2+ increases in acute tolerance were maximal (factor 7.2) and significant. Acclimation for seven generations to the same acclimation concentrations did result in an increased chronic cadmium tolerance (21 days EC 50 values increased). Organisms acclimated to 1.93 nM Cd 2+ were equally or more sensitive than non-acclimated daphnids in acute and chronic toxicity tests. Cadmium contents in D. magna increased significantly as a function of the acclimation concentration. Maximum body burdens of 236±30 μg Cd/g dry weight were measured in organisms exposed to 4.60 nM Cd 2+ , but detoxification mechanisms were only successful up to 82±20 μg Cd/g dry weight as this concentration did not cause major decreases in survival and reproduction in chronic toxicity tests. As the potential positive effect of acclimation on cadmium tolerance disappeared with successive acclimation generations and increasing acclimation concentrations, it is concluded that multi-generation acclimation studies are important for the evaluation of the long-term effects of environmental toxicants. - Multi-generation acclimation studies are important for evaluating long-term effects of aquatic pollutants
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Performance assessment of a new solar energy-based multigeneration system
International Nuclear Information System (INIS)
Ozlu, Sinan; Dincer, Ibrahim
2016-01-01
In this study, a thermodynamic analysis is conducted on a multigeneration energy system based on renewable energy sources. The proposed system is developed for residential applications, including individual- and multi-building complexes, utilizing solar energy to produce useful outputs, namely electricity, heat, fresh water and hydrogen. Hydrogen is used for the purpose of storing energy to offset the mismatch between demand and supply when dealt with renewables, such as solar energy. The system is modeled thermodynamically to obtain the optimal energy and exergy efficiencies, heat and work outputs for the overall system. Moreover, greenhouse gas emissions caused by conventional energy systems utilized for the same outputs are calculated and compared with the studied systems. A solar collector area of 24 m 2 is considered for the present system and its analysis. The maximum energy efficiency is 36% and the maximum exergy efficiency is 44%. The total work output for electricity is 116 kW, and hence the CO 2 reduction achieved by this system is 476 tons per year. It can produce 0.04 kg/s desalinated water. The optimum number of suites, as an application for a building complex, which can be sustained with the proposed system is determined as 106 suites. - Highlights: • A solar energy based multigeneration system is proposed. • Energy, exergy efficiencies, heat, work outputs of the system are determined. • Optimization is done on efficiencies and work output. • Domestic heating, desalination, hydrogen, electricity is obtained. • Overall system energy and exergy efficiency is found to be 36% and 44%.
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2018-01-23
Hereditary colorectal cancer can be divded into two categories based on the presence or absence of polyps. The first category is characterized by the development of polyposis, which includes familial adenomatous polyposis (FAP); The second category is nonpolyposis colorectal cancer, which is represented by Lynch syndrome. "Consensus on clinical diagnosis, treatment and pedigree management of hereditary colorectal cancer in China" developed by the Genetics Group of the Committee of Colorectal Cancer, Chinese Anti-cancer Association, is composed of three sections, including hereditary nonpolyposis syndrome, polyposis syndrome as well as genetic evaluation of hereditary colorectal cancer. The consensus aims to provide recommendations on management of the respective hereditary syndromes in terms of definition, clinical and pathological features, diagnostic standards, treatment, and follow-ups. In addition to describing diagnostic and treatment strategies, prophylactic treatment as well as genetic screening and pedigree monitoring is highly recommended. Through the establishment of this expert consensus, we hope to promote better understanding of hereditary colorectal cancer for clinicians and encourage standardized treatment through multidisciplinery approaches, eventually improving clinical treatment and pedigree management of hereditary colorectal cancer in China.
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Nechiporuk, A; Fain, P; Kort, E; Nee, L E; Frommelt, E; Polinsky, R J; Korenberg, J R; Pulst, S M
1993-05-01
Alzheimer disease (AD) is a devastating neurodegenerative disease leading to global dementia. In addition to sporadic forms of AD, familial forms (FAD) have been recognized. Mutations in the amyloid precursor protein (APP) gene on chromosome (CHR) 21 have been shown to cause early-onset AD in a small number of pedigrees. Recently, linkage to markers on CHR 14 has been established in several early-onset FAD pedigrees. We now report lod scores for CHR 14 markers in two large early-onset FAD pedigrees. Pairwise linkage analysis suggested that in these pedigrees the mutation is tightly linked to the loci D14S43 and D14S53. However, assumptions regarding marker allele frequencies had a major and often unpredictable effect on calculated lod scores. Therefore, caution needs to be exercised when single pedigrees are analyzed with marker allele frequencies determined from the literature or from a pool of spouses.
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PyPedal, an open source software package for pedigree analysis
The open source software package PyPedal (http://pypedal.sourceforge.net/) was first released in 2002, and provided users with a set of simple tools for manipulating pedigrees. Its flexibility has been demonstrated by its used in a number of settings for large and small populations. After substantia...
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Yu, T; Wang, X; Ding, Q; Fu, Q; Dai, J; Lu, Y; Xi, X; Wang, H
2009-11-01
Factor VII deficiency which transmitted as an autosomal recessive disorder is a rare haemorrhagic condition. The aim of this study was to identify the molecular genetic defect and determine its functional consequences in a Chinese pedigree with FVII deficiency. The proband was diagnosed as inherited coagulation FVII deficiency by reduced plasma levels of FVII activity (4.4%) and antigen (38.5%). All nine exons and their flanking sequence of F7 gene were amplified by polymerase chain reaction (PCR) for the proband and the PCR products were directly sequenced. The compound heterozygous mutations of F7 (NM_000131.3) c.572-1G>A and F7 (NM_000131.3) c.1165T>G; p.Cys389Gly were identified in the proband's F7 gene. To investigate the splicing patterns associated with F7 c.572-1G>A, ectopic transcripts in leucocytes of the proband were analyzed. F7 minigenes, spanning from intron 4 to intron 7 and carrying either an A or a G at position -1 of intron 5, were constructed and transiently transfected into human embryonic kidney (HEK) 293T cells, followed by RT-PCR analysis. The aberrant transcripts from the F7 c.572-1G>A mutant allele were not detected by ectopic transcription study. Sequencing of the RT-PCR products from the mutant transfectant demonstrated the production of an erroneously spliced mRNA with exon 6 skipping, whereas a normal splicing occurred in the wide type transfectant. The aberrant mRNA produced from the F7 c.572-1G>A mutant allele is responsible for the factor VII deficiency in this pedigree.
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2015-05-06
45 viii ix Abstract Generation members are born , start school, enter the workforce, have children, and retire at about the...and Army acquisition workforce has evolved into a multigenerational workforce of young (Millennials, born 1980–2000), middle age (Generation X, 1965...younger workforce. Editors of TDn2K, a restaurant workforce data and analytics provider firm ( Restaurant Hospitality, 2014), quoting Sarah Atkinson
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Moser, Kathy L.; Neas, Barbara R.; Salmon, Jane E.; Yu, Hua; Gray-McGuire, Courtney; Asundi, Neeraj; Bruner, Gail R.; Fox, Jerome; Kelly, Jennifer; Henshall, Stephanie; Bacino, Debra; Dietz, Myron; Hogue, Robert; Koelsch, Gerald; Nightingale, Lydia; Shaver, Tim; Abdou, Nabih I.; Albert, Daniel A.; Carson, Craig; Petri, Michelle; Treadwell, Edward L.; James, Judith A.; Harley, John B.
1998-01-01
Systemic lupus erythematosus (SLE) is an autoimmune disorder characterized by production of autoantibodies against intracellular antigens including DNA, ribosomal P, Ro (SS-A), La (SS-B), and the spliceosome. Etiology is suspected to involve genetic and environmental factors. Evidence of genetic involvement includes: associations with HLA-DR3, HLA-DR2, Fcγ receptors (FcγR) IIA and IIIA, and hereditary complement component deficiencies, as well as familial aggregation, monozygotic twin concordance >20%, λs > 10, purported linkage at 1q41–42, and inbred mouse strains that consistently develop lupus. We have completed a genome scan in 94 extended multiplex pedigrees by using model-based linkage analysis. Potential [log10 of the odds for linkage (lod) > 2.0] SLE loci have been identified at chromosomes 1q41, 1q23, and 11q14–23 in African-Americans; 14q11, 4p15, 11q25, 2q32, 19q13, 6q26–27, and 12p12–11 in European-Americans; and 1q23, 13q32, 20q13, and 1q31 in all pedigrees combined. An effect for the FcγRIIA candidate polymorphism) at 1q23 (lod = 3.37 in African-Americans) is syntenic with linkage in a murine model of lupus. Sib-pair and multipoint nonparametric analyses also support linkage (P 2.0). Our results are consistent with the presumed complexity of genetic susceptibility to SLE and illustrate racial origin is likely to influence the specific nature of these genetic effects. PMID:9843982
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Identification of Mendelian inconsistencies between SNP and pedigree Information of Sibs
Calus, M.P.L.; Mulder, H.A.; Bastiaansen, J.W.M.
2011-01-01
Background Using SNP genotypes to apply genomic selection in breeding programs is becoming common practice. Tools to edit and check the quality of genotype data are required. Checking for Mendelian inconsistencies makes it possible to identify animals for which pedigree information and genotype
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Project InterActions: A Multigenerational Robotic Learning Environment
Bers, Marina U.
2007-12-01
This paper presents Project InterActions, a series of 5-week workshops in which very young learners (4- to 7-year-old children) and their parents come together to build and program a personally meaningful robotic project in the context of a multigenerational robotics-based community of practice. The goal of these family workshops is to teach both parents and children about the mechanical and programming aspects involved in robotics, as well as to initiate them in a learning trajectory with and about technology. Results from this project address different ways in which parents and children learn together and provide insights into how to develop educational interventions that would educate parents, as well as children, in new domains of knowledge and skills such as robotics and new technologies.
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Hammerly, Susan C; Morrow, Michael E; Johnson, Jeff A
2013-11-01
The primary goal of captive breeding programmes for endangered species is to prevent extinction, a component of which includes the preservation of genetic diversity and avoidance of inbreeding. This is typically accomplished by minimizing mean kinship in the population, thereby maintaining equal representation of the genetic founders used to initiate the captive population. If errors in the pedigree do exist, such an approach becomes less effective for minimizing inbreeding depression. In this study, both pedigree- and DNA-based methods were used to assess whether inbreeding depression existed in the captive population of the critically endangered Attwater's Prairie-chicken (Tympanuchus cupido attwateri), a subspecies of prairie grouse that has experienced a significant decline in abundance and concurrent reduction in neutral genetic diversity. When examining the captive population for signs of inbreeding, variation in pedigree-based inbreeding coefficients (f(pedigree)) was less than that obtained from DNA-based methods (f(DNA)). Mortality of chicks and adults in captivity were also positively correlated with parental relatedness (r(DNA)) and f(DNA), respectively, while no correlation was observed with pedigree-based measures when controlling for additional variables such as age, breeding facility, gender and captive/release status. Further, individual homozygosity by loci (HL) and parental rDNA values were positively correlated with adult mortality in captivity and the occurrence of a lethal congenital defect in chicks, respectively, suggesting that inbreeding may be a contributing factor increasing the frequency of this condition among Attwater's Prairie-chickens. This study highlights the importance of using DNA-based methods to better inform management decisions when pedigrees are incomplete or errors may exist due to uncertainty in pairings. © 2013 John Wiley & Sons Ltd.
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Voges, S; Distl, O
2009-10-01
The objective of this study was to analyse genetic diversity for the three scent-hound breeds Bavarian mountain hound (BMH), Hanoverian hound (HH) and Tyrolean hound (TH) using all available pedigree information from scent-hound kennel clubs for these three breeds throughout Europe. The pedigree data of the BMH and the HH date back to 1912 and 1894, respectively. Pedigree data of the TH were available from the 1960s onwards. The reference populations included all BMH (n = 3231), HH (n = 1371) and TH (n = 1167) dogs registered between 1992 and 2004. Average generation intervals were 5.3 years for the BMH and 5.0 years for the HH and TH. Average inbreeding coefficients for the reference populations were 4.5%, 6.8% and 9.5% for the BMH, HH and TH. The effective numbers of founders, ancestors and founder genomes were lowest for the TH and highest for the BMH. The effective numbers of founder genomes were 10.9, 5.6 and 4.3 for the BMH, HH and TH. Effective population size was largest for the BMH with 72.7 effective breeding animals, followed by the HH with 50.9 and TH with 26.5. The most important ten ancestors had genetic contributions to the reference populations of 54.4%, 65.2% and 77.9% in the BMH, HH and TH. The results of our study indicate the need for careful breed management in these highly specialized hound breeds to maintain genetic diversity. European stud books should be established for these dog breeds in order to avoid inbreeding due to missing pedigree records.
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Boehnke, M; Moll, P P; Kottke, B A; Weidman, W H
1987-04-01
Fasting plasma glucose measurements made in 1972-1977 on normoglycemic individuals in three-generation Caucasian pedigrees from Rochester, Minnesota were analyzed. The authors determined the contributions of polygenic loci and environmental factors to fasting plasma glucose variability in these pedigrees. To that end, fasting plasma glucose measurements were normalized by an inverse normal scores transformation and then regressed separately for males and females on measured concomitants including age, body mass index (weight/height2), season of measurement, sex hormone use, and diuretic use. The authors found that 27.7% of the variability in normalized fasting plasma glucose in these pedigrees is explained by these measured concomitants. Subsequent variance components analysis suggested that unmeasured polygenic loci and unmeasured shared environmental factors together account for at least an additional 36.7% of the variability in normalized fasting plasma glucose, with genes alone accounting for at least 27.3%. These results are consistent with the known familiality of diabetes, for which fasting plasma glucose level is an important predictor. Further, these familial factors provide an explanation for at least half the variability in normalized fasting plasma glucose which remains after regression on known concomitants.
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International Nuclear Information System (INIS)
Chen Xiulan; Yang Hefeng; He Zhentian; Han Yuepeng; Liu Xueyu
2002-01-01
The percentage of homologous series of early mutants (PHSEM) induced by irradiation was closely related to its pedigree. This study showed that PHSEM for varieties with the same pedigree were similar, and there were three different level of dominance (high, low and normal) in the homologous series induced from different pedigree. The PHSEM for varieties derived form distant-relative-parents were higher than that derived from close-relative-parents. There was the dominance pedigree for the induction of homologous series of early mutants. IR8(Peta x DGWG), IR127 (Cpslo x Sigadis) and IR24 (IR8 x IR127) were dominant pedigree, and varieties derived from them could be easily induced the homologous series of early mutants
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Cultural Transmission and Evolution of Melodic Structures in Multi-generational Signaling Games.
Lumaca, Massimo; Baggio, Giosuè
2017-01-01
It has been proposed that languages evolve by adapting to the perceptual and cognitive constraints of the human brain, developing, in the course of cultural transmission, structural regularities that maximize or optimize learnability and ease of processing. To what extent would perceptual and cognitive constraints similarly affect the evolution of musical systems? We conducted an experiment on the cultural evolution of artificial melodic systems, using multi-generational signaling games as a laboratory model of cultural transmission. Signaling systems, using five-tone sequences as signals, and basic and compound emotions as meanings, were transmitted from senders to receivers along diffusion chains in which the receiver in each game became the sender in the next game. During transmission, structural regularities accumulated in the signaling systems, following principles of proximity, symmetry, and good continuation. Although the compositionality of signaling systems did not increase significantly across generations, we did observe a significant increase in similarity among signals from the same set. We suggest that our experiment tapped into the cognitive and perceptual constraints operative in the cultural evolution of musical systems, which may differ from the mechanisms at play in language evolution and change.
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Two pedigrees of familial advanced sleep phase syndrome in Japan.
Satoh, Kohtoku; Mishima, Kazuo; Inoue, Yuichi; Ebisawa, Takashi; Shimizu, Tetsuo
2003-06-15
To determine whether a known missense mutation (bp2106 A/G) in hPer2 (a human homolog of the Drosophila period gene) for familial advanced sleep phase syndrome in a Caucasian family is involved in Japanese familial advanced sleep phase syndrome pedigrees. We identified 2 new Japanese families with advanced sleep phase syndrome, and a systematic survey was carried out in 28 relatives of theses 2 families. A total of 9 affected subjects were identified. The affected members showed significantly strong morningness tendencies compared with the unaffected members in various circadian parameters including the Horne-Ostberg Morningness-Eveningness Questionnaire score (77.3 +/- 4.8 vs 57.5 +/- 7.6, p sleep-onset time (20:45 +/- 75 min vs 23:16 +/- 64 min, p DNA samples were obtained from 7 affected and 7 unaffected subjects. None of the tested subjects possessed the missense mutation (bp2106 A/G) in hPer2. Furthermore, there is no significant linkage between affected subjects with hPer2 region by 2-point mapping and by direct sequencing of 23 exons of hPer2. These findings support the notion of genetic heterogeneity of familial advanced sleep phase syndrome cases in humans. The search for more familial advanced sleep phase syndrome cases and for loci other than hPer2 are necessary to further examine the roles of circadian-related genes in genetically determined human circadian rhythm disorders.
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Cultural Transmission and Evolution of Melodic Structures in Multi-generational Signaling Games
DEFF Research Database (Denmark)
Lumaca, Massimo; Baggio, G.
2017-01-01
, and basic and compound emotions as meanings, were transmitted from senders to receivers along diffusion chains in which the receiver in each game became the sender in the next game. During transmission, structural regularities accumulated in the signaling systems, following principles of proximity, symmetry...... and cognitive constraints similarly affect the evolution of musical systems? We conducted an experiment on the cultural evolution of artificial melodic systems, using multi-generational signaling games as a laboratory model of cultural transmission. Signaling systems, using five-tone sequences as signals...
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Multigenerational transmission of family size in contemporary Sweden.
Kolk, Martin
2014-03-01
The study of the intergenerational transmission of fertility has a long history in demography, but until now research has focused primarily on parents' influence on their children's fertility patterns and has largely overlooked the possible influence of other kin. This study examines the transmission of fertility patterns from parents, grandparents, uncles, and aunts, using event history models to determine the risk of first, second, and third births. Swedish register data are used to study the 1970-82 birth cohorts. The findings indicate strong associations between the fertility of index persons and that of their parents, and also independent associations between the completed fertility of index persons and that of their grandparents and parents' siblings. The results suggest that, when examining background effects in fertility research, it is relevant to take a multigenerational perspective and to consider the characteristics of extended kin.
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Sohi, R; Trompf, J; Marriott, H; Bervan, A; Godoy, B I; Weerasinghe, M; Desai, A; Jois, M
2017-11-01
The objectives of this study were to validate the application of Bluetooth technology to determine maternal pedigree and to determine ewe-lamb spatial relationships in extensive farming systems. A total of 35 first-cross Merino ewes (Merino × Border Leicester and East Friesian) and 23 of their lambs aged 1 to 3 wk were fitted with activity monitors equipped with Bluetooth (BT) technology (ActiGraph wGT3X-BT) by means of halters and collars, respectively. The BT devices on lambs were programmed to receive wireless signals once every minute from nearby BT units on ewes, which were programmed as beacons sending BT signals 4 times every second. Ewes and lambs fitted with sensors were dispatched into the paddocks, and after 10 d, the sensor units were retrieved and the BT signals received by lambs were downloaded using the ActiGraph software. The maternal pedigree of the lambs was determined as the ewe from which the lamb received the most BT signals. The distance between the lamb receiving the signal and the ewe sending the signal was estimated from the strength of BT signal received. The pedigree determined by BT was compared with the pedigree determined by DNA profiling and verification. The results showed that the accuracy of maternal pedigree determined by BT signals reached 100% within the first 15 min of returning animals to pasture of ewes and lambs fitted with sensors. Maternal signals (counts/d) received by 1-, 2-, and 3-wk-old lambs were 617 ± 102, 603 ± 54, and 498 ± 36, respectively, and the corresponding nonmaternal signals received were 140 ± 27, 106 ± 30, and 155 ± 39, respectively. Maternal signals received during the dark period were significantly higher than the maternal signals received during the light period ( wireless networking is a fast and reliable method for the determination of maternal pedigree of lambs in extensive farming systems. In addition, wireless BT technology is also useful in determining mother-offspring spatial
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Computer simulation of airflow through a multi-generation tracheobronchial conducting airway
Energy Technology Data Exchange (ETDEWEB)
Fan, B.; Cheng, Yung-Sung; Yeh, Hsu-Chi
1995-12-01
Knowledge of airflow patterns in the human lung is important for an analysis of lung diseases and drug delivery of aerosolized medicine for medical treatment. However, very little systematic information is available on the pattern of airflow in the lung and on how this pattern affects the deposition of toxicants in the lung, and the efficacy of aerosol drug therapy. Most previous studies have only considered the airflow through a single bifurcating airway. However, the flow in a network of more than one bifurcation is more complicated due to the effect of interrelated lung generations. Because of the variation of airway geometry and flow condition from generation to generation, a single bifurcating airway cannot be taken as a representative for the others in different generations. The flow in the network varies significantly with airway generations because of a redistribution of axial momentum by the secondary flow motions. The influence of the redistribution of flow is expected in every generation. Therefore, a systematic information of the airflow through a multi-generation tracheobronchial conducting airway is needed, and it becomes the purpose of this study. This study has provided information on airflow in a lung model which is necessary to the study of the deposition of toxicants and therapeutic aerosols.
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Computer simulation of airflow through a multi-generation tracheobronchial conducting airway
International Nuclear Information System (INIS)
Fan, B.; Cheng, Yung-Sung; Yeh, Hsu-Chi.
1995-01-01
Knowledge of airflow patterns in the human lung is important for an analysis of lung diseases and drug delivery of aerosolized medicine for medical treatment. However, very little systematic information is available on the pattern of airflow in the lung and on how this pattern affects the deposition of toxicants in the lung, and the efficacy of aerosol drug therapy. Most previous studies have only considered the airflow through a single bifurcating airway. However, the flow in a network of more than one bifurcation is more complicated due to the effect of interrelated lung generations. Because of the variation of airway geometry and flow condition from generation to generation, a single bifurcating airway cannot be taken as a representative for the others in different generations. The flow in the network varies significantly with airway generations because of a redistribution of axial momentum by the secondary flow motions. The influence of the redistribution of flow is expected in every generation. Therefore, a systematic information of the airflow through a multi-generation tracheobronchial conducting airway is needed, and it becomes the purpose of this study. This study has provided information on airflow in a lung model which is necessary to the study of the deposition of toxicants and therapeutic aerosols
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Digital Inequality on the US-Mexico Border: A Multigenerational Case Study in Laredo, Texas
María de los Ángeles Flores; Viviana Rojas; Joseph Straubhaar
2017-01-01
The purpose of the present study is to determine the cultural and social barriers that are preventing Laredoans from accessing the digital world. This multigenerational study examines how three generations within 16 families relate culturally and socially to technology. Three members from the same family were invited to voluntarily participate in the study, ...
Bound volatile precursors in genotypes in the pedigree of 'Marion' blackberry (Rubus sp.).
Du, Xiaofen; Finn, Chad E; Qian, Michael C
2010-03-24
Glycosidically bound volatiles and precursors in genotypes representing the pedigree for 'Marion' blackberry were investigated over two growing seasons. The volatile precursors were isolated using a C18 solid-phase extraction column. After enzymatic hydrolysis, the released volatiles were analyzed using stir bar sorptive extraction gas chromatography-mass spectrometry (GC-MS) and direct microvial insert thermal desorption GC-MS. The most abundant volatile precursors in the genotypes were alcohols, followed by shikimic acid derivatives. High amounts of furanone glycosides were also detected, while norisoprenoids only existed in a small amount in blackberries. The volatile precursor composition in the genotypes in the 'Marion' pedigree was very similar to their free volatile distribution. 'Logan' and 'Olallie' predominantly had bound norisoprenoids. Wild 'Himalaya' predominated with terpene alcohol and furaneol glycosides, whereas 'Santiam' and 'Chehalem' contained a high level of terpene alcohol glycosides. A similar inheritance pattern was also observed for some volatile precursors in the genotypes in the 'Marion' pedigree. A high content of linalool, hydroxylinalool, and alpha-ionol glycosides in 'Olallie' and a low content in 'Chehalem' resulted in a moderate level in their offspring 'Marion', while a low content of (E)-linalool oxide precursor in 'Olallie' and a high content in 'Chehalem' also resulted in a moderate level in 'Marion'. However, the concentration of furaneol glycosides in 'Marion' exceeded that of its two parents.
ePedigree Traceability System for the Agricultural Food Supply Chain to Ensure Consumer Health
Directory of Open Access Journals (Sweden)
Umar Farooq
2016-08-01
Full Text Available Sustainability relies on the environmental, social and economical systems: the three pillars of sustainability. The social sustainability mostly advocates the people’s welfare, health, safety, and quality of life. In the agricultural food industry, the aspects of social sustainability, such as consumer health and safety have gained substantial attention due to the frequent cases of food-borne diseases. The food-borne diseases due to the food degradation, chemical contamination and adulteration of food products pose a serious threat to the consumer’s health, safety, and quality of life. To ensure the consumer’s health and safety, it is essential to develop an efficient system which can address these critical social issues in the food distribution networks. This research proposes an ePedigree (electronic pedigree traceability system based on the integration of RFID and sensor technology for real-time monitoring of the agricultural food to prevent the distribution of hazardous and adulterated food products. The different aspects regarding implementation of the proposed system in food chains are analyzed and a feasible integrated solution is proposed. The performance of the proposed system is evaluated and finally, a comprehensive analysis of the proposed ePedigree system’s impact on the social sustainability in terms of consumer health and safety is presented.
Inheritance of RFLP loci in a loblolly pine three-generation pedigree
M.D. Devey; K.D. Jermstad; C.G. Tauer; D.B. Neale
1991-01-01
A high-density restriction fragment length polymorphism (RFLP) linkage map is being constructed for loblolly pine (Pinus taeda L.). Loblolly pine cDNA and genomic DNA clones were used as probes in hybridizations to genomic DNAs prepared from grandparents, parents, and progeny of a three-generation outbred pedigree. Approximately 200 probes were...
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Multigeneration feeding studies with an irradiated whole diet
International Nuclear Information System (INIS)
Aravindakshan, M.; Chaubey, R.C.; Chauhan, P.S.; Sundaram, K.
1978-01-01
Multigeneration feeding studies have been carried out to investigate the effects of long-term feeding of an irradiated whole diet in Wistar rats. The parent and the four successive generations were fed on a nutritionally adequate test diet exposed to either 0.2 or 2.5Mrad gamma radiation and the effects, if any, on various parameters of animal health were assessed. In addition to an unirradiated test control, a historical control group fed on stock laboratory rations was also employed for comparison. The test diet consisted of various components including some of the basic ingredients of human diet in India. Exposure of the test diet to 0.2 or 2.5Mrad did not affect the food efficiency ratio and there were no significant differences in the growth rates of animals fed on unirradiated or irradiated diets. Reproductive performance of the rats fed on irradiated or unirradiated diets belonging to the parent, first, second or third generations were also comparable. Mortality rates and reproductive function in relation to age were also not altered due to feeding of irradiated whole diets. The haematological profile and the serum enzymes of the animals of all the generations fed irradiated diets were within normal limits. Though some differences were observed in the relative weights of some organs, these effects were limited to a particular generation, did not show any definite pattern and could not be related to the ingestion of irradiated diets. First-generation rats examined at 100-104 weeks for gross pathological manifestations including tumour incidence also did not indicate any significant differences among groups. (author)
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Familial atrophia maculosa varioliformis cutis: case report and pedigree analysis.
Qu, T; Wang, B; Fang, K
2005-10-01
Atrophia maculosa varioliformis cutis (AVMC) was first described in 1918, as a rarely reported form of idiopathic macular atrophy on the cheeks. Nineteen patients have been reported in the past 86 years. Recently we diagnosed a 25-year-old woman as AMVC and investigated her family history. We collected the clinical data of the pedigree and presumed that AVMV is in a autosomal dominant inheritance.
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[Clinical features of a Chinese pedigree with Waardenburg syndrome type 2].
Yang, Shu-zhi; Yuan, Hui-jun; Bai, Lin-na; Cao, Ju-yang; Xu, Ye; Shen, Wei-dong; Ji, Fei; Yang, Wei-yan
2005-10-12
To investigate detailed clinical features of a Chinese pedigree with Waardenburg syndrome type 2. Members of this pedigree were interviewed to identify personal or family medical histories of hearing loss, the use of aminoglycosides, and other clinical abnormalities by filling questionnaire. The audiological and other clinical evaluations of the proband and other members of this family were conducted, including pure-tone audiometry, immittance and auditory brain-stem response and ophthalmological, dermatologic, hair, temporal bone CT examinations. This family is categorized as Waardenburg syndrome type 2 according to its clinical features. It's an autosomal dominant disorder with incomplete penetrance. The clinical features varied greatly among family members and characterized by sensorineural hearing loss, heterochromia irides, freckle on the face and premature gray hair. Hearing loss can be unilateral or bilateral, congenital or late onset in this family. This Chinese family has some unique clinical features comparing with the international diagnostic criteria for Waardenburg syndrome. This study may provide some evidences to amend the diagnostic criteria for Waardenburg syndrome in Chinese population.
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DEFF Research Database (Denmark)
Druley, Todd E; Wang, Lihua; Lin, Shiow J
2016-01-01
from six pedigrees. OBFC1 (chromosome 10) is involved in telomere maintenance, and falls within a linkage peak recently reported from an analysis of telomere length in LLFS families. Two different algorithms for single gene associations identified three genes with an enrichment of variation......BACKGROUND: The Long Life Family Study (LLFS) is an international study to identify the genetic components of various healthy aging phenotypes. We hypothesized that pedigree-specific rare variants at longevity-associated genes could have a similar functional impact on healthy phenotypes. METHODS......: We performed custom hybridization capture sequencing to identify the functional variants in 464 candidate genes for longevity or the major diseases of aging in 615 pedigrees (4,953 individuals) from the LLFS, using a multiplexed, custom hybridization capture. Variants were analyzed individually...
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Genetic drift. Descent, lineage, and pedigree of the Trojans in Homer's Iliad.
Bazopoulou-Kyrkanidou, Euterpe
2007-12-15
Homer's Iliad, is an epic poem that describes the last 70 days of the Trojan War, which was waged against the city of Troy by the Achaeans. Here, the descent, lineage, and the pedigree of the Trojans are presented. In the Illiad, they are said to have originated from Zeus. Beginning with him, the Trojan pedigree comprised 17 men in 8 generations with Dardanus, founder of Dardania in the second generation; Tros, King of the Trojans in the fourth generation; and the two heroes Hector and Aeneas in the eighth generation. In the seventh generation, Priam, as King of the Trojans, had a huge family, including 50 sons: 19 children with his wife Hecabe, other sons with many different wives, and some daughters as well. Hector, the first born, became leader of the Trojans. Hector's brother, Paris, in abducting Helen of Sparta, the wife of King Menelaus, caused the Trojan War to break out. (c) 2007 Wiley-Liss, Inc.
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Directory of Open Access Journals (Sweden)
Amanda Vinson
Full Text Available The rhesus macaque is an important model for human atherosclerosis but genetic determinants of relevant phenotypes have not yet been investigated in this species. Because lipid levels are well-established and heritable risk factors for human atherosclerosis, our goal was to assess the heritability of lipoprotein cholesterol and triglyceride levels in a single, extended pedigree of 1,289 Indian-origin rhesus macaques. Additionally, because increasing evidence supports sex differences in the genetic architecture of lipid levels and lipid metabolism in humans and macaques, we also explored sex-specific heritability for all lipid measures investigated in this study. Using standard methods, we measured lipoprotein cholesterol and triglyceride levels from fasted plasma in a sample of 193 pedigreed rhesus macaques selected for membership in large, paternal half-sib cohorts, and maintained on a low-fat, low cholesterol chow diet. Employing a variance components approach, we found moderate heritability for total cholesterol (h²=0.257, P=0.032, LDL cholesterol (h²=0.252, P=0.030, and triglyceride levels (h²=0.197, P=0.034 in the full sample. However, stratification by sex (N=68 males, N=125 females revealed substantial sex-specific heritability for total cholesterol (0.644, P=0.004, females only, HDL cholesterol (0.843, P=0.0008, females only, VLDL cholesterol (0.482, P=0.018, males only, and triglyceride levels (0.705, P=0.001, males only that was obscured or absent when sexes were combined in the full sample. We conclude that genes contribute to spontaneous variation in circulating lipid levels in the Indian-origin rhesus macaque in a sex-specific manner, and that the rhesus macaque is likely to be a valuable model for sex-specific genetic effects on lipid risk factors for human atherosclerosis. These findings are a first-ever report of heritability for cholesterol levels in this species, and support the need for expanded analysis of these traits in
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International Nuclear Information System (INIS)
Buisset-Goussen, Adeline
2014-01-01
The environmental risk assessment of chronic exposure to ionizing radiation (natural and ubiquitous phenomenon enhanced by human activities) has become a major concern. Few studies relating to chronic exposure over several generations - essential knowledge to better understand the disruption caused by ionizing radiation and its possible consequences on the population - exist. In addition, it has become necessary to understand the mechanisms of disturbances related to ionizing radiation at the molecular and cellular level. Without this mechanistic understanding, it is difficult to extrapolate the effects observed between the different levels of biological organization and between different species. The aim of this PhD was to study the multi-generational effects of chronic gamma radiation in an integrated manner (to the life history traits from the subcellular mechanisms) in a model organism, the nematode Caenorhabditis elegans. A two-step strategy was implemented. First, studying the effects of chronic gamma radiation on the life history traits of C. elegans was performed. The objective of this experiment was to test the hypothesis of an increase of the sensitivity according generations. For that, three generations have been exposed to different dose rates. In parallel, two generations have been placed in 'control' environment after parental exposure to test a possible transmission of maternal effects. The second part of this thesis aimed to characterize the different subcellular mechanisms that could explain the observed effects on the life history traits after multi-generational exposure. The results showed that (i) the cumulative number of larvae was the most sensitive endpoint to gamma radiation, (ii) an increase in radiosensitivity was observed over three exposed generations and (iii) the effects of the parental generation were transmitted to the non-exposed generations. An increase in apoptosis, a reduction in the stock of sperm, and to a lesser
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Engelsma, K.A.; Veerkamp, R.F.; Calus, M.P.L.; Windig, J.J.
2011-01-01
Up to now, prioritization of animals for conservation has been mainly based on pedigree information; however, genomic information may improve prioritization. In this study, we used two Holstein populations to investigate the consequences for genetic diversity when animals are prioritized with
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Pedigrees, propaganda, and paranoia: family studies in a historical context.
Lombardo, P A
2001-01-01
This article reviews the uses of family studies carried out in the early 20th century under the banner of eugenics, a companion discipline to early genetics. It explores how, in an attempt to analyze and quantify purportedly biologic bases of social problems, the eugenicists constructed pedigree charts of notoriously "defective" families. Investigation of individuals with suspect traits formed the basis for instruction of field workers who linked those traits to larger groups. The resulting eugenic family studies provided a "scientific" face for a popular hereditarian mythology that claimed to explain all social failure in systematic terms. The eugenicists were successful in fueling public fear about the growing "army of idiots and imbeciles" graphically depicted in their pedigree charts. Their success was the result of a finely crafted educational program--propaganda that reduced science to simplistic terms. The tendency to oversimplify concepts of genetic causation and the rush to amplify the significance of research findings through the popular media is also apparent today. What begins as publicity has the potential to be transformed into propaganda. Although many in the scientific community are understandably reluctant to revisit the abuses of the past, that community must confront the history of eugenics as a necessary antidote to the genetic hype that surrounds us.
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Starks, Florida Elizabeth
2014-01-01
The purpose of this quantitative study is to broaden multigenerational workforce research involving factors affecting employee learning and interaction by using a population of Baby Boomer, Generation X, and Millennial faculty and staff age cohorts employed at two-year public community college organizations. Researchers have studied…
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Kooshavar, Daniz; Razipour, Masoumeh; Movasat, Morteza; Keramatipour, Mohammad
2018-01-01
Usher syndrome (USH) is characterized by congenital hearing loss and retinitis pigmentosa (RP) with a later onset. It is an autosomal recessive trait with clinical and genetic heterogeneity which makes the molecular diagnosis much difficult. In this study, we introduce a pedigree with two affected members with USH type 1 and represent a cost and time effective approach for genetic diagnosis of USH as a genetically heterogeneous disorder. Target region capture in the genes of interest, followed by next generation sequencing (NGS) was used to determine the causative mutations in one of the probands. Then segregation analysis in the pedigree was conducted using PCR-Sanger sequencing. Targeted NGS detected a novel homozygous nonsense variant c.4513G > T (p.Glu1505Ter) in MYO7A. The variant is segregating in the pedigree with an autosomal recessive pattern. In this study, a novel stop gained variant c.4513G > T (p.Glu1505Ter) in MYO7A was found in an Iranian pedigree with two affected members with USH type 1. Bioinformatic as well as pedigree segregation analyses were in line with pathogenic nature of this variant. Targeted NGS panel was showed to be an efficient method for mutation detection in hereditary disorders with locus heterogeneity. Copyright © 2017 Elsevier B.V. All rights reserved.
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Heinrich, Verena; Kamphans, Tom; Mundlos, Stefan; Robinson, Peter N; Krawitz, Peter M
2017-01-01
Next generation sequencing technology considerably changed the way we screen for pathogenic mutations in rare Mendelian disorders. However, the identification of the disease-causing mutation amongst thousands of variants of partly unknown relevance is still challenging and efficient techniques that reduce the genomic search space play a decisive role. Often segregation- or linkage analysis are used to prioritize candidates, however, these approaches require correct information about the degree of relationship among the sequenced samples. For quality assurance an automated control of pedigree structures and sample assignment is therefore highly desirable in order to detect label mix-ups that might otherwise corrupt downstream analysis. We developed an algorithm based on likelihood ratios that discriminates between different classes of relationship for an arbitrary number of genotyped samples. By identifying the most likely class we are able to reconstruct entire pedigrees iteratively, even for highly consanguineous families. We tested our approach on exome data of different sequencing studies and achieved high precision for all pedigree predictions. By analyzing the precision for varying degrees of relatedness or inbreeding we could show that a prediction is robust down to magnitudes of a few hundred loci. A java standalone application that computes the relationships between multiple samples as well as a Rscript that visualizes the pedigree information is available for download as well as a web service at www.gene-talk.de CONTACT: heinrich@molgen.mpg.deSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.
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Noll, Jennie G.; Trickett, Penelope K.; Harris, William W.; Putnam, Frank W.
2009-01-01
This multigenerational study empirically demonstrates the extent to which offspring whose parents experienced childhood abuse are at increased risk of being abused or neglected. Females with substantiated childhood sexual abuse and nonabused comparison females were assessed at six points spanning 18 years in a prospective, longitudinal study.…
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Pedigree and genomic analyses of feed consumption and residual feed intake in laying hens.
Wolc, Anna; Arango, Jesus; Jankowski, Tomasz; Settar, Petek; Fulton, Janet E; O'Sullivan, Neil P; Fernando, Rohan; Garrick, Dorian J; Dekkers, Jack C M
2013-09-01
Efficiency of production is increasingly important with the current escalation of feed costs and demands to minimize the environmental footprint. The objectives of this study were 1) to estimate heritabilities for daily feed consumption and residual feed intake and their genetic correlations with production and egg-quality traits; 2) to evaluate accuracies of estimated breeding values from pedigree- and marker-based prediction models; and 3) to localize genomic regions associated with feed efficiency in a brown egg layer line. Individual feed intake data collected over 2-wk trial periods were available for approximately 6,000 birds from 8 generations. Genetic parameters were estimated with a multitrait animal model; methods BayesB and BayesCπ were used to estimate marker effects and find genomic regions associated with feed efficiency. Using pedigree information, feed efficiency was found to be moderately heritable (h(2) = 0.46 for daily feed consumption and 0.47 for residual feed intake). Hens that consumed more feed and had greater residual feed intake (lower efficiency) had a genetic tendency to lay slightly more eggs with greater yolk weights and albumen heights. Regions on chromosomes 1, 2, 4, 7, 13, and Z were found to be associated with feed intake and efficiency. The accuracy from genomic prediction was higher and more persistent (better maintained across generations) than that from pedigree-based prediction. These results indicate that genomic selection can be used to improve feed efficiency in layers.
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Peter, Beate; Raskind, Wendy H.
2011-01-01
Purpose To evaluate phenotypic expressions of speech sound disorder (SSD) in multigenerational families with evidence of familial forms of SSD. Method Members of five multigenerational families (N = 36) produced rapid sequences of monosyllables and disyllables and tapped computer keys with repetitive and alternating movements. Results Measures of repetitive and alternating motor speed were correlated within and between the two motor systems. Repetitive and alternating motor speeds increased in children and decreased in adults as a function of age. In two families with children who had severe speech deficits consistent with disrupted praxis, slowed alternating, but not repetitive, oral movements characterized most of the affected children and adults with a history of SSD, and slowed alternating hand movements were seen in some of the biologically related participants as well. Conclusion Results are consistent with a familial motor-based SSD subtype with incomplete penetrance, motivating new clinical questions about motor-based intervention not only in the oral but also the limb system. PMID:21909176
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Broad scan linkage analysis in a large Tourette family pedigree
Energy Technology Data Exchange (ETDEWEB)
Peiffer, A.; Leppert, M. [Univ. of Utah Health Sciences Center, Salt Lake City, UT (United States); Wetering, B.J.M. van der [Univ. Hospital Rotterdam (Netherlands)
1994-09-01
Attempts to find a gene causing Tourette syndrome (TS) using linkage analysis have been unsuccessful even though as much as 65% of the autosomal genetic map has been excluded by the pooled results from several laboratories collaborating worldwide. One reason for this failure may be the misclassification of affection status of marry-in spouses. Specifically, we have found that six unrelated spouses in our Utah TS pedigree suffer from TS, obsessive-compulsive disorder or chronic motor tics. In light of these findings we decided to conduct a complete genomic scan from this Utah kindred with polymorphic markers in three related sibships in which there was no assortative mating. A linkage study assuming autosomal dominant inheritance was done using tetranucleotide repeat markers developed at the University of Utah. We selected markers that were less than 300 bp in size and that gave a heterozygosity of over 70% upon analysis in 4 CEPH families. Results to date with 95 markers run at an interval of 30 cM (covering 61% of the genome) show no evidence of linkage. We intend to extend the coverage to 100% of the genome. Pending completion of this scan, failure to provide evidence of linkage in our TS pedigree might then be attributed to phenotypic misclassification or erroneous assumptions regarding the genetic model of transmission.
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Shamseldin, Hanan E.
2016-11-12
Ectodermal dysplasia is a highly heterogeneous group of disorders that variably affect the derivatives of the ectoderm, primarily skin, hair, nails and teeth. TP63, itself mutated in ectodermal dysplasia, links many other ectodermal dysplasia disease genes through a regulatory network that maintains the balance between proliferation and differentiation of the epidermis and other ectodermal derivatives. The ectodermal knockout phenotype of five mouse genes that regulate and/or are regulated by TP63 (Irf6, Ikkα, Ripk4, Stratifin, and Kdf1) is strikingly similar and involves abnormal balance towards proliferation at the expense of differentiation, but only the first three have corresponding ectodermal phenotypes in humans. We describe a multigenerational Saudi family with an autosomal dominant form of hypohidrotic ectodermal dysplasia in which positional mapping and exome sequencing identified a novel variant in KDF1 that fully segregates with the phenotype. The recapitulation of the phenotype we observe in this family by the Kdf1−/− mouse suggests a causal role played by the KDF1 variant.
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Shamseldin, Hanan E; Khalifa, Ola; Binamer, Yousef M; Almutawa, Abdulmonem; Arold, Stefan T; Zaidan, Hamad; Alkuraya, Fowzan S
2017-01-01
Ectodermal dysplasia is a highly heterogeneous group of disorders that variably affect the derivatives of the ectoderm, primarily skin, hair, nails and teeth. TP63, itself mutated in ectodermal dysplasia, links many other ectodermal dysplasia disease genes through a regulatory network that maintains the balance between proliferation and differentiation of the epidermis and other ectodermal derivatives. The ectodermal knockout phenotype of five mouse genes that regulate and/or are regulated by TP63 (Irf6, Ikkα, Ripk4, Stratifin, and Kdf1) is strikingly similar and involves abnormal balance towards proliferation at the expense of differentiation, but only the first three have corresponding ectodermal phenotypes in humans. We describe a multigenerational Saudi family with an autosomal dominant form of hypohidrotic ectodermal dysplasia in which positional mapping and exome sequencing identified a novel variant in KDF1 that fully segregates with the phenotype. The recapitulation of the phenotype we observe in this family by the Kdf1-/- mouse suggests a causal role played by the KDF1 variant.
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Cell organisation in the colonic crypt: a theoretical comparison of the pedigree and niche concepts.
Directory of Open Access Journals (Sweden)
Richard C van der Wath
Full Text Available The intestinal mucosa is a monolayer of rapidly self-renewing epithelial cells which is not only responsible for absorption of water and nutrients into the bloodstream but also acts as a protective barrier against harmful microbes entering the body. New functional epithelial cells are produced from stem cells, and their proliferating progeny. These stem cells are found within millions of crypts (tubular pits spaced along the intestinal tract. The entire intestinal epithelium is replaced every 2-3 days in mice (3-5 days in humans and hence cell production, differentiation, migration and turnover need to be tightly regulated. Malfunctions in this regulation are strongly linked to inflammatory bowel diseases and to the formation of adenomas and ultimately cancerous tumours. Despite a great deal of biological experimentation and observation, precisely how colonic crypts are regulated to produce mature colonocytes remains unclear. To assist in understanding how cell organisation in crypts is achieved, two very different conceptual models of cell behaviour are developed here, referred to as the 'pedigree' and the 'niche' models. The pedigree model proposes that crypt cells are largely preprogrammed and receive minimal prompting from the environment as they move through a routine of cell differentiation and proliferation to become mature colonocytes. The niche model proposes that crypt cells are primarily influenced by the local microenvironments along the crypt, and that predetermined cell behaviour plays a negligible role in their development. In this paper we present a computational model of colonic crypts in the mouse, which enables a comparison of the quality and controllability of mature coloncyte production by crypts operating under these two contrasting conceptual models of crypt regulation.
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Barmentlo, S.H.; van Gestel, C.A.M.; Alvarez-Rogel, J.; Gonzalez Alcaraz, M.N.
2017-01-01
This study aimed at assessing the effects of increased air temperature and reduced soil moisture content on the multi-generation toxicity of a soil polluted by metal/metalloid mining wastes. Enchytraeus crypticus was exposed to dilution series of the polluted soil in Lufa 2.2 soil under different
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Familial epilepsy in Algeria: Clinical features and inheritance profiles.
Chentouf, Amina; Dahdouh, Aïcha; Guipponi, Michel; Oubaiche, Mohand Laïd; Chaouch, Malika; Hamamy, Hanan; Antonarakis, Stylianos E
2015-09-01
To document the clinical characteristics and inheritance pattern of epilepsy in multigeneration Algerian families. Affected members from extended families with familial epilepsy were assessed at the University Hospital of Oran in Algeria. Available medical records, neurological examination, electroencephalography and imaging data were reviewed. The epilepsy type was classified according to the criteria of the International League Against Epilepsy and modes of inheritance were deduced from pedigree analysis. The study population included 40 probands; 23 male (57.5%) and 17 female subjects (42.5%). The mean age of seizure onset was 9.5 ± 6.1 years. According to seizure onset, 16 patients (40%) had focal seizures and 20 (50%) had generalized seizures. Seizure control was achieved for two patients (5%) for 10 years, while 28 (70%) were seizure-free for 3 months. Eleven patients (27.5%) had prior febrile seizures, 12 were diagnosed with psychiatric disorders and four families had syndromic epilepsy. The consanguinity rate among parents of affected was 50% with phenotypic concordance observed in 25 families (62.5%). Pedigree analysis suggested autosomal dominant (AD) inheritance with or without reduced penetrance in 18 families (45%), probable autosomal recessive (AR) inheritance in 14 families (35%), and an X-linked recessive inheritance in one family. This study reveals large Algerian families with multigenerational inheritance of epilepsy. Molecular testing such as exome sequencing would clarify the genetic basis of epilepsy in some of our families. Copyright © 2015 British Epilepsy Association. Published by Elsevier Ltd. All rights reserved.
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Pedigree analysis on the population of Gir cattle in Northeast Brazil
Directory of Open Access Journals (Sweden)
Aracele Prates de Oliveira
2012-05-01
Full Text Available The objective of this study was to characterize the population genetic structure of the Gir breed in the Northeast of Brazil. The data used in this study were taken from pedigree information of 8,897 Gir animals between 1957 and 2007, obtained from the Brazilian Zebu Breeders Association (ABCZ. The program ENDOG was used to estimate the parameters based on the probability gene origin. From the amount of the studied animals, 67.22%, 18.41% and 3.15% had complete pedigree only on the first, second and third parentage, respectively. The number of ancestors that contributed for the reference population was 2,755, of which only 171 explain the 50% genetic variability of the population. The actual number of founder herds was 168 and the effective number of founder herds was 22.3. The number of sire supplier herds was 22.16, 8.66 and 5.36 for fathers, grandfathers and great-grandfathers, respectively. The average coefficient of relatedness was estimated at 0.22%; the highest individual coefficient was 1.49%. The little variability of the current population is a result of the small number of effective founders and ancestors indicating the population evolved from a narrow genetic base.
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Lo, David; Weng, Jingning; Liu, xiaohong; Yang, Juhua; He, Fen; Wang, Yun; Liu, Xuyang
2016-01-01
PURPOSE To detect the disease-causing gene in a Chinese pedigree with autosomal-recessive retinitis pigmentosa (ARRP). METHODS All subjects in this family underwent a complete ophthalmic examination. Targeted-capture next generation sequencing (NGS) was performed on the proband to detect variants. All variants were verified in the remaining family members by PCR amplification and Sanger sequencing. RESULTS All the affected subjects in this pedigree were diagnosed with retinitis pigmentosa (RP). The compound heterozygous c.138delA (p.Asp47IlefsX24) and c.1841G>T (p.Gly614Val) mutations in the Crumbs homolog 1 (CRB1) gene were identified in all the affected patients but not in the unaffected individuals in this family. These mutations were inherited from their parents, respectively. CONCLUSION The novel compound heterozygous mutations in CRB1 were identified in a Chinese pedigree with ARRP using targeted-capture next generation sequencing. After evaluating the significant heredity and impaired protein function, the compound heterozygous c.138delA (p.Asp47IlefsX24) and c.1841G>T (p.Gly614Val) mutations are the causal genes of early onset ARRP in this pedigree. To the best of our knowledge, there is no previous report regarding the compound mutations. PMID:27806333
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DEFF Research Database (Denmark)
Christensen, Ole Fredslund
2012-01-01
Single-step methods for genomic prediction have recently become popular because they are conceptually simple and in practice such a method can completely replace a pedigree-based method for routine genetic evaluation. An issue with single-step methods is compatibility between the marker-based rel...
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Directory of Open Access Journals (Sweden)
Junbao Yu
2011-09-01
Full Text Available Manila clam Ruditapes philippinarum is one of the most important economic species in shellfishery in China due to its wide geographic distribution and high tolerance to environmental changes (e.g., salinity, temperature. In addition, Manila clam is a good biomonitor/bioindicator in “Mussel Watch Programs” and marine environmental toxicology. However, there are several pedigrees of R. philippinarum distributed in the marine environment in China. No attention has been paid to the biological differences between various pedigrees of Manila clams, which may introduce undesirable biological variation in toxicology studies. In this study, we applied NMR-based metabolomics to detect the biological differences in two main pedigrees (White and Zebra of R. philippinarum and their differential responses to heavy metal exposures (Cadmium and Zinc using adductor muscle as a target tissue to define one sensitive pedigree of R. philippinarum as biomonitor for heavy metals. Our results indicated that there were significant metabolic differences in adductor muscle tissues between White and Zebra clams, including higher levels of alanine, glutamine, hypotaurine, phosphocholine and homarine in White clam muscles and higher levels of branched chain amino acids (valine, leucine and isoleucine, succinate and 4-aminobutyrate in Zebra clam muscles, respectively. Differential metabolic responses to heavy metals between White and Zebra clams were also found. Overall, we concluded that White pedigree of clam could be a preferable bioindicator/biomonitor in marine toxicology studies and for marine heavy metals based on the relatively high sensitivity to heavy metals.
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Directory of Open Access Journals (Sweden)
Camp Nicola J
2006-04-01
Full Text Available Abstract Background We present a general approach to perform association analyses in pedigrees of arbitrary size and structure, which also allows for a mixture of pedigree members and independent individuals to be analyzed together, to test genetic markers and qualitative or quantitative traits. Our software, PedGenie, uses Monte Carlo significance testing to provide a valid test for related individuals that can be applied to any test statistic, including transmission disequilibrium statistics. Single locus at a time, composite genotype tests, and haplotype analyses may all be performed. We illustrate the validity and functionality of PedGenie using simulated and real data sets. For the real data set, we evaluated the role of two tagging-single nucleotide polymorphisms (tSNPs in the DNA repair gene, NBS1, and their association with female breast cancer in 462 cases and 572 controls selected to be BRCA1/2 mutation negative from 139 high-risk Utah breast cancer families. Results The results from PedGenie were shown to be valid both for accurate p-value calculations and consideration of pedigree structure in the simulated data set. A nominally significant association with breast cancer was observed with the NBS1 tSNP rs709816 for carriage of the rare allele (OR = 1.61, 95% CI = 1.10–2.35, p = 0.019. Conclusion PedGenie is a flexible and valid statistical tool that is intuitively simple to understand, makes efficient use of all the data available from pedigrees without requiring trimming, and is flexible to the types of tests to which it can be applied. Further, our analyses of real data indicate NBS1 may play a role in the genetic etiology of heritable breast cancer.
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Molecular Reconstruction of an Old Pedigree of Diploid and Triploid Hydrangea macrophylla Genotypes
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Peter Hempel
2018-04-01
Full Text Available The ornamental crop species Hydrangea macrophylla exhibits diploid and triploid levels of ploidy and develops lacecap (wild type or mophead inflorescences. In order to characterize a H. macrophylla germplasm collection, we determined the inflorescence type and the 2C DNA content of 120 plants representing 43 cultivars. We identified 78 putative diploid and 39 putative triploid plants by flow cytometry. In our collection 69 out of 98 flowering plants produced lacecap inflorescences, whereas 29 plants developed mophead inflorescences. Surprisingly, 12 cultivars included diploid as well as triploid plants, while 5 cultivars contained plants with different inflorescence types. We genotyped this germplasm collection using 12 SSR markers that detected 2–7 alleles per marker, and identified 51 different alleles in this collection. We detected 62 distinct fingerprints, revealing a higher genetic variation than the number of cultivars suggested. Only one genotype per cultivar is expected due to the vegetative propagation of Hydrangea cultivars; however we identified 25 cultivars containing 2–4 different genotypes. These different genotypes explained the variation in DNA content and inflorescence type. Diploid and triploid plants with the same cultivar name were exclusively mix-ups. We therefor assume, that 36% of the tested plants were mislabeled. Based on the “Wädenswil” pedigree, which includes 31 of the tested cultivars, we predicted cultivar-specific fingerprints and identified at least 21 out of 31 cultivars by SSR marker-based reconstruction of the “Wädenswil” pedigree. Furthermore, we detected 4 putative interploid crosses between diploid and triploid plants in this pedigree. These interploid crosses resulted in diploid or/and triploid offspring, suggesting that crosses with triploids were successfully applied in breeding of H. macrophylla.
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Inbreeding and Genetic Diversity in Three Imported Swine Breeds in China Using Pedigree Data
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G. Q. Tang
2013-06-01
Full Text Available The accumulation of inbreeding and the loss of genetic diversity is a potential problem in the modern swine breeds in China. Therefore, the purpose of this study was to analyze the pedigrees of Chinese Duroc (CD, Landrace (CL and Yorkshire (CY swine to estimate the past and current rates of inbreeding, and to identify the main causes of genetic diversity loss. Pedigree files from CD, CL and CY containing, 4529, 16,776 and 22,600 records, respectively, were analyzed. Pedigree completeness indexes of the three breeds, accounting for one generation back, were 83.72, 93.93 and 93.59%, respectively. The estimated average annual inbreeding rates for CD, CL and CY in recent three years were 0.21, 0.19 and 0.13%, respectively. The estimated average percentage of genetic diversity loss within each breed in recent three years was about 8.92, 2.19, and 3.36%, respectively. The average relative proportion of genetic diversity loss due to unequal contributions of founders in CD, CL and CY was 69.09, 57.95 and 60.57%, and due to random genetic drift was 30.91, 42.05 and 39.43%, respectively. The estimated current effective population size for CD, CL and CY was 76, 117 and 202, respectively. Therefore, CD has been found to have lost considerable genetic diversity, demanding priority for optimizing the selection and mating to control future coancestry and inbreeding. Unequal contribution of founders was a major cause of genetic diversity loss in Chinese swine breeds and random genetic drift also showed substantial impact on the loss of diversity.
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Efficient Maximum Likelihood Estimation for Pedigree Data with the Sum-Product Algorithm.
Engelhardt, Alexander; Rieger, Anna; Tresch, Achim; Mansmann, Ulrich
2016-01-01
We analyze data sets consisting of pedigrees with age at onset of colorectal cancer (CRC) as phenotype. The occurrence of familial clusters of CRC suggests the existence of a latent, inheritable risk factor. We aimed to compute the probability of a family possessing this risk factor as well as the hazard rate increase for these risk factor carriers. Due to the inheritability of this risk factor, the estimation necessitates a costly marginalization of the likelihood. We propose an improved EM algorithm by applying factor graphs and the sum-product algorithm in the E-step. This reduces the computational complexity from exponential to linear in the number of family members. Our algorithm is as precise as a direct likelihood maximization in a simulation study and a real family study on CRC risk. For 250 simulated families of size 19 and 21, the runtime of our algorithm is faster by a factor of 4 and 29, respectively. On the largest family (23 members) in the real data, our algorithm is 6 times faster. We introduce a flexible and runtime-efficient tool for statistical inference in biomedical event data with latent variables that opens the door for advanced analyses of pedigree data. © 2017 S. Karger AG, Basel.
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Leveraging multi-generational workforce values in interactive information societies
Directory of Open Access Journals (Sweden)
Sophie van der Walt
2010-11-01
Objectives: This article advocates the need for generational awareness and addresses how this awareness presents benefits to companies, such as, increased productivity, improved succession planning policies and strategies to recruit and retain a diverse workforce. The research problem is directed at how diversity management influences Traditionalists, Baby Boomers, Generation X and Generation Y in terms of their work performance and co-worker relationships. Method: The research design combines Critical Theory and Generational Theory within the mixed-method paradigm. The sequential exploratory design was decided upon as it studies the unknown relationships between different generations of employees. The literature review was followed by a quantitative empirical research component and data was collected by means of a questionnaire. Results: The findings highlight specific differences between generations regarding their perspectives on work values and co-worker relationships, rewards, work-life balance and retirement. Conclusion: The article concludes with recommendations on the role diversity management plays in terms of work performance and co-worker relationships. By leveraging generational awareness in the interactive information society organizations with a multi-generational workforce will succeed in the competitive business environment.
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Heidaritabar, M.; Vereijken, A.; Muir, W.M.; Meuwissen, T.H.E.; Cheng, H.; Megens, H.J.W.C.; Groenen, M.; Bastiaansen, J.W.M.
2014-01-01
Genomic selection (GS) is a DNA-based method of selecting for quantitative traits in animal and plant breeding, and offers a potentially superior alternative to traditional breeding methods that rely on pedigree and phenotype information. Using a 60¿K SNP chip with markers spaced throughout the
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Yamamoto, Toshio; Nagasaki, Hideki; Yonemaru, Jun-ichi; Ebana, Kaworu; Nakajima, Maiko; Shibaya, Taeko; Yano, Masahiro
2010-04-27
caused by a recent human selection in rice breeding. The definition of pedigree haplotypes by means of genome-wide SNPs will facilitate next-generation breeding of rice and other crops.
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Goodspeed, Danielle; Seferovic, Maxim D.; Holland, William; Mcknight, Robert A.; Summers, Scott A.; Branch, D. Ware; Lane, Robert H.; Aagaard, Kjersti M.
2015-01-01
Intrauterine growth restriction (IUGR) confers heritable alterations in DNA methylation, rendering risk of adult metabolic syndrome (MetS). Because CpG methylation is coupled to intake of essential nutrients along the one-carbon pathway, we reasoned that essential nutrient supplementation (ENS) may abrogate IUGR-conferred multigenerational MetS. Pregnant Sprague-Dawley rats underwent bilateral uterine artery ligation causing IUGR in F1. Among the F2 generation, IUGR lineage rats were underweight at birth (6.7 vs. 8.0 g, P 30% elevated, P 5-fold less central fat mass, normal hepatic glucose efflux, and >70% reduced circulating triglycerides and very-LDLs compared with IUGR control-fed F2 offspring (P intrauterine growth-restricted rats. PMID:25395450
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Directory of Open Access Journals (Sweden)
Shen Wang
2015-02-01
Full Text Available Subsynchronous oscillation (SSO of generators caused by high voltage direct current (HVDC systems can be solved by applying supplemental subsynchronous damping controller (SSDC. SSDC application in mitigating SSO of single-generator systems has been studied intensively. This paper focuses on SSDC application in mitigating SSO of multi-generator systems. The phase relationship of the speed signals of the generators under their common mechanical natural frequencies is a key consideration in SSDC design. The paper studies in detail the phase relationship of the speed signals of two generators in parallel under their shared mechanical natural frequency, revealing regardless of whether the two generators are identical or not, there always exists a common-mode and an anti-mode under their common natural frequency, and the phase relationship of the speed signals of the generators depends on the extent to which the anti-mode is stimulated. The paper further demonstrates that to guarantee the effectiveness of SSDC, the anti-phase mode component of its input signal should be eliminated. Based on the above analysis, the paper introduces the design process of SSDC for multi-generator systems and verifies its effectiveness through simulation in Power Systems Computer Aided Design/Electromagnetic Transients including Direct Current (PSCAD/EMTDC.
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Noll, Laura K; Clark, Caron A C; Skowron, Elizabeth A
2015-11-01
Despite burgeoning evidence linking early exposure to child maltreatment (CM) to deficits in self-regulation, the pathways to strong regulatory development in these children are not well understood, and significant heterogeneity is observed in their outcomes. Experiences of autonomy may play a key role in transmitting self-regulatory capacity across generations and help explain individual differences in maltreatment outcomes. In this study, we investigated multigenerational associations between Generation 1 (G1)-Generation 2 (G2) mothers' early experience of warmth and autonomy in relation to their own mothers and their Generation 3 (G3) children's autonomic physiological regulation in CM (n = 85) and non-CM (n = 128) families. We found that G2 mothers who recalled greater autonomy in their childhood relationship with their G1 mothers had preschool-age G3 children with higher respiratory sinus arrhythmia at baseline when alone while engaged in individual challenge tasks, during social exchanges with their mother in joint challenge tasks, and during the portions of the strange situation procedure when the mother was present. Although no clear mediators of this association emerged, multigenerational links among G1-G2 relations, maternal representations of her child, child behavior, and child respiratory sinus arrhythmia differed by maltreatment status, thus possibly representing important targets for future research and intervention.
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Multigeneric Intertextuality in Advertising: Discourse Strategy from a Cognitive Perspective
Directory of Open Access Journals (Sweden)
Katarína Nemčoková
2014-07-01
Full Text Available Advert recipients have wide-ranging experiences of perceiving other texts. When these experiences become the basis of perceiving advert messages, we speak of intertextuality operating as a discourse strategy. This paper studies multigeneric intertextuality in printed advertising, i.e. delivering an advert message through a register or text-form typical of other genres, for which discourse analysis and the genre studies perspective are adapted. From the cognitive linguistics perspective, it focuses on how the experience becomes the basis of building an emotive and attitudinal layer of meaning via exploring the recipient's mental space. The article studies cues signalling intertextual processing, specifically cues of socially determined discourses such as cooking recipes, warning signs, computer-mediated communication, scientific discussions or travel brochures, which may function as mental space inducing cues in the collected adverts. It also deals with how intertextuality in adverts can be scaled and how the level of explicitness relates to promoting various categories of products.
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Rooster Semen Cryopreservation: Effect of Pedigree Line and Male Age on Post-Thaw Sperm Function
The fertility rates of cryopreserved poultry semen are highly variable and not reliable for use in preservation of commercial genetic stocks. Our objective was to evaluate the cryosurvival of semen from 8 pedigreed layer lines at the onset and end of production. Semen from 160 roosters (20/line) was...
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Mutations in LOXHD1, a Recessive-Deafness Locus, Cause Dominant Late-Onset Fuchs Corneal Dystrophy
Riazuddin, S. Amer; Parker, David S.; McGlumphy, Elyse J.; Oh, Edwin C.; Iliff, Benjamin W.; Schmedt, Thore; Jurkunas, Ula; Schleif, Robert; Katsanis, Nicholas; Gottsch, John D.
2012-01-01
Fuchs corneal dystrophy (FCD) is a genetic disorder of the corneal endothelium and is the most common cause of corneal transplantation in the United States. Previously, we mapped a late-onset FCD locus, FCD2, on chromosome 18q. Here, we present next-generation sequencing of all coding exons in the FCD2 critical interval in a multigenerational pedigree in which FCD segregates as an autosomal-dominant trait. We identified a missense change in LOXHD1, a gene causing progressive hearing loss in humans, as the sole variant capable of explaining the phenotype in this pedigree. We observed LOXHD1 mRNA in cultured human corneal endothelial cells, whereas antibody staining of both human and mouse corneas showed staining in the corneal epithelium and endothelium. Corneal sections of the original proband were stained for LOXHD1 and demonstrated a distinct increase in antibody punctate staining in the endothelium and Descemet membrane; punctate staining was absent from both normal corneas and FCD corneas negative for causal LOXHD1 mutations. Subsequent interrogation of a cohort of >200 sporadic affected individuals identified another 15 heterozygous missense mutations that were absent from >800 control chromosomes. Furthermore, in silico analyses predicted that these mutations reside on the surface of the protein and are likely to affect the protein's interface and protein-protein interactions. Finally, expression of the familial LOXHD1 mutant allele as well as two sporadic mutations in cells revealed prominent cytoplasmic aggregates reminiscent of the corneal phenotype. All together, our data implicate rare alleles in LOXHD1 in the pathogenesis of FCD and highlight how different mutations in the same locus can potentially produce diverse phenotypes. PMID:22341973
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Optimal Genetic Contribution Selection in Danish Holstein Depends on Pedigree Qualtiy
DEFF Research Database (Denmark)
Sørensen, M K; Sørensen, A C; Baumung, R
2008-01-01
. In the analyses earlier breeding decisions were considered by including all AI waiting- and young bulls and contract matings. Twenty potential sires, 2169 potential dams, 1421 AI-bulls and 754 contract matings plus pedigree animals were included. Results showed that the outcome was very dependent on quality...... the increase in future inbreeding. The more weight put on the average additive genetic relationship in next generation relative to genetic merit, the lower the average merit of the matings, and the lower average additive genetic relationship among the chosen matings and the present breeding animals...
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Haplotype inference in general pedigrees with two sites
Directory of Open Access Journals (Sweden)
Doan Duong D
2011-04-01
Full Text Available Abstract Background Genetic disease studies investigate relationships between changes in chromosomes and genetic diseases. Single haplotypes provide useful information for these studies but extracting single haplotypes directly by biochemical methods is expensive. A computational method to infer haplotypes from genotype data is therefore important. We investigate the problem of computing the minimum number of recombination events for general pedigrees with two sites for all members. Results We show that this NP-hard problem can be parametrically reduced to the Bipartization by Edge Removal problem and therefore can be solved by an O(2k · n2 exact algorithm, where n is the number of members and k is the number of recombination events. Conclusions Our work can therefore be useful for genetic disease studies to track down how changes in haplotypes such as recombinations relate to genetic disease.
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Larmuseau, M H D; Van Geystelen, A; van Oven, M; Decorte, R
2013-04-01
In this article, we promote the implementation of extensive genealogical data in population genetic studies. Genealogical records can provide valuable information on the origin of DNA donors in a population genetic study, going beyond the commonly collected data such as residence, birthplace, language, and self-reported ethnicity. Recent studies demonstrated that extended genealogical data added to surname analysis can be crucial to detect signals of (past) population stratification and to interpret the population structure in a more objective manner. Moreover, when in-depth pedigree data are combined with haploid markers, it is even possible to disentangle signals of temporal differentiation within a population genetic structure during the last centuries. Obtaining genealogical data for all DNA donors in a population genetic study is a labor-intensive task but the vastly growing (genetic) genealogical databases, due to the broad interest of the public, are making this job more time-efficient if there is a guarantee for sufficient data quality. At the end, we discuss the advantages and pitfalls of using genealogy within sampling campaigns and we provide guidelines for future population genetic studies. Copyright © 2013 Wiley Periodicals, Inc.
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Miar, Younes; Sargolzaei, Mehdi; Schenkel, Flavio S
2017-04-01
Phasing genotypes to haplotypes is becoming increasingly important due to its applications in the study of diseases, population and evolutionary genetics, imputation, and so on. Several studies have focused on the development of computational methods that infer haplotype phase from population genotype data. The aim of this study was to compare phasing algorithms implemented in Beagle, Findhap, FImpute, Impute2, and ShapeIt2 software using 50k and 777k (HD) genotyping data. Six scenarios were considered: no-parents, sire-progeny pairs, sire-dam-progeny trios, each with and without pedigree information in Holstein cattle. Algorithms were compared with respect to their phasing accuracy and computational efficiency. In the studied population, Beagle and FImpute were more accurate than other phasing algorithms. Across scenarios, phasing accuracies for Beagle and FImpute were 99.49-99.90% and 99.44-99.99% for 50k, respectively, and 99.90-99.99% and 99.87-99.99% for HD, respectively. Generally, FImpute resulted in higher accuracy when genotypic information of at least one parent was available. In the absence of parental genotypes and pedigree information, Beagle and Impute2 (with double the default number of states) were slightly more accurate than FImpute. Findhap gave high phasing accuracy when parents' genotypes and pedigree information were available. In terms of computing time, Findhap was the fastest algorithm followed by FImpute. FImpute was 30 to 131, 87 to 786, and 353 to 1,400 times faster across scenarios than Beagle, ShapeIt2, and Impute2, respectively. In summary, FImpute and Beagle were the most accurate phasing algorithms. Moreover, the low computational requirement of FImpute makes it an attractive algorithm for phasing genotypes of large livestock populations. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.
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Forecasting Model of Risk of Cancer in Lung Cancer Pedigree in a Case-control Study
Directory of Open Access Journals (Sweden)
Huan LIN
2011-07-01
Full Text Available Background and objective Annual lung screening using spiral computed tomography (CT, has a high sensitivity of detecting early lung cancer (LC, but its high rates of false-positive often lead to unnecessary surgery. The aim of this study is to create a forecasting model of high risk individuals to lung cancer. Methods The pathologic diagnoses of LC in Guangdong Lung Cancer Institute were consecutively chosen as the probands. All the members of the first-degree relatives of probands' and their spouses' were enrolled in this study. These pedigrees consisted of 633 probands' pedigrees and 565 spouses' pedigrees. Unless otherwise stated, analyses were performed using the SPSS 17.0 statistical software package. Results Compared with the control, a family history of carcinoma in first-degree relatives was significantly associated with LC risk (OR=1.71, P<0.001, the sub-group of either one infected individual or more than two infected individuals in first-degree relatives showed significantly statistical differences (P=0.005, P=0.002. In the forecasting model, the risk compared to that in Chinese population was from 0.38 to 63.08 folds. In the population whose risk was more than 10 times to the Chinese population, the accuracy rate of prediction was 88.1%. Conclusion A family history of carcinoma in first-degree relatives was significantly associated with increased LC risk. The more infected individuals exist in first-degree relatives, the more risk was showed. In the forecasting model, smokers especially heavy ones whose risk were more than 10 times to the Chinese population should be receive annual screening. The population are positive at least any two conditions which including male, lung disease history, occupation expose and history of cancer in first-degree relative.
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Crossa, José; Campos, Gustavo de Los; Pérez, Paulino; Gianola, Daniel; Burgueño, Juan; Araus, José Luis; Makumbi, Dan; Singh, Ravi P; Dreisigacker, Susanne; Yan, Jianbing; Arief, Vivi; Banziger, Marianne; Braun, Hans-Joachim
2010-10-01
The availability of dense molecular markers has made possible the use of genomic selection (GS) for plant breeding. However, the evaluation of models for GS in real plant populations is very limited. This article evaluates the performance of parametric and semiparametric models for GS using wheat (Triticum aestivum L.) and maize (Zea mays) data in which different traits were measured in several environmental conditions. The findings, based on extensive cross-validations, indicate that models including marker information had higher predictive ability than pedigree-based models. In the wheat data set, and relative to a pedigree model, gains in predictive ability due to inclusion of markers ranged from 7.7 to 35.7%. Correlation between observed and predictive values in the maize data set achieved values up to 0.79. Estimates of marker effects were different across environmental conditions, indicating that genotype × environment interaction is an important component of genetic variability. These results indicate that GS in plant breeding can be an effective strategy for selecting among lines whose phenotypes have yet to be observed.
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McInnes, LA; Escamilla, MA; Service, SK; Reus, [No Value; Leon, P; Silva, S; Rojas, E; Spesny, M; Baharloo, S; Blankenship, K; Peterson, A; Tyler, D; Shimayoshi, N; Tobey, C; Batki, S; Vinogradov, S; Meza, L; Gallegos, A; Fournier, E; Smith, LB; Barondes, SH; Sandkuijl, LA; Freimer, NB
1996-01-01
Bipolar mood disorder (BP) is a debilitating syndrome characterized by episodes of mania and depression. We designed a multistage study to detect all major loci predisposing to severe BP (termed BP-I) in two pedigrees drawn from the Central Valley of Costa Rica, where the population is largely
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Genetic diversity analysis of two commercial breeds of pigs using genomic and pedigree data.
Zanella, Ricardo; Peixoto, Jane O; Cardoso, Fernando F; Cardoso, Leandro L; Biegelmeyer, Patrícia; Cantão, Maurício E; Otaviano, Antonio; Freitas, Marcelo S; Caetano, Alexandre R; Ledur, Mônica C
2016-03-30
Genetic improvement in livestock populations can be achieved without significantly affecting genetic diversity if mating systems and selection decisions take genetic relationships among individuals into consideration. The objective of this study was to examine the genetic diversity of two commercial breeds of pigs. Genotypes from 1168 Landrace (LA) and 1094 Large White (LW) animals from a commercial breeding program in Brazil were obtained using the Illumina PorcineSNP60 Beadchip. Inbreeding estimates based on pedigree (F x) and genomic information using runs of homozygosity (F ROH) and the single nucleotide polymorphisms (SNP) by SNP inbreeding coefficient (F SNP) were obtained. Linkage disequilibrium (LD), correlation of linkage phase (r) and effective population size (N e ) were also estimated. Estimates of inbreeding obtained with pedigree information were lower than those obtained with genomic data in both breeds. We observed that the extent of LD was slightly larger at shorter distances between SNPs in the LW population than in the LA population, which indicates that the LW population was derived from a smaller N e . Estimates of N e based on genomic data were equal to 53 and 40 for the current populations of LA and LW, respectively. The correlation of linkage phase between the two breeds was equal to 0.77 at distances up to 50 kb, which suggests that genome-wide association and selection should be performed within breed. Although selection intensities have been stronger in the LA breed than in the LW breed, levels of genomic and pedigree inbreeding were lower for the LA than for the LW breed. The use of genomic data to evaluate population diversity in livestock animals can provide new and more precise insights about the effects of intense selection for production traits. Resulting information and knowledge can be used to effectively increase response to selection by appropriately managing the rate of inbreeding, minimizing negative effects of inbreeding
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Genomic and pedigree-based prediction for leaf, stem, and stripe rust resistance in wheat.
Juliana, Philomin; Singh, Ravi P; Singh, Pawan K; Crossa, Jose; Huerta-Espino, Julio; Lan, Caixia; Bhavani, Sridhar; Rutkoski, Jessica E; Poland, Jesse A; Bergstrom, Gary C; Sorrells, Mark E
2017-07-01
Genomic prediction for seedling and adult plant resistance to wheat rusts was compared to prediction using few markers as fixed effects in a least-squares approach and pedigree-based prediction. The unceasing plant-pathogen arms race and ephemeral nature of some rust resistance genes have been challenging for wheat (Triticum aestivum L.) breeding programs and farmers. Hence, it is important to devise strategies for effective evaluation and exploitation of quantitative rust resistance. One promising approach that could accelerate gain from selection for rust resistance is 'genomic selection' which utilizes dense genome-wide markers to estimate the breeding values (BVs) for quantitative traits. Our objective was to compare three genomic prediction models including genomic best linear unbiased prediction (GBLUP), GBLUP A that was GBLUP with selected loci as fixed effects and reproducing kernel Hilbert spaces-markers (RKHS-M) with least-squares (LS) approach, RKHS-pedigree (RKHS-P), and RKHS markers and pedigree (RKHS-MP) to determine the BVs for seedling and/or adult plant resistance (APR) to leaf rust (LR), stem rust (SR), and stripe rust (YR). The 333 lines in the 45th IBWSN and the 313 lines in the 46th IBWSN were genotyped using genotyping-by-sequencing and phenotyped in replicated trials. The mean prediction accuracies ranged from 0.31-0.74 for LR seedling, 0.12-0.56 for LR APR, 0.31-0.65 for SR APR, 0.70-0.78 for YR seedling, and 0.34-0.71 for YR APR. For most datasets, the RKHS-MP model gave the highest accuracies, while LS gave the lowest. GBLUP, GBLUP A, RKHS-M, and RKHS-P models gave similar accuracies. Using genome-wide marker-based models resulted in an average of 42% increase in accuracy over LS. We conclude that GS is a promising approach for improvement of quantitative rust resistance and can be implemented in the breeding pipeline.
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Leading a multigenerational workforce: strategies for attracting and retaining millennials.
Cahill, Terrence F; Sedrak, Mona
2012-01-01
Over the past several years, leaders in healthcare have noticed an increase in generational tension among employees, most often focused on the attitudes and behaviors of the arriving millennials (generation Y). While these employee relations issues were a nuisance, they rarely rose to the level of a priority demanding leadership intervention. Some leaders, in fact, hoped that the issues would resolve themselves as these young employees settled in and learned that they had to demonstrate new behaviors to be successful in the workplace. Most organizations adopted this wait-and-see attitude. Not so today. As the boomer generation has begun its exodus from the workplace, organizations are increasingly looking at the millennials as not a problem but a solution to the workplace manpower transition that is under way. Our problem is that we don't yet know how best to lead such a diverse, multigenerational workforce. This article examines the generational topic and provides advice concerning a variety of changes that leaders may implement to advance their organization's ability to attract and to retain the millennials.
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Directory of Open Access Journals (Sweden)
Hilary Browne Hutchinson
2005-03-01
Full Text Available The challenges encountered in building the InternationalChildren’s Digital Library (ICDL, a freely availableonline library of children’s literature are described. Thesechallenges include selecting and processing books fromdifferent countries, handling and presenting multiplelanguages simultaneously, and addressing cultural differences. Unlike other digital libraries that present content from one or a few languages and cultures, and focuson either adult or child audiences, ICDL must serve amultilingual, multicultural, multigenerational audience.The research is presented as a case study for addressingthese design criteria; current solutions and plans forfuture work are described.
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International Nuclear Information System (INIS)
Hassoun, Anwar; Dincer, Ibrahim
2015-01-01
This paper develops a new Organic Rankine Cycle (ORC) based multigenerational system to meet the demands of a net zero energy building and assesses such a system for an application to a net zero energy house in Lebanon. Solar energy is the prime source for the integrated system to achieve multigeneration to supply electricity, fresh and hot water, seasonal heating and cooling. The study starts by optimizing the power system with and without grid connection. Then, a comprehensive thermodynamic analysis through energy and exergy, and a parametric study to assess the sensitivity and improvements of the overall system are conducted. Furthermore, exergoeconomic analysis and a follow-up optimization study for optimizing the total system cost to the overall system efficiency using genetic algorithm to obtain the optimal design or a set of optimal designs (Pareto Front), are carried out. The present results show that the optimum solar energy system for a total connected load to the house of 90 kWh/day using a combination of ORC, batteries, convertor has a total net present cost of US $52,505.00 (based on the prices in 2013) with a renewable energy fraction of 1. Moreover, the optimization for the same connected load with ORC, batteries and converter configuration with grid connection results in a total net present cost of $50,868.00 (2013) with a renewable energy fraction of 0.992 with 169 kg/yr of CO 2 emissions. In addition, exergoeconomic analysis of the overall system yields a cost of $117,700.00 (2013), and the multi-objective optimization provides the overall exergetic efficiency by 14% at a total system cost increase of $10,500.00 (2013). - Highlights: • To develop a new Organic Rankine Cycle (ORC) based multigenerational system to meet the demands of a net zero energy building. • To perform a comprehensive thermodynamic analysis through energy and exergy approaches. • To apply an exergoeconomic model for exergy-based cost accounting. • To undertake
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Corry, Justine; Green, Melissa; Roberts, Gloria; Fullerton, Janice M.; Schofield, Peter R.; Mitchell, Philip B.
2017-01-01
Background Bipolar disorder (BD) and the anxiety disorders are highly comorbid. The present study sought to examine perfectionism and goal attainment values as potential mechanisms of known associations between anxiety, stress and BD symptomatology. Measures of perfectionism and goal attainment values were administered to 269 members of BD pedigrees, alongside measures of anxiety and stress, and BD mood symptoms. Regression analyses were used to determine whether perfectionism and goal attain...
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Directory of Open Access Journals (Sweden)
James L. Mills
2010-06-01
Full Text Available OBJECTIVE: To document the existence and clinical characteristics of three large families with multigenerational inheritance of early-onset type 2 diabetes in Jamaica. METHODS: Three probands from large families with multigenerational inheritance of early-onset type 2 diabetes in at least three generations were detected at the University Hospital of the West Indies in Jamaica. Each proband at the time of diagnosis was OBJETIVO: Documentar la presencia de herencia multigeneracional de la diabetes de tipo II de inicio temprano en tres familias jamaiquinas grandes y describir sus características clínicas. MÉTODOS: En el Hospital Universitario de West Indies en Jamaica, se detectaron tres probandos de familias grandes en las que se observó herencia multigeneracional de la diabetes tipo 2 de inicio temprano en al menos tres generaciones. Al momento del diagnóstico, cada probando tenía # 25 años de edad, era delgado y no necesitó insulinoterapia. Se emprendieron estudios clínicos, metabólicos y genéticos con el fin de determinar las características particulares de la diabetes que presentan estas tres familias. RESULTADOS: Se investigaron tres árboles genealógicos -BK, SU y CA- conformados por 38, 48 y 113 miembros, respectivamente. Cada árbol presentaba herencia multigeneracional de diabetes tipo 2 de inicio temprano en al menos tres generaciones. En los tres árboles genealógicos, la media de la edad al momento del diagnóstico fue de 31,5 ± 2,9 años y 10 personas tenían menos de 25 años. Se observaron signos indicativos de sobrepeso, resistencia insulínica, baja secreción de insulina, dislipidemia y obesidad intrabdominal leve. No se hallaron anticuerpos contra las células de los islotes ni variantes en la secuencia de los genes MODY1 a MODY6. CONCLUSIONES: Algunas familias grandes de la población jamaiquina presentan herencia multigeneracional de la diabetes y otras características indicativas de diabetes tipo 2 de inicio
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A. Groover; M. Devey; T. Fiddler; J. Lee; R. Megraw; T. Mitchel-Olds; B. Sherman; S. Vujcic; C. Williams; D. Neale
1994-01-01
We report the identification of quantitative trait loci (QTL) influencing wood specific gravity (WSG) in an outbred pedigree of loblolly pine (Pinus taeda L.) . QTL mapping in an outcrossing species is complicated by the presence of multiple alleles (>2) at QTL and marker loci. Multiple alleles at QTL allow the examination of interaction among...
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Energy Technology Data Exchange (ETDEWEB)
Stein, J.; Hecht, T. [Univ. of Texas, Houston, TX (United States); Stal, S. [Texas Children`s Hospital, Houston, TX (United States)] [and others
1995-08-01
Nonsyndromic cleft lip with or without cleft palate (CL/P) is a common craniofacial developmental defect. Recent segregation analyses have suggested that major genes play a role in the etiology of CL/P. Linkage to 22 candidate genes was tested in 11 multigenerational families with CL/P, and 21 of these candidates were excluded. APOC2, 19q13.1, which is linked to the proto-oncogene BCL3, gave suggestive evidence for linkage to CL/P. The study was expanded to include a total of 39 multigenerational CL/P families. Linkage was tested in all families, using anonymous marker, D19S178, and intragenic markers in BCL3 and APOC2. Linkage was tested under two models, autosomal dominant with reduced penetrance and affecteds-only model. Both models showed evidence of heterogeneity, with 43% of families linked at zero recombination to BCL3 when marker data from BCL3 and APOC2 were included. A maximum multipoint LOD score of 7.00 at BCL3 was found among the 17 families that had posterior probabilities {ge}50% in favor of linkage. The transmission disequilibrium test provided additional evidence for linkage with the 3 allele of BCL3 more often transmitted to affected children. These results suggest that BCL3, or a nearby gene, plays a role in the etiology of CL/P in some families. 39 refs., 8 figs., 4 tabs.
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DEFF Research Database (Denmark)
Lythcke-Jørgensen, Christoffer Ernst; Münster, Marie; Ensinas, Adriano Viana
2016-01-01
This paper presents a novel, simple method for reducing external operating condition datasets to be used in multi-generation system optimization models. The method, called the Characteristic Operating Pattern (CHOP) method, is a visually-based aggregation method that clusters reference data based...... on parameter values rather than time of occurrence, thereby preserving important information on short-term relations between the relevant operating parameters. This is opposed to commonly used methods where data are averaged over chronological periods (months or years), and extreme conditions are hidden...... in the averaged values. The CHOP method is tested in a case study where the operation of a fictive Danish combined heat and power plant is optimized over a historical 5-year period. The optimization model is solved using the full external operating condition dataset, a reduced dataset obtained using the CHOP...
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HindIII identifies a two allele DNA polymorphism of the human cannabinoid receptor gene (CNR)
Energy Technology Data Exchange (ETDEWEB)
Caenazzo, L.; Hoehe, M.R.; Hsieh, W.T.; Berrettini, W.H.; Bonner, T.I.; Gershon, E.S. (National Inst. of Health, Bethesda, MD (United States))
1991-09-11
HCNR p5, a 0.9 kb BamHI/EcoRI fragment from the human cannabinoid receptor gene inserted into pUC19, was used as probe. The fragment is located in an intron approximately 14 kb 5{prime} of the initiation codon. This fragment is a clean single copy sequence by genomic blotting. Hybridization of human genomic DNA digested with HindIII identified a two allele RFLP with bands at 5.5 (A1) and 3.3 kb (A2). The human cannabinoid receptor gene has been genetically mapped in CEPH reference pedigrees to the centromeric/q region of chromosome 6. In situ hybridization localizes it to 6q14-q15. Codominant segregation has been observed in 26 informative two- and three-generation CEPH pedigrees and in 14 medium-sized disease families.
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van der Spek, Mijndert; Ramirez, Andrea; Faaij, André
2016-01-01
This article aims to improve uncertainty evaluation of process models by combining a quantitative uncertainty evaluation method (data validation) with a qualitative uncertainty evaluation method (pedigree analysis). The approach is tested on a case study of monoethanolamine based postcombustion CO2
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Liu, Ting; Li, Qi; Song, Junlin; Yu, Hong
2017-02-01
There is an increasing requirement for traceability of aquaculture products, both for consumer protection and for food safety. There are high error rates in the conventional traceability systems depending on physical labels. Genetic traceability technique depending on DNA-based tracking system can overcome this problem. Genealogy information is essential for genetic traceability, and microsatellite DNA marker is a good choice for pedigree analysis. As increasing genotyping throughput of microsatellites, microsatellite multiplex PCR has become a fast and cost-effective technique. As a commercially important cultured aquatic species, Pacific oyster Crassostrea gigas has the highest global production. The objective of this study was to develop microsatellite multiplex PCR panels with dye-labeled universal primer for pedigree analysis in C. gigas, and these multiplex PCRs were validated using 12 full-sib families with known pedigrees. Here we developed six informative multiplex PCRs using 18 genomic microsatellites in C. gigas. Each multiplex panel contained a single universal primer M13(-21) used as a tail on each locus-specific forward primer and a single universal primer M13(-21) labeled with fluorophores. The polymorphisms of the markers were moderate, with an average of 10.3 alleles per locus and average polymorphic information content of 0.740. The observed heterozygosity per locus ranged from 0.492 to 0.822. Cervus simulations revealed that the six panels would still be of great value when massive families were analysed. Pedigree analysis of real offspring demonstrated that 100% of the offspring were unambiguously allocated to their parents when two multiplex PCRs were used. The six sets of multiplex PCRs can be an important tool for tracing cultured individuals, population genetic analysis, and selective breeding program in C. gigas.
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Zhang, J; Wang, Y N; Wang, J S; Wu, L; Wei, N; Fu, L; Gao, Z; Chen, J H; Pei, R J; Wang, Z
2016-07-01
To investigate the significance of pedigree genetic screening and rapid immunological parameters in the diagnosis of primary hemophagocytic lymphohistiocytosis (HLH). Four cases of primary HLH patients with PRF1, UNC13D and SH2D1A gene mutations were conducted pedigree investigation, including family genetic screening and detections of immunological parameters (NK cell activity, CD107a degranulation and expression of HLH related defective protein), to evaluate the significance of these different indicators in the diagnosis of primary HLH and explore their correlations. The DNA mutations of the four families included missense mutation c.T172C (p.S58P) and non- frameshift deletions c.1083_1094del (p.361_365del), missense mutation c.C1349T (p.T450M) and frameshift mutation c.1090_1091delCT (p.T364fsX93) in PRF1 gene, missense mutation c.G2588A (p.G863D) in UNC13D gene and hemizygous mutation c.32T>G (p.I11S) in SH2D1A gene. The patients and their family members presented decreased NK cell activities. Individuals who carried mutations of PRF1 gene and SH2D1A gene showed low expression of perforin (PRF1) and signaling lymphocytic activation molecule associated protein (SAP). And the patient with UNC13D gene mutation and his family member with identical mutation showed significant reducing cytotoxic degranulation function (expression of CD107a). Pedigree genetic screening and rapid detection of immunological parameters might play an important role in the diagnosis of primary HLH, and both of them had good consistency. As an efficient detection means, the rapid immunological detection indicators would provide reliable basis for the early diagnosis of the primary HLH.
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DEFF Research Database (Denmark)
Rorije, Emiel; Muller, André; Beekhuijzen, Manon E.W.
2011-01-01
The possible impact on classification and labelling decisions of effects observed in second generation parental (P1) and offspring (F2) parameters in multi-generation studies was investigated. This was done for 50 substances classified as reproductive toxicants in Europe, for which a multi-genera...... and reduced animal use, provide strong further support for replacement of the classical two-generation reproductive toxicity study by the EOGRTS in regulatory reproductive toxicity assessment....
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Reverse-namaskar: A new sign in Ehlers-Danlos syndrome: A family pedigree study of four generations
Directory of Open Access Journals (Sweden)
Premalatha S
2010-01-01
Full Text Available Ehlers-Danlos Syndrome (EDS is a rare group of inheritable connective tissue disorder of defective collagen. Skin, joints and blood vessels are most commonly affected. Clinical signs such as Gorlin sign and Metenier sign have been described in this syndrome. We report another new clinical sign called ′Reverse-Namaskar′ sign as an important clinical finding in EDS, based on the family pedigree study of the proband.
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Pedigree Analysis of Holstein Bulls in Slovakia
Directory of Open Access Journals (Sweden)
Ivan Pavlík
2012-05-01
Full Text Available The aim of the study was to evaluate the genetic diversity in Holstein bulls population in Slovakia by the methods of pedigree analysis. The population was represented by the bulls with reserve of frozen semen doses in AI centers. Whole reference population consisted of 169 bulls born from 1997 to 2009. For calculation of diversity parameters the program Endog v.4.8 (Gutiérrez, Goyache, 2005 was used. An average maximal number of generations traced was 9.35, 3.06 complete generations and equivalent number of generations traced was 5.71. An average coefficient of inbreeding was 2.48%, individual increase in inbreeding was 0.53% and average relatedness was 2.72%. The 167 bulls from 169 were inbred (98.82%. An average number of offsprings per bull was 107.70 with maximal number 1,641 offsprings. The effective population size computed via individual increase in inbreeding was 94.50. The effective number of founders was 88, effective number of ancestors 31 and only 13 ancestors described 50% of diversity. From these results we can conclude that the diversity of Holstein bulls is reduced by more factors (inbreeding, high relatedness, bottlenecks. Obtained results point out the need to use new outbred bull lines for mating cows.
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Midro, Alina T; Zollino, Marcella; Wiland, Ewa; Panasiuk, Barbara; Iwanowski, Piotr S; Murdolo, Marina; Śmigiel, Robert; Sąsiadek, Maria; Pilch, Jacek; Kurpisz, Maciej
2016-02-01
The purpose of this study was to compare meiotic segregation in sperm cells from two carriers with t(4;8)(p16;p23.1) reciprocal chromosome translocations (RCTs), differing in localization of the breakpoint positions at the 4p subband-namely, 4p16.3 (carrier 1) and 4p16.1 (carrier 2)-and to compare data of the pedigree analyses performed by direct method. Three-color fluorescent in situ hybridization (FISH) on sperm cells and FISH mapping for the evaluation of the breakpoint positions, data from pedigrees, and direct segregation analysis of the pedigrees were performed. Similar proportions of normal/balanced and unbalanced sperm cells were found in both carriers. The most common was an alternate type of segregation (about 52 % and about 48 %, respectively). Unbalanced adjacent I and adjacent II karyotypes were found in similar proportions about 15 %. The direct segregation analysis (following Stengel-Rutkowski) of the pedigree of carriers of t(4;8)(p16.1;p23.1) was performed and results were compared with the data of the pedigree segregation analysis obtained earlier through the indirect method. The probability of live-born progeny with unbalanced karyotype for carriers of t(4;8)(p16.1;p23.1) was moderately high at 18.8 %-comparable to the value obtained using the indirect method for the same carriership, which was 12 %. This was, however, markedly lower than the value of 41.2 % obtained through the pedigree segregation indirect analysis estimated for carriers of t(4;8)(p16.3;p23.1), perhaps due to the unique composition of genes present within the 4p16.1-4p 16.3 region. Revealed differences in pedigree segregation analysis did not correspond to the very similar profile of meiotic segregation patterns presented by carrier 1 and carrier 2. Most probably, such discordances may be due to differences in embryo survival rates arising from different genetic backgrounds.
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Tempo and mode of genomic mutations unveil human evolutionary history.
Hara, Yuichiro
2015-01-01
Mutations that have occurred in human genomes provide insight into various aspects of evolutionary history such as speciation events and degrees of natural selection. Comparing genome sequences between human and great apes or among humans is a feasible approach for inferring human evolutionary history. Recent advances in high-throughput or so-called 'next-generation' DNA sequencing technologies have enabled the sequencing of thousands of individual human genomes, as well as a variety of reference genomes of hominids, many of which are publicly available. These sequence data can help to unveil the detailed demographic history of the lineage leading to humans as well as the explosion of modern human population size in the last several thousand years. In addition, high-throughput sequencing illustrates the tempo and mode of de novo mutations, which are producing human genetic variation at this moment. Pedigree-based human genome sequencing has shown that mutation rates vary significantly across the human genome. These studies have also provided an improved timescale of human evolution, because the mutation rate estimated from pedigree analysis is half that estimated from traditional analyses based on molecular phylogeny. Because of the dramatic reduction in sequencing cost, sequencing on-demand samples designed for specific studies is now also becoming popular. To produce data of sufficient quality to meet the requirements of the study, it is necessary to set an explicit sequencing plan that includes the choice of sample collection methods, sequencing platforms, and number of sequence reads.
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Ouaras, K.; Lombardi, G.; Hassouni, K.
2018-03-01
For the first time, we demonstrate that tungsten (W) nanoparticles (NPs) are created when a tungsten target is exposed to low-pressure, high density hydrogen plasma. The plasma was generated using a novel dual plasma system combining a microwave discharge and a pulsed direct-current (DC) discharge. The tungsten surface originates in the multi-generational formation of a significant population of 30-70 nm diameter particles when the W cathode is biased at ~ -1 kV and submitted to ~1020 m2 s-1 H+/H2+ /H3+ ions flux. The evidenced NPs formation should be taking into account as one of the consequence of the plasma surface interaction outcomes, especially for fusion applications.
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Genomic view of bipolar disorder revealed by whole genome sequencing in a genetic isolate.
Directory of Open Access Journals (Sweden)
Benjamin Georgi
2014-03-01
Full Text Available Bipolar disorder is a common, heritable mental illness characterized by recurrent episodes of mania and depression. Despite considerable effort to elucidate the genetic underpinnings of bipolar disorder, causative genetic risk factors remain elusive. We conducted a comprehensive genomic analysis of bipolar disorder in a large Old Order Amish pedigree. Microsatellite genotypes and high-density SNP-array genotypes of 388 family members were combined with whole genome sequence data for 50 of these subjects, comprising 18 parent-child trios. This study design permitted evaluation of candidate variants within the context of haplotype structure by resolving the phase in sequenced parent-child trios and by imputation of variants into multiple unsequenced siblings. Non-parametric and parametric linkage analysis of the entire pedigree as well as on smaller clusters of families identified several nominally significant linkage peaks, each of which included dozens of predicted deleterious variants. Close inspection of exonic and regulatory variants in genes under the linkage peaks using family-based association tests revealed additional credible candidate genes for functional studies and further replication in population-based cohorts. However, despite the in-depth genomic characterization of this unique, large and multigenerational pedigree from a genetic isolate, there was no convergence of evidence implicating a particular set of risk loci or common pathways. The striking haplotype and locus heterogeneity we observed has profound implications for the design of studies of bipolar and other related disorders.
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Genomic View of Bipolar Disorder Revealed by Whole Genome Sequencing in a Genetic Isolate
Georgi, Benjamin; Craig, David; Kember, Rachel L.; Liu, Wencheng; Lindquist, Ingrid; Nasser, Sara; Brown, Christopher; Egeland, Janice A.; Paul, Steven M.; Bućan, Maja
2014-01-01
Bipolar disorder is a common, heritable mental illness characterized by recurrent episodes of mania and depression. Despite considerable effort to elucidate the genetic underpinnings of bipolar disorder, causative genetic risk factors remain elusive. We conducted a comprehensive genomic analysis of bipolar disorder in a large Old Order Amish pedigree. Microsatellite genotypes and high-density SNP-array genotypes of 388 family members were combined with whole genome sequence data for 50 of these subjects, comprising 18 parent-child trios. This study design permitted evaluation of candidate variants within the context of haplotype structure by resolving the phase in sequenced parent-child trios and by imputation of variants into multiple unsequenced siblings. Non-parametric and parametric linkage analysis of the entire pedigree as well as on smaller clusters of families identified several nominally significant linkage peaks, each of which included dozens of predicted deleterious variants. Close inspection of exonic and regulatory variants in genes under the linkage peaks using family-based association tests revealed additional credible candidate genes for functional studies and further replication in population-based cohorts. However, despite the in-depth genomic characterization of this unique, large and multigenerational pedigree from a genetic isolate, there was no convergence of evidence implicating a particular set of risk loci or common pathways. The striking haplotype and locus heterogeneity we observed has profound implications for the design of studies of bipolar and other related disorders. PMID:24625924
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Miljkovic-Gacic, Iva; Wang, Xiaojing; Kammerer, Candace M; Bunker, Clareann H; Wheeler, Victor W; Patrick, Alan L; Kuller, Lewis H; Evans, Rhobert W; Zmuda, Joseph M
2007-02-01
Adiponectin, an adipose-specific protein, is negatively associated with adiposity, insulin sensitivity, and diabetes. Very few studies have examined the role of heredity in the regulation of adiponectin and its association with body fat among individuals of African heritage. Thus, we measured fasting serum adiponectin levels by radioimmunoassay and body composition by dual-energy x-ray absorptiometry (DEXA) in 402 individuals aged 18 to 103 years belonging to 7 multigenerational families of African heritage in the relatively homogeneous island population of Tobago. Heritability of adiponectin was 33.2% (P genetic factors are a significant source of interindividual differences in circulating adiponectin among Afro-Caribbeans. Adiponectin may serve as a promising quantitative intermediate trait in studies designed to map the genes underlying diabetes and obesity in this population.
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Goyal, Tarang; Varshney, Anupam; Bakshi, S K
2012-01-01
Familial atrophia maculosa varioliformis cutis is a very rare disorder with less than 28 cases being reported in the literature worldwide and remains a mystery both as far as genetics and the virtue of its pathogenesis is concerned. We present a case of mother and son, both having this disorder with presentations unique in terms of sites involved and try to draw a five generations pedigree chart for the same. We further support its inheritance pattern as autosomal dominant. Also, we propose oral isotretinoin as an effective treatment modality for the same.
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Directory of Open Access Journals (Sweden)
Tarang Goyal
2012-01-01
Full Text Available Familial atrophia maculosa varioliformis cutis is a very rare disorder with less than 28 cases being reported in the literature worldwide and remains a mystery both as far as genetics and the virtue of its pathogenesis is concerned. We present a case of mother and son, both having this disorder with presentations unique in terms of sites involved and try to draw a five generations pedigree chart for the same. We further support its inheritance pattern as autosomal dominant. Also, we propose oral isotretinoin as an effective treatment modality for the same.
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Directory of Open Access Journals (Sweden)
Ronaldo Carvalho dos Santos
2005-01-01
Full Text Available Genetic diversity in cocoa (Theobroma cacao L. has been assessed based on morphological and molecular markers for germplasm management and breeding purposes. Pedigree data is available in cocoa but it has not been used for assessing genetic relatedness. The geneitic diversity of 30 clonal cocoa accessions resistant to witche´ broom disease, from the CEPEC series, were studied on the basis of RAPD data and pedigree information. Twenty of these accessions descend from the TSA-644 clone, originated from a cross between the Upper Amazon germplasm called Scavina-6, the main source of resistance to witches' broom disease, and IMC-67. The ten remaining clones come from different sources including Amazon and Trinitario germplasm. RAPD data was collected using 16 primers and pedigree information was obtained from the International Cocoa Germplasm Database. Genetic similarities, genetic distances and coefficient of parentage were calculated using available software. Relatively low genetic diversity was observed in this germplasm set, probably because of great genetic relatedness amongst accessions studied and the poor representation of the germplasm. The TSA-644 descendants were more diverse than the other accessions used in the study. This might be due to the origin of the TSA clone, which was derived from highly divergent genotypes. Association between genetic similarities based on RAPD data and coefficient of parentage, based on pedigree data, was very low, probably due to the homogeneity of the breeding stocks and poor pedigree information. These findings are useful to cocoa breeders in planning crosses for the development of hybrid and clonal cultivars.A diversidade genética em cacau (Theobroma cacao L., embasada em dados morfológicos e em marcadores moleculares, tem sido avaliada com fins de manejo de germoplasma e uso no melhoramento genético. Dados de genealogia de cacau, embora disponíveis, não têm sido utilizados. Foi analisada a
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2010-04-01
... 26 Internal Revenue 11 2010-04-01 2010-04-01 true Taxation of U.S. persons that are shareholders of PFICs that are not pedigreed QEFs. 1.1291-1 Section 1.1291-1 Internal Revenue INTERNAL REVENUE... Determining Capital Gains and Losses § 1.1291-1 Taxation of U.S. persons that are shareholders of PFICs that...
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Bamashmus, M A; Downey, L M; Inglehearn, C F; Gupta, S R; Mansfield, D C
2000-04-01
Familial exudative vitreoretinopathy (FEVR) is associated with mutations in the Norrie disease gene in X linked pedigrees and with linkage to the EVR1 locus at 11q13 in autosomal dominant cases. A large autosomal dominant FEVR family was studied, both clinically and by linkage analysis, to determine whether it differed from the known forms of FEVR. Affected members and obligate gene carriers from this family were examined by slit lamp biomicroscopy, indirect ophthalmoscopy, and in some cases fluorescein angiography. Patient DNAs were genotyped for markers at the EVR1 locus on chromosome 11q13. The clinical evaluation in this family is consistent with previous descriptions of FEVR pedigrees, but linkage analysis proves that it has a form of FEVR genetically distinct from the EVR1 locus on 11q. This proves that there are at least three different loci associated with comparable FEVR phenotypes, a situation similar to that existing for many forms of retinal degeneration.
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DEFF Research Database (Denmark)
Frenck, Georg; van der Linden, Leon; Mikkelsen, Teis Nørgaard
2013-01-01
Functional plant traits are likely to adapt under the sustained pressure imposed by environmental changes through natural selection. Employing Brassica napus as a model, a multi-generational study was performed to investigate the potential trajectories of selection at elevated [CO2] in two differ...... ameliorate depressions in plant reproductive fitness caused by higher temperatures in situations where both factors co-occur....
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Jasinska, A.J.; Service, S.; Jawaheer, D.; DeYoung, J.; Levinson, M.; Zhang, Z.; Kremeyer, B.; Muller, H.; Aldana, I.; Garcia, J.; Restrepo, G.; Lopez, C.; Palacio, C.; Duque, C.; Parra, M.; Vega, J.; Ortiz, D.; Bedoya, G.; Mathews, C.; Davanzo, P.; Fournier, E.; Bejarano, J.; Ramirez, M.; Ortiz, C. Araya; Araya, X.; Molina, J.; Sabatti, C.; Reus, V.; Ospina, J.; Macaya, G.; Ruiz-Linares, A.; Freimer, N.B.
2016-01-01
We previously reported linkage of bipolar disorder to 5q33-q34 in families from two closely related population isolates, the Central Valley of Costa Rica (CVCR) and Antioquia, Colombia (CO). Here we present follow up results from fine-scale mapping in large CVCR and CO families segregating severe bipolar disorder, BP-I, and in 343 population trios/duos from CVCR and CO. Employing densely spaced SNPs to fine map the prior linkage peak region increases linkage evidence and clarifies the position of the putative BP-I locus. We performed two-point linkage analysis with 1134 SNPs in an approximately 9 Mb region between markers D5S410 and D5S422. Combining pedigrees from CVCR and CO yields a LOD score of 4.9 at SNP rs10035961. Two other SNPs (rs7721142 and rs1422795) within the same 94 kb region also displayed LOD scores greater than 4. This linkage peak coincides with our prior microsatellite results and suggests a narrowed BP-I susceptibility regions in these families. To investigate if the locus implicated in the familial form of BP-I also contributes to disease risk in the population, we followed up the family results with association analysis in duo and trio samples, obtaining signals within 2 Mb of the peak linkage signal in the pedigrees; rs12523547 and rs267015 (P = 0.00004 and 0.00016, respectively) in the CO sample and rs244960 in the CVCR sample and the combined sample, with P = 0.00032 and 0.00016, respectively. It remains unclear whether these association results reflect the same locus contributing to BP susceptibility within the extended pedigrees. PMID:19319892
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A Large PROP1 Gene Deletion in a Turkish Pedigree
Directory of Open Access Journals (Sweden)
Suheyla Gorar
2018-01-01
Full Text Available Pituitary-specific paired-like homeodomain transcription factor, PROP1, is associated with multiple pituitary hormone deficiency. Alteration of the gene encoding the PROP1 may affect somatotropes, thyrotropes, and lactotropes, as well as gonadotropes and corticotropes. We performed genetic analysis of PROP1 gene in a Turkish pedigree with three siblings who presented with short stature. Parents were first degree cousins. Index case, a boy, had somatotrope, gonadotrope, thyrotrope, and corticotrope deficiency. However, two elder sisters had somatotroph, gonadotroph, and thyrotroph deficiency and no corticotroph deficiency. On pituitary magnetic resonance, partial empty sella was detected with normal bright spot in all siblings. In genetic analysis, we found a gross deletion involving PROP1 coding region. In conclusion, we report three Turkish siblings with a gross deletion in PROP1 gene. Interestingly, although little boy with combined pituitary hormone deficiency has adrenocorticotropic hormone (ACTH deficiency, his elder sisters with the same gross PROP1 deletion have no ACTH deficiency. This finding is in line with the fact that patients with PROP1 mutations may have different phenotype/genotype correlation.
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Digital Inequality on the US-Mexico Border: A Multigenerational Case Study in Laredo, Texas
Directory of Open Access Journals (Sweden)
María de los Ángeles Flores
2017-09-01
Full Text Available
The purpose of the present study is to determine the cultural and social barriers that are preventing Laredoans from accessing the digital world. This multigenerational study examines how three generations within 16 families relate culturally and socially to technology. Three members from the same family were invited to voluntarily participate in the study, with a total of 48 in-depth, face-to-face interviews being conducted. The present study identified several barriers such as low educational level, low income, lack of English language proficiency, lack of relevant content available in other languages besides English, preference to communicate face-to-face, fear of violence, and endless working hours. Laredo is the least connected city in the nation with 40.2% non-connectivity rate. Research is needed to understand this digital inequity situation in this borderland city. The theoretical framework used is rooted on Straubhaar’s concepts of techno-field, techno-disposition, and techno-capital.
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Carcinogenesis in C57BL mice after multigeneration exposure of the male germinal line to tritium
International Nuclear Information System (INIS)
Mewissen, D.J.; Ugarte, A.S.; Rust, J.J.
1986-01-01
The occurrence of a heritable, multiple intestinal adenocarcinoma (HMIA) was observed in the offspring of an outcross between a male (or female) parent originating from our C57 Black/6M strain and his female (or male) mating counterpart originating from an experimental subline of the same strain, propagated with multigeneration exposure of the male parent to low-level tritium. Multiple intestinal malignancy was observed with a high-expression frequency in all animals examined in five subsequent generations, irrespective of the sex of the initial ascendant originating from the experimental subline, exposed to tritiated water. A digenic inheritance with partial penetrance is postulated, involving at least a two-stage process of tumorigenesis, namely, a dominant mutation at one locus and a second mutation to a recessive which, as long as it remained homozygous, prevented expression of the tumorigenic dominant gene. 10 refs., 2 tabs
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Rooster semen cryopreservation: effect of pedigree line and male age on postthaw sperm function.
Long, J A; Bongalhardo, D C; Pelaéz, J; Saxena, S; Settar, P; O'Sullivan, N P; Fulton, J E
2010-05-01
The fertility rates of cryopreserved poultry semen are highly variable and not reliable for use in preservation of commercial genetic stocks. Our objective was to evaluate the cryosurvival of semen from 8 pedigreed layer lines at 2 different ages: the onset and end of commercial production. Semen from 160 roosters (20/line) was frozen individually with 11% glycerol at 6 and 12 mo of age. Glycerol was removed from thawed semen by Accudenz gradient centrifugation. The viability of thawed sperm from each male was determined using fluorescent live-dead staining and flow cytometry; sperm velocity parameters were measured using computerized motion analysis. The fertilizing ability of thawed sperm was evaluated in vitro by assessing hydrolysis of the inner perivitelline membrane. The postthaw function of sperm from the elite lines varied widely, despite the fact that fresh semen from all of these lines typically yielded high fertility rates. The percentage of thawed sperm with intact plasma membranes ranged from 27.8 + or - 2.1 to 49.6 + or - 1.9 and varied among lines and between age groups. Thawed sperm from 2 lines consistently demonstrated the highest and lowest motility parameters, whereas the velocity parameters of the remaining 6 lines varied widely. The mean number of hydrolysis points per square millimeter of inner perivitelline membrane ranged from 12.5 + or - 4.1 (line 2) to 103.3 + or - 30.2 (line 6). Age effects were observed for 4 out of 8 lines; however, improved postthaw sperm function at 12 mo of age was not consistent for all 3 assays. These results demonstrate variability among pedigreed lines in withstanding glycerol-based semen cryopreservation and provide a model for delineating genotypic and phenotypic factors affecting sperm cryosurvival.
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Directory of Open Access Journals (Sweden)
Catherine Cukras
Full Text Available Retinitis Pigmentosa (RP is a common form of retinal degeneration characterized by photoreceptor degeneration and retinal pigment epithelium (RPE atrophy causing loss of visual field and acuities. Exome sequencing identified a novel homozygous splice site variant (c.111+1G>A in the gene encoding retinol binding protein 4 (RBP4. This change segregated with early onset, progressive, and severe autosomal recessive retinitis pigmentosa (arRP in an eight member consanguineous pedigree of European ancestry. Additionally, one patient exhibited developmental abnormalities including patent ductus arteriosus and chorioretinal and iris colobomas. The second patient developed acne from young age and extending into the 5(th decade. Both patients had undetectable levels of RBP4 in the serum suggesting that this mutation led to either mRNA or protein instability resulting in a null phenotype. In addition, the patients exhibited severe vitamin A deficiency, and diminished serum retinol levels. Circulating transthyretin levels were normal. This study identifies the RBP4 splice site change as the cause of RP in this pedigree. The presence of developmental abnormalities and severe acne in patients with retinal degeneration may indicate the involvement of genes that regulate vitamin A absorption, transport and metabolism.
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Cukras, Catherine; Gaasterland, Terry; Lee, Pauline; Gudiseva, Harini V; Chavali, Venkata R M; Pullakhandam, Raghu; Maranhao, Bruno; Edsall, Lee; Soares, Sandra; Reddy, G Bhanuprakash; Sieving, Paul A; Ayyagari, Radha
2012-01-01
Retinitis Pigmentosa (RP) is a common form of retinal degeneration characterized by photoreceptor degeneration and retinal pigment epithelium (RPE) atrophy causing loss of visual field and acuities. Exome sequencing identified a novel homozygous splice site variant (c.111+1G>A) in the gene encoding retinol binding protein 4 (RBP4). This change segregated with early onset, progressive, and severe autosomal recessive retinitis pigmentosa (arRP) in an eight member consanguineous pedigree of European ancestry. Additionally, one patient exhibited developmental abnormalities including patent ductus arteriosus and chorioretinal and iris colobomas. The second patient developed acne from young age and extending into the 5(th) decade. Both patients had undetectable levels of RBP4 in the serum suggesting that this mutation led to either mRNA or protein instability resulting in a null phenotype. In addition, the patients exhibited severe vitamin A deficiency, and diminished serum retinol levels. Circulating transthyretin levels were normal. This study identifies the RBP4 splice site change as the cause of RP in this pedigree. The presence of developmental abnormalities and severe acne in patients with retinal degeneration may indicate the involvement of genes that regulate vitamin A absorption, transport and metabolism.
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International Nuclear Information System (INIS)
Taheri, M.H.; Mosaffa, A.H.; Farshi, L. Garousi
2017-01-01
In this work, a novel integrated biomass based multigeneration energy system is presented and investigated for power, cooling and hydrogen production. The proposed system consists of a combination of biomass integrated gasifier-gas turbine cycle, a Rankine cycle, a cascade organic Rankine cycle, an absorption refrigeration system and a PEM to produce hydrogen. This system uses cold energy of LNG as a thermal sink. Comprehensive thermodynamic and economic analyses as well as an optimization are performed. The effects of operating parameters on thermodynamic performance and total cost rate are investigated for overall system and subsystems. The results show that the fuel mass flow rate is the dominant factor affecting the variation of energy efficiency and total cost rate. An increase in fuel mass flow rate from 4 kg s"−"1 to 10 kg s"−"1 leads to a decrease of 8.5% and an increase of 122.8% overall energy efficiency and total cost rate, respectively. Also, the largest increase in exergy efficiency occurs when gas turbine inlet temperature increases. The results of optimization showed that the highest net power output, mass flow rate of natural gas delivered to city and the flue gas temperature discharged to the environment are obtained for the exergy efficiency optimal design. - Highlights: • A novel multigeneration system is investigated and optimized thermodynamically and economically. • This system is proposed for power, cooling and hydrogen production. • Proposed system uses LNG cold energy thermal sink that can generate power after vaporization. • The effects of operating parameters on energy and exergy efficiencies and total cost rate are investigated. • An optimization is applied based on the energy, exergy and economic viewpoints.
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Phenotypic variation in a large Swedish pedigree due to SNCA duplication and triplication
DEFF Research Database (Denmark)
Fuchs, J; Nilsson, C; Kachergus, J
2007-01-01
complex. The genetic basis for familial parkinsonism is an SNCA-MMRN11 multiplication, but whereas SNCA-MMRN1 duplication in the Swedish proband (Branch J) leads to late-onset autonomic dysfunction and parkinsonism, SNCA-MMRN1 triplication in the Swedish American family (Branch I) leads to early......BACKGROUND: The "Lister family complex," an extensive Swedish family with autosomal dominant Parkinson disease, was first described by Henry Mjönes in 1949. On the basis of clinical, molecular, and genealogic findings on a Swedish and an American family branch, we provide genetic evidence...... that explains the parkinsonism in this extended pedigree. METHODS: Clinical methods included a detailed neurologic exam of the proband of the Swedish family branch, MRI, and ([123]I)-beta-CIT SPECT imaging. Genomic analysis included alpha-synuclein sequencing, SNCA real-time PCR dosage, chromosome 4q21...
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Estimating Heritability from Nuclear Family and Pedigree Data.
Bochud, Murielle
2017-01-01
Heritability is a measure of familial resemblance. Estimating the heritability of a trait could be one of the first steps in the gene mapping process. This chapter describes how to estimate heritability for quantitative traits from nuclear and pedigree data using the ASSOC program in the Statistical Analysis in Genetic Epidemiology (S.A.G.E.) software package. Estimating heritability rests on the assumption that the total phenotypic variance of a quantitative trait can be partitioned into independent genetic and environmental components. In turn, the genetic variance can be divided into an additive (polygenic) genetic variance, a dominance variance (nonlinear interaction effects between alleles at the same locus) and an epistatic variance (interaction effects between alleles at different loci). The last two are often assumed to be zero. The additive genetic variance represents the average effects of individual alleles on the phenotype and reflects transmissible resemblance between relatives. Heritability in the narrow sense (h 2 ) refers to the ratio of the additive genetic variance to the total phenotypic variance. Heritability is a dimensionless population-specific parameter. ASSOC estimates association parameters (regression coefficients) and variance components from family data. ASSOC uses a linear regression model in which the total residual variance is partitioned, after regressing on covariates, into the sum of random components such as an additive polygenic component, a random sibship component, random nuclear family components, a random marital component, and an individual-specific random component. Assortative mating, nonrandom ascertainment of families, and failure to account for key confounding factors may bias heritability estimates.
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Multi-generational effects of rice harboring Bph15 on brown planthopper, Nilaparvata lugens.
Li, Jie; Shang, Keke; Liu, Jia; Jiang, Tingru; Hu, Dingbang; Hua, Hongxia
2014-02-01
The brown planthopper (BPH), Nilaparvata lugens, is one of the most devastating rice pests in Asia. Resistant cultivars are an effective way of managing BPH. Bph15 is a BPH resistance gene and has been introgressed into rice variety Minghui 63 (MH63). The multi-generational effects of rice line MH63::15 (harboring Bph15) on BPH were investigated and compared with its parental line MH63. U-test analysis indicated that, over seven generations, the developmental duration of BPH nymphs was significantly prolonged by MH63::15. The results of a two-way analysis indicated that, over seven generations, MH63::15 had significant negative effects on the hatchability, emergence rate, copulation rate, weight of adults and fecundity of BPH, but no significant effects on the survival rate of nymphs or female ratio of BPH. In addition, the development of ovary was significantly retarded by MH63::15, and the expression of oogenesis genes were either down-regulated (three genes) or up-regulated (one genes) by MH63::15 compared with MH63. After being reared continuously on MH63::15 for seven generations, most of the life parameters of BPH were negatively affected by MH63::15, especially fecundity and ovary development. These results indicate that MH63::15 rice has potential for use in the control of BPH. © 2013 Society of Chemical Industry.
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Directory of Open Access Journals (Sweden)
Sarah L. Nickerson
2015-10-01
Full Text Available Autosomal recessive cerebellar ataxia encompasses a large and heterogeneous group of neurodegenerative disorders. We employed single nucleotide polymorphism (SNP analysis and whole exome sequencing to investigate a consanguineous Maori pedigree segregating ataxia. We identified a novel mutation in exon 10 of the SACS gene: c.7962T>G p.(Tyr2654*, establishing the diagnosis of autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS. Our findings expand both the genetic and phenotypic spectrum of this rare disorder, and highlight the value of high-density SNP analysis and whole exome sequencing as powerful and cost-effective tools in the diagnosis of genetically heterogeneous disorders such as the hereditary ataxias.
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Rix, Rachel R; Cutler, G Christopher
2018-02-01
Hormetic preconditioning, whereby exposure to mild stress primes an organism to better tolerate subsequent stress, is well documented. It is unknown if exposure to hormetic concentrations of insecticide can trans-generationally prime insects to better tolerate insecticide exposure, or whether exposure to hormetic concentrations of insecticide can induce mutations in genes responsible for insecticide resistance. Using the aphid Myzus persicae (Sulzer) and the insecticide imidacloprid as a model, we examined if exposure to mildly toxic and hormetic concentrations of imidacloprid reduced aphid susceptibility to insecticides across four generations, and whether such exposures induced mutations in the imidacloprid binding site in post-synaptic nicotinic acetylcholine receptors. Chronic, multigenerational exposure of aphids to hormetic concentrations of imidacloprid primed offspring to better survive exposure to certain concentrations of imidacloprid, but not exposure to spirotetramat, an insecticide with a different mode of action. Exposure to hormetic and mildly toxic concentrations of imidacloprid did not result in mutations in any of the examined nicotinic acetylcholine receptor subunits. Our findings demonstrate that exposure to hormetic concentrations of insecticide can prime insects to better withstand subsequent chemical stress, but this is dependent upon the insecticide exposure scenario, and may be subtle over generations. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.
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Rules for resolving Mendelian inconsistencies in nuclear pedigrees typed for two-allele markers.
Directory of Open Access Journals (Sweden)
Sajjad Ahmad Khan
Full Text Available Gene-mapping studies, regularly, rely on examination for Mendelian transmission of marker alleles in a pedigree as a way of screening for genotyping errors and mutations. For analysis of family data sets, it is, usually, necessary to resolve or remove the genotyping errors prior to consideration. At the Center of Inherited Disease Research (CIDR, to deal with their large-scale data flow, they formalized their data cleaning approach in a set of rules based on PedCheck output. We scrutinize via carefully designed simulations that how well CIDR's data cleaning rules work in practice. We found that genotype errors in siblings are detected more often than in parents for less polymorphic SNPs and vice versa for more polymorphic SNPs. Through computer simulations, we conclude that some of the CIDR's rules work poorly in some circumstances, and we suggest a set of modified data cleaning rules that may work better than CIDR's rules.
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Fernández, E N; Legarra, A; Martínez, R; Sánchez, J P; Baselga, M
2017-06-01
Inbreeding generates covariances between additive and dominance effects (breeding values and dominance deviations). In this work, we developed and applied models for estimation of dominance and additive genetic variances and their covariance, a model that we call "full dominance," from pedigree and phenotypic data. Estimates with this model such as presented here are very scarce both in livestock and in wild genetics. First, we estimated pedigree-based condensed probabilities of identity using recursion. Second, we developed an equivalent linear model in which variance components can be estimated using closed-form algorithms such as REML or Gibbs sampling and existing software. Third, we present a new method to refer the estimated variance components to meaningful parameters in a particular population, i.e., final partially inbred generations as opposed to outbred base populations. We applied these developments to three closed rabbit lines (A, V and H) selected for number of weaned at the Polytechnic University of Valencia. Pedigree and phenotypes are complete and span 43, 39 and 14 generations, respectively. Estimates of broad-sense heritability are 0.07, 0.07 and 0.05 at the base versus 0.07, 0.07 and 0.09 in the final generations. Narrow-sense heritability estimates are 0.06, 0.06 and 0.02 at the base versus 0.04, 0.04 and 0.01 at the final generations. There is also a reduction in the genotypic variance due to the negative additive-dominance correlation. Thus, the contribution of dominance variation is fairly large and increases with inbreeding and (over)compensates for the loss in additive variation. In addition, estimates of the additive-dominance correlation are -0.37, -0.31 and 0.00, in agreement with the few published estimates and theoretical considerations. © 2017 Blackwell Verlag GmbH.
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International Nuclear Information System (INIS)
Yuan Huijun; Chen Jing; Liu Xin; Cheng Jing; Wang Xinjian; Yang Li; Yang Shuzhi; Cao Juyang; Kang Dongyang; Dai Pu; Zha, Suoqiang; Han Dongyi; Young Wieyen; Guan Minxin
2007-01-01
Mutations in mitochondrial DNA are one of the important causes of hearing loss. We report here the clinical, genetic, and molecular characterization of two Han Chinese pedigrees with maternally transmitted aminoglycoside-induced and nonsyndromic bilateral hearing loss. Clinical evaluation revealed the wide range of severity, age-at-onset, and audiometric configuration of hearing impairment in matrilineal relatives in these families. The penetrances of hearing loss in these pedigrees were 20% and 18%, when aminoglycoside-induced deafness was included. When the effect of aminoglycosides was excluded, the penetrances of hearing loss in these seven pedigrees were 10% and 15%. Sequence analysis of the complete mitochondrial genomes in these pedigrees showed the presence of the deafness-associated 12S rRNA C1494T and CO1/tRNA Ser(UCN) G7444A mutations. Their distinct sets of mtDNA polymorphism belonged to Eastern Asian haplogroup C4a1, while other previously identified six Chinese mitochondrial genomes harboring the C1494T mutation belong to haplogroups D5a2, D, R, and F1, respectively. This suggested that the C1494T or G7444A mutation occurred sporadically and multiplied through evolution of the mitochondrial DNA (mtDNA). The absence of functionally significant mutations in tRNA and rRNAs or secondary LHON mutations in their mtDNA suggest that these mtDNA haplogroup-specific variants may not play an important role in the phenotypic expression of the 12S rRNA C1494T and CO1/tRNA Ser(UCN) G7444A mutations in those Chinese families. However, aminoglycosides and other nuclear modifier genes play a modifying role in the phenotypic manifestation of the C1494T mutation in these Chinese families
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Druml, T; Baumung, R; Sölkner, J
2009-10-01
The pedigree of the current Austrian Noriker draught horse population comprising 2808 horses was traced back to the animals considered as founders of this breed. In total, the number of founders was 1991, the maximum pedigree length was 31 generations, with an average of 12.3 complete generations. Population structure in this autochthonous Austrian draught horse breed is defined by seven breeding regions (Carinthia, Lower Austria, Salzburg, Styria, Tyrol, Upper Austria and Vorarlberg) or through six coat colour groups (Bay, Black, Chestnut, Roan, Leopard, Tobiano). Average inbreeding coefficients within the breeding regions ranged from 4.5% to 5.5%; for the colour groups, the coefficients varied from 3.5% to 5.9%. Other measures of genetic variability like the effective number of founders, ancestors and founder genomes revealed a slightly different genetic background of the subpopulations. Average co-ancestries between and within breeding areas showed that the Salzburg population may be considered as the nucleus or original stock whereas all other subpopulations showed high relationship to horses from Salzburg. The target of draught horse breeding in the 21st century does not meet the breeding concept of maximizing genetic gains any more. Stabilizing selection takes place. In this study, we show that demographic factors as well as structure given by different coat colours helped to maintain genetic diversity in this endangered horse breed.
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Chen, Yong; Yang, Fuwei; Zheng, Hexin; Zhu, Ganghua; Hu, Peng; Wu, Weijing
2015-12-01
To explore the molecular etiology of two pedigrees affected with type II Waardenburg syndrome (WS2) and to provide genetic diagnosis and counseling. Blood samples were collected from the proband and his family members. Following extraction of genomic DNA, the coding sequences of PAX3, MITF, SOX10 and SNAI2 genes were amplified with PCR and subjected to DNA sequencing to detect potential mutations. A heterozygous deletional mutation c.649_651delAGA in exon 7 of the MITF gene has been identified in all patients from the first family, while no mutation was found in the other WS2 related genes including PAX3, MITF, SOX10 and SNAI2. The heterozygous deletion mutation c.649_651delAGA in exon 7 of the MITF gene probably underlies the disease in the first family. It is expected that other genes may also underlie WS2.
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Detection of bias in animal model pedigree indices of heifers
Directory of Open Access Journals (Sweden)
M. LIDAUER
2008-12-01
Full Text Available The objective of the study was to test whether the pedigree indices (PI of heifers are biased, and if so, whether the magnitude of the bias varies in different groups of heifers. Therefore, two animal model evaluations with two different data sets were computed. Data with all the records from the national evaluation in December 1994 was used to obtain estimated breeding values (EBV for 305-days' milk yield and protein yield. In the second evaluation, the PIs were estimated for cows calving the first time in 1993 by excluding all their production records from the data. Three different statistics, a simple t-test, the linear regression of EBV on PI, and the polynomial regression of the difference in the predictions (EBV-PI on PI, were computed for three groups of first parity Ayrshire cows: daughters of proven sires, daughters of young sires, and daughters of bull dam candidates. A practically relevant bias was found only in the PIs for the daughters of young sires. On average their PIs were biased upwards by 0.20 standard deviations (78.8 kg for the milk yield and by 0.21 standard deviations (2.2 kg for the protein yield. The polynomial regression analysis showed that the magnitude of the bias in the PIs changed somewhat with the size of the PIs.;
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Baron, Robert V; Conley, Yvette P; Gorin, Michael B; Weeks, Daniel E
2015-03-18
When studying the genetics of a human trait, we typically have to manage both genome-wide and targeted genotype data. There can be overlap of both people and markers from different genotyping experiments; the overlap can introduce several kinds of problems. Most times the overlapping genotypes are the same, but sometimes they are different. Occasionally, the lab will return genotypes using a different allele labeling scheme (for example 1/2 vs A/C). Sometimes, the genotype for a person/marker index is unreliable or missing. Further, over time some markers are merged and bad samples are re-run under a different sample name. We need a consistent picture of the subset of data we have chosen to work with even though there might possibly be conflicting measurements from multiple data sources. We have developed the dbVOR database, which is designed to hold data efficiently for both genome-wide and targeted experiments. The data are indexed for fast retrieval by person and marker. In addition, we store pedigree and phenotype data for our subjects. The dbVOR database allows us to select subsets of the data by several different criteria and to merge their results into a coherent and consistent whole. Data may be filtered by: family, person, trait value, markers, chromosomes, and chromosome ranges. The results can be presented in columnar, Mega2, or PLINK format. dbVOR serves our needs well. It is freely available from https://watson.hgen.pitt.edu/register . Documentation for dbVOR can be found at https://watson.hgen.pitt.edu/register/docs/dbvor.html .
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Bai, Ying; Chen, Yibing; Kong, Xiangdong
2018-02-02
It has been reported that mutations in arginine vasopressin type 2 receptor (AVPR2) cause congenital X-linked nephrogenic diabetes insipidus (NDI). However, only a few cases of AVPR2 deletion have been documented in China. An NDI pedigree was included in this study, including the proband and his mother. All NDI patients had polyuria, polydipsia, and growth retardation. PCR mapping, long range PCR and sanger sequencing were used to identify genetic causes of NDI. A novel 22,110 bp deletion comprising AVPR2 and ARH4GAP4 genes was identified by PCR mapping, long range PCR and sanger sequencing. The deletion happened perhaps due to the 4-bp homologous sequence (TTTT) at the junctions of both 5' and 3' breakpoints. The gross deletion co-segregates with NDI. After analyzing available data of putative clinical signs of AVPR2 and ARH4GAP4 deletion, we reconsider the potential role of AVPR2 deletion in short stature. We identified a novel 22.1-kb deletion leading to X-linked NDI in a Chinese pedigree, which would increase the current knowledge in AVPR2 mutation.
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Bamashmus, M; Downey, L; Inglehearn, C; Gupta, S; Mansfield, D
2000-01-01
BACKGROUND/AIMS—Familial exudative vitreoretinopathy (FEVR) is associated with mutations in the Norrie disease gene in X linked pedigrees and with linkage to the EVR1 locus at 11q13 in autosomal dominant cases. A large autosomal dominant FEVR family was studied, both clinically and by linkage analysis, to determine whether it differed from the known forms of FEVR. METHODS—Affected members and obligate gene carriers from this family were examined by slit lamp biomicroscopy, indirect ophthalmos...
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Li, D.; Fang, N. Z.
2017-12-01
Dallas-Fort Worth Metroplex (DFW) has a population of over 7 million depending on many water supply reservoirs. The reservoir inflow plays a vital role in water supply decision making process and long-term strategic planning for the region. This paper demonstrates a method of utilizing deep learning algorithms and multi-general circulation model (GCM) platform to forecast reservoir inflow for three reservoirs within the DFW: Eagle Mountain Lake, Lake Benbrook and Lake Arlington. Ensemble empirical mode decomposition was firstly employed to extract the features, which were then represented by the deep belief networks (DBNs). The first 75 years of the historical data (1940 -2015) were used to train the model, while the last 2 years of the data (2016-2017) were used for the model validation. The weights of each DBN gained from the training process were then applied to establish a neural network (NN) that was able to forecast reservoir inflow. Feature predictors used for the forecasting model were generated from weather forecast results of the downscaled multi-GCM platform for the North Texas region. By comparing root mean square error (RMSE) and mean bias error (MBE) with the observed data, the authors found that the deep learning with downscaled multi-GCM platform is an effective approach in the reservoir inflow forecasting.
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Bentley, M; Gavin, L; Black, M M; Teti, L
1999-10-01
The early introduction of non-milk foods among African-American infants has been well documented. Several studies report the addition of semi-solids as early as 1-2 weeks of age. This study investigated, through ethnographic, repeat indepth interviews with teen mothers and grandmothers of infants, the determinants of such feeding practices and the inter-generational factors involved in infant feeding decision-making. Nineteen adolescent mothers were recruited from Baltimore City WIC programs. The teen mothers were interviewed in their homes during four separate visits and the grandmothers at least twice. Ethnographic field guides focused on questions about what, why and how infants were fed and on the 'ethnotheories' of parenting and infant care in this population. All interviews were taped and transcripts were analyzed using text retrieval software. Results confirmed that it is the cultural norm to feed cereal in the bottle and to feed other semi-solid foods within the first month of life. Most grandmothers played the dominant role in deciding what the infant should eat and the timing of the introduction of solids. This pattern occurred both because grandmothers had extensive physical access to their grandchildren and because teen mothers were dependent upon grandmothers. The use of qualitative research methods, with an ecological, multi-generational focus, provides a rich description of the context within which infant feeding decisions are made.
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Directory of Open Access Journals (Sweden)
Tom Cattaert
Full Text Available We propose a novel multifactor dimensionality reduction method for epistasis detection in small or extended pedigrees, FAM-MDR. It combines features of the Genome-wide Rapid Association using Mixed Model And Regression approach (GRAMMAR with Model-Based MDR (MB-MDR. We focus on continuous traits, although the method is general and can be used for outcomes of any type, including binary and censored traits. When comparing FAM-MDR with Pedigree-based Generalized MDR (PGMDR, which is a generalization of Multifactor Dimensionality Reduction (MDR to continuous traits and related individuals, FAM-MDR was found to outperform PGMDR in terms of power, in most of the considered simulated scenarios. Additional simulations revealed that PGMDR does not appropriately deal with multiple testing and consequently gives rise to overly optimistic results. FAM-MDR adequately deals with multiple testing in epistasis screens and is in contrast rather conservative, by construction. Furthermore, simulations show that correcting for lower order (main effects is of utmost importance when claiming epistasis. As Type 2 Diabetes Mellitus (T2DM is a complex phenotype likely influenced by gene-gene interactions, we applied FAM-MDR to examine data on glucose area-under-the-curve (GAUC, an endophenotype of T2DM for which multiple independent genetic associations have been observed, in the Amish Family Diabetes Study (AFDS. This application reveals that FAM-MDR makes more efficient use of the available data than PGMDR and can deal with multi-generational pedigrees more easily. In conclusion, we have validated FAM-MDR and compared it to PGMDR, the current state-of-the-art MDR method for family data, using both simulations and a practical dataset. FAM-MDR is found to outperform PGMDR in that it handles the multiple testing issue more correctly, has increased power, and efficiently uses all available information.
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Human lymphocyte polymorphisms detected by quantitative two-dimensional electrophoresis
International Nuclear Information System (INIS)
Goldman, D.; Merril, C.R.
1983-01-01
A survey of 186 soluble lymphocyte proteins for genetic polymorphism was carried out utilizing two-dimensional electrophoresis of 14 C-labeled phytohemagglutinin (PHA)-stimulated human lymphocyte proteins. Nineteen of these proteins exhibited positional variation consistent with independent genetic polymorphism in a primary sample of 28 individuals. Each of these polymorphisms was characterized by quantitative gene-dosage dependence insofar as the heterozygous phenotype expressed approximately 50% of each allelic gene product as was seen in homozygotes. Patterns observed were also identical in monozygotic twins, replicate samples, and replicate gels. The three expected phenotypes (two homozygotes and a heterozygote) were observed in each of 10 of these polymorphisms while the remaining nine had one of the homozygous classes absent. The presence of the three phenotypes, the demonstration of gene-dosage dependence, and our own and previous pedigree analysis of certain of these polymorphisms supports the genetic basis of these variants. Based on this data, the frequency of polymorphic loci for man is: P . 19/186 . .102, and the average heterozygosity is .024. This estimate is approximately 1/3 to 1/2 the rate of polymorphism previously estimated for man in other studies using one-dimensional electrophoresis of isozyme loci. The newly described polymorphisms and others which should be detectable in larger protein surveys with two-dimensional electrophoresis hold promise as genetic markers of the human genome for use in gene mapping and pedigree analyses
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DEFF Research Database (Denmark)
Ribbenstedt, Anton; Mustajärvi, Lukas; Breitholtz, Magnus
2017-01-01
to test the applicability of passive dosing to maintain stable concentrations of the organochlorine bacteriocide triclosan in the water phase during a 6-week multi-generation population development test with the harpacticoid copepod Nitocra spinipes. Triclosan was loaded into silicone (1000 mg), which...... was used as passive dosing phase in the exposure vials. The distribution ratio for triclosan between silicone and water (Dsilicone-water ) was 10466 ± 1927. A population development test was conducted at three concentration levels of triclosan that were measured to be 3-5 µg L(-1) , 7-11 µg L(-1) and 16...... exerted on juvenile development. Progressively lower development index values in the populations exposed to increasing triclosan concentrations suggest developmental retardation. Our results further stress the need for chronic exposure during ecotoxicity testing in chemical risk assessment as even...
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Rankin, William
2017-06-01
The International Map of the World was a hugely ambitious scheme to create standardized maps of the entire world. It was first proposed in 1891 and remained a going concern until 1986. Over the course of the project's official life, nearly every country in the world took part, and map sheets were published showing all but a few areas of the planet. But the project ended quite unceremoniously, repudiated by cartographers and mapping institutions alike, and it is now remembered as a 'sad story' of network failure. How can we evaluate this kind of sprawling, multigenerational project? In order to move beyond practitioners' (and historians') habit of summarizing the entire endeavor using the blunt categories of success and failure, I propose a more temporally aware reading, one that both disaggregates the (persistent) project from the (always changing) network and sees project and network as invertible, with the possibility of zombie projects and negative networks that can remain robust even when disconnected from their original goals. I therefore see the abandonment of the International Map of the World as resulting from vigorous collaboration and new norms in cartography, not from lack of cooperation or other resources. New categories are required for analyzing science over the long durée.
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Multi-generational responses of a marine polychaete to a rapid change in seawater pCO2.
Rodríguez-Romero, Araceli; Jarrold, Michael D; Massamba-N'Siala, Gloria; Spicer, John I; Calosi, Piero
2016-10-01
Little is known of the capacity that marine metazoans have to evolve under rapid p CO 2 changes. Consequently, we reared a marine polychaete, Ophryotrocha labronica , previously cultured for approximately 33 generations under a low/variable pH regime, under elevated and low p CO 2 for six generations. The strain used was found to be tolerant to elevated p CO 2 conditions. In generations F1 and F2 females' fecundity was significantly lower in the low p CO 2 treatment. However, from generation F3 onwards there were no differences between p CO 2 treatments, indicating that trans-generational effects enabled the restoration and maintenance of reproductive output. Whilst the initial fitness recovery was likely driven by trans-generational plasticity (TGP), the results from reciprocal transplant assays, performed using F7 individuals, made it difficult to disentangle between whether TGP had persisted across multiple generations, or if evolutionary adaptation had occurred. Nonetheless, both are important mechanisms for persistence under climate change. Overall, our study highlights the importance of multi-generational experiments in more accurately determining marine metazoans' responses to changes in p CO 2 , and strengthens the case for exploring their use in conservation, by creating specific p CO 2 tolerant strains of keystone ecosystem species.
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Flockhart, D. T. Tyler; Wassenaar, Leonard I.; Martin, Tara G.; Hobson, Keith A.; Wunder, Michael B.; Norris, D. Ryan
2013-01-01
Insect migration may involve movements over multiple breeding generations at continental scales, resulting in formidable challenges to their conservation and management. Using distribution models generated from citizen scientist occurrence data and stable-carbon and -hydrogen isotope measurements, we tracked multi-generational colonization of the breeding grounds of monarch butterflies (Danaus plexippus) in eastern North America. We found that monarch breeding occurrence was best modelled with geographical and climatic variables resulting in an annual breeding distribution of greater than 12 million km2 that encompassed 99% occurrence probability. Combining occurrence models with stable isotope measurements to estimate natal origin, we show that butterflies which overwintered in Mexico came from a wide breeding distribution, including southern portions of the range. There was a clear northward progression of monarchs over successive generations from May until August when reproductive butterflies began to change direction and moved south. Fifth-generation individuals breeding in Texas in the late summer/autumn tended to originate from northern breeding areas rather than regions further south. Although the Midwest was the most productive area during the breeding season, monarchs that re-colonized the Midwest were produced largely in Texas, suggesting that conserving breeding habitat in the Midwest alone is insufficient to ensure long-term persistence of the monarch butterfly population in eastern North America. PMID:23926146
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Directory of Open Access Journals (Sweden)
Paulino Pérez
2010-09-01
Full Text Available The availability of dense molecular markers has made possible the use of genomic selection in plant and animal breeding. However, models for genomic selection pose several computational and statistical challenges and require specialized computer programs, not always available to the end user and not implemented in standard statistical software yet. The R-package BLR (Bayesian Linear Regression implements several statistical procedures (e.g., Bayesian Ridge Regression, Bayesian LASSO in a unified framework that allows including marker genotypes and pedigree data jointly. This article describes the classes of models implemented in the BLR package and illustrates their use through examples. Some challenges faced when applying genomic-enabled selection, such as model choice, evaluation of predictive ability through cross-validation, and choice of hyper-parameters, are also addressed.
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Directory of Open Access Journals (Sweden)
Jason Ezra Hawkes
2013-06-01
Full Text Available Approximately 10% of melanoma cases are familial, but only 25-40% of familial melanoma cases can be attributed to germ-line mutations in the CDKN2A - the most significant high-risk melanoma susceptibility locus identified to date. The pathogenic mutation(s in most of the remaining familial melanoma pedigrees have not yet been identified. The most common mutations in nevi and sporadic melanoma are found in BRAF and NRAS, both of which result in constitutive activation of the MAPK pathway. However, these mutations are not found in uveal melanomas or the intradermal melanocytic proliferations known as blue nevi. Rather, multiple studies report a strong association between these lesions and somatic mutations in Guanine nucleotide-binding protein G(q subunit alpha (GNAQ, Guanine nucleotide-binding protein G(q subunit alpha-11 (GNA11 and BRCA1 associated protein-1 (BAP1. Recently, germ-line mutations in BAP1, the gene encoding a tumor suppressing deubiquitinating enzyme, have been associated with predisposition to a variety of cancers including uveal melanoma, but no studies have examined the association of germ-line mutations in GNAQ and GNA11 with uveal melanoma and blue nevi. We have now done so by sequencing exon 5 of both of these genes in 13 unique familial melanoma pedigrees, members of which have had either uveal or cutaneous melanoma and/or blue nevi. Germ-line DNA from a total of 22 individuals was used for sequencing; however no deleterious mutations were detected. Nevertheless, such candidate gene studies and the discovery of novel germ-line mutations associated with an increased MM susceptibility can lead to a better understanding of the pathways involved in melanocyte transformation, formulation of risk assessment, and the development of specific drug therapies.
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Payne, Jennifer L; Klein, Sarah R; Zamoiski, Rachel B; Zandi, Peter P; Bienvenu, Oscar J; Mackinnon, Dean F; Mondimore, Francis M; Schweizer, Barbara; Swartz, Karen L; Crowe, Raymond P; Scheftner, William A; Weissman, Myrna M; Levinson, Douglas F; DePaulo, J Raymond; Potash, James B
2009-02-01
We sought to determine whether premenstrual mood symptoms exhibit familial aggregation in bipolar disorder or major depression pedigrees. Two thousand eight hundred seventy-six women were interviewed with the Diagnostic Interview for Genetic Studies as part of either the NIMH Genetics Initiative Bipolar Disorder Collaborative study or the Genetics of Early Onset Major Depression (GenRED) study and asked whether they had experienced severe mood symptoms premenstrually. In families with two or more female siblings with bipolar disorder (BP) or major depressive disorder (MDD), we examined the odds of having premenstrual mood symptoms given one or more siblings with these symptoms. For the GenRED MDD sample we also assessed the impact of personality as measured by the NEO-FFI. Premenstrual mood symptoms did not exhibit familial aggregation in families with BP or MDD. We unexpectedly found an association between high NEO openness scores and premenstrual mood symptoms, but neither this factor, nor NEO neuroticism influenced evidence for familial aggregation of symptoms. Limitations include the retrospective interview, the lack of data on premenstrual dysphoric disorder, and the inability to control for factors such as medication use.
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Genetic Candidate Variants in Two Multigenerational Families with Childhood Apraxia of Speech.
Directory of Open Access Journals (Sweden)
Beate Peter
Full Text Available Childhood apraxia of speech (CAS is a severe and socially debilitating form of speech sound disorder with suspected genetic involvement, but the genetic etiology is not yet well understood. Very few known or putative causal genes have been identified to date, e.g., FOXP2 and BCL11A. Building a knowledge base of the genetic etiology of CAS will make it possible to identify infants at genetic risk and motivate the development of effective very early intervention programs. We investigated the genetic etiology of CAS in two large multigenerational families with familial CAS. Complementary genomic methods included Markov chain Monte Carlo linkage analysis, copy-number analysis, identity-by-descent sharing, and exome sequencing with variant filtering. No overlaps in regions with positive evidence of linkage between the two families were found. In one family, linkage analysis detected two chromosomal regions of interest, 5p15.1-p14.1, and 17p13.1-q11.1, inherited separately from the two founders. Single-point linkage analysis of selected variants identified CDH18 as a primary gene of interest and additionally, MYO10, NIPBL, GLP2R, NCOR1, FLCN, SMCR8, NEK8, and ANKRD12, possibly with additive effects. Linkage analysis in the second family detected five regions with LOD scores approaching the highest values possible in the family. A gene of interest was C4orf21 (ZGRF1 on 4q25-q28.2. Evidence for previously described causal copy-number variations and validated or suspected genes was not found. Results are consistent with a heterogeneous CAS etiology, as is expected in many neurogenic disorders. Future studies will investigate genome variants in these and other families with CAS.
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Genetic Candidate Variants in Two Multigenerational Families with Childhood Apraxia of Speech.
Peter, Beate; Wijsman, Ellen M; Nato, Alejandro Q; Matsushita, Mark M; Chapman, Kathy L; Stanaway, Ian B; Wolff, John; Oda, Kaori; Gabo, Virginia B; Raskind, Wendy H
2016-01-01
Childhood apraxia of speech (CAS) is a severe and socially debilitating form of speech sound disorder with suspected genetic involvement, but the genetic etiology is not yet well understood. Very few known or putative causal genes have been identified to date, e.g., FOXP2 and BCL11A. Building a knowledge base of the genetic etiology of CAS will make it possible to identify infants at genetic risk and motivate the development of effective very early intervention programs. We investigated the genetic etiology of CAS in two large multigenerational families with familial CAS. Complementary genomic methods included Markov chain Monte Carlo linkage analysis, copy-number analysis, identity-by-descent sharing, and exome sequencing with variant filtering. No overlaps in regions with positive evidence of linkage between the two families were found. In one family, linkage analysis detected two chromosomal regions of interest, 5p15.1-p14.1, and 17p13.1-q11.1, inherited separately from the two founders. Single-point linkage analysis of selected variants identified CDH18 as a primary gene of interest and additionally, MYO10, NIPBL, GLP2R, NCOR1, FLCN, SMCR8, NEK8, and ANKRD12, possibly with additive effects. Linkage analysis in the second family detected five regions with LOD scores approaching the highest values possible in the family. A gene of interest was C4orf21 (ZGRF1) on 4q25-q28.2. Evidence for previously described causal copy-number variations and validated or suspected genes was not found. Results are consistent with a heterogeneous CAS etiology, as is expected in many neurogenic disorders. Future studies will investigate genome variants in these and other families with CAS.
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Genealogical data in population medical genetics: field guidelines
Directory of Open Access Journals (Sweden)
Fernando A. Poletta
2014-01-01
Full Text Available This is a guide for fieldwork in Population Medical Genetics research projects. Data collection, handling, and analysis from large pedigrees require the use of specific tools and methods not widely familiar to human geneticists, unfortunately leading to ineffective graphic pedigrees. Initially, the objective of the pedigree must be decided, and the available information sources need to be identified and validated. Data collection and recording by the tabulated method is advocated, and the involved techniques are presented. Genealogical and personal information are the two main components of pedigree data. While the latter is unique to each investigation project, the former is solely represented by gametic links between persons. The triad of a given pedigree member and its two parents constitutes the building unit of a genealogy. Likewise, three ID numbers representing those three elements of the triad is the record field required for any pedigree analysis. Pedigree construction, as well as pedigree and population data analysis, varies according to the pre-established objectives, the existing information, and the available resources.
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Basha, Piler Mahaboob; Rai, Puja; Begum, Shabana
2011-12-01
High-fluoride (100 and 200 ppm) water was administered to rats orally to study the fluoride-induced changes on the thyroid hormone status, the histopathology of discrete brain regions, the acetylcholine esterase activity, and the learning and memory abilities in multigeneration rats. Significant decrease in the serum-free thyroxine (FT4) and free triiodothyronine (FT3) levels and decrease in acetylcholine esterase activity in fluoride-treated group were observed. Presence of eosinophilic Purkinje cells, degenerating neurons, decreased granular cells, and vacuolations were noted in discrete brain regions of the fluoride-treated group. In the T-maze experiments, the fluoride-treated group showed poor acquisition and retention and higher latency when compared with the control. The alterations were more profound in the third generation when compared with the first- and second-generation fluoride-treated group. Changes in the thyroid hormone levels in the present study might have imbalanced the oxidant/antioxidant system, which further led to a reduction in learning memory ability. Hence, presence of generational or cumulative effects of fluoride on the development of the offspring when it is ingested continuously through multiple generations is evident from the present study.
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Dreger, Dayna L.; Rimbault, Maud; Davis, Brian W.; Bhatnagar, Adrienne; Parker, Heidi G.
2016-01-01
ABSTRACT In the decade following publication of the draft genome sequence of the domestic dog, extraordinary advances with application to several fields have been credited to the canine genetic system. Taking advantage of closed breeding populations and the subsequent selection for aesthetic and behavioral characteristics, researchers have leveraged the dog as an effective natural model for the study of complex traits, such as disease susceptibility, behavior and morphology, generating unique contributions to human health and biology. When designing genetic studies using purebred dogs, it is essential to consider the unique demography of each population, including estimation of effective population size and timing of population bottlenecks. The analytical design approach for genome-wide association studies (GWAS) and analysis of whole-genome sequence (WGS) experiments are inextricable from demographic data. We have performed a comprehensive study of genomic homozygosity, using high-depth WGS data for 90 individuals, and Illumina HD SNP data from 800 individuals representing 80 breeds. These data were coupled with extensive pedigree data analyses for 11 breeds that, together, allowed us to compute breed structure, demography, and molecular measures of genome diversity. Our comparative analyses characterize the extent, formation and implication of breed-specific diversity as it relates to population structure. These data demonstrate the relationship between breed-specific genome dynamics and population architecture, and provide important considerations influencing the technological and cohort design of association and other genomic studies. PMID:27874836
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DEFF Research Database (Denmark)
Frenck, Georg; van der Linden, Leon; Mikkelsen, Teis Nørgaard
2013-01-01
different temperature regimes. To reveal phenotypic divergence at the manipulated [CO2] and temperature conditions, a full-factorial natural selection regime was established in a phytotron environment over the range of four generations. It is demonstrated that a directional response to selection at elevated......Functional plant traits are likely to adapt under the sustained pressure imposed by environmental changes through natural selection. Employing Brassica napus as a model, a multi-generational study was performed to investigate the potential trajectories of selection at elevated [CO2] in two...... subjected to increased levels of CO2 over the generational range investigated. The results of this study suggest that phenotypic divergence of plants selected under elevated atmospheric CO2 concentration may drive the future functions of plant productivity to be different from projections that do...
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Directory of Open Access Journals (Sweden)
Zhang Yanming
2010-11-01
Full Text Available Abstract Background The plateau pika (Ochotona curzoniae is an underground-dwelling mammal, native to the Tibetan plateau of China. A set of 10 polymorphic microsatellite loci has been developed earlier. Its reliability for parentage assignment has been tested in a plateau pika population. Two family groups with a known pedigree were used to validate the power of this set of markers. Results The error in parentage assignment using a combination of these 10 loci was very low as indicated by their power of discrimination (0.803 - 0.932, power of exclusion (0.351 - 0.887, and an effectiveness of the combined probability of exclusion in parentage assignment of 99.999%. Conclusion All the offspring of a family could be assigned to their biological mother; and their father or relatives could also be identified. This set of markers therefore provides a powerful and efficient tool for parentage assignment and other population analyses in the plateau pika.
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Timing of the uv mutagenesis in yeast: a pedigree analysis of induced recessive mutation
International Nuclear Information System (INIS)
James, A.P.; Kilbey, B.J.
1977-01-01
The mechanism of uv-induced mutation in eukaryotes was studied in individual yeast cells by a procedure that combined pedigree analysis and tetrad analysis. The technique involved the induction of recessive lethals and semilethals in G1 diploid cells. Induced frequencies were 25 and 61% at survival levels of 90 and 77%, respectively. No evidence of gross chromosome aberrations was detected. Recessive mutations that affect only one strand or that affect both strands of the DNA molecule are induced much at random among a population of cells, and both types can occur within the same cell. However, the data confirm that two-strand mutations are in the majority after a low level of irradiation. The simplest explanation involves a mechanism whereby most mutations are fixed in both strands prior to the first round of post-irradiation DNA replication. The recessive mutational consequences of irradiation are exhausted at the conclusion of the first post-irradiation cell division, although dominant-lethal sectoring continues at a high level through the second post-irradiation division. It is concluded that pyrimidine dimers that persist to the second round of DNA replication are rare or ineffective
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The timing of UV mutagenesis in yeast: a pedigree analysis of induced recessive mutation.
James, A P; Kilbey, B J
1977-10-01
The mechanism of UV-induced mutation in eukaryotes was studied in individual yeast cells by a procedure that combined pedigree analysis and tetrad analysis. The technique involved the induction of recessive lethals and semilethals in G1 diploid cells. Induced frequencies were 25 and 61 percent at survival levels of 90 and 77 percent, respectively. No evidence of gross chromosome aberrations was detected. Recessive mutations that affect only one strand or that affect both strands of the DNA molecule are induced much at random among a population of cells, and both types can occur within the same cell. However, the data confirm that two-strand mutations are in the majority after a low level of irradiation. The simplest explanation involves a mechanism whereby most mutations are fixed in both strands prior to the first round of post-irradiation DNA replication. The recessive mutational consequences of irradiation are exhausted at the conclusion of the first post-irradiation cell division, although dominant-lethal sectoring continues at a high level through the second post-irradiation division. It is concluded that pyrimidine dimers that persist to the second round of DNA replication are rare or ineffective.
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2013-06-01
This paper explores the analysis of an obese woman who came to experience her flesh as a bodying forth of personal and multigenerational family and cultural experiences of helplessness. The paper discusses the ideas and images that formed the basis of how I engaged with these themes as they presented countertransferentially. My thesis is that clinical approaches which draw on spatial metaphors for the psyche offer valuable tools for working with people whose inner world expresses itself somatically because such metaphors can be used to engage simultaneously with the personal, cultural, and ancestral dimensions of these unconscious communications. The paper builds on Jung's view of the psyche as comprised of pockets of inner otherness (complexes), on Redfearn's image of psyche as landscape-like and on Samuels' thinking on embodied countertransference and on the political psyche. It also draws on Butler's work on the body as a social phenomenon and on the theme of being a helpless non-person or nobody as explored in Tom Stoppard's play Rosencrantz and Guildenstern are Dead which retells Shakespeare's Hamlet from the perspective of two of the play's 'bit' characters. © 2013, The Society of Analytical Psychology.
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Directory of Open Access Journals (Sweden)
IDG Ugrasena
2017-02-01
Full Text Available The molecular and pedigree analyses in a Javanese Chinese family were carried oul on glucose-6-phosphate dehydrogenase deficiencies. By method of MPTP scanning without the sequencing steps, those variants could be confirmed. Two out of three sons were clinically jaundiced at birth due to G6PD deficiency and identified to have a G to T nucleotide change al 1376th nucleotide 01 the G6PD gene (GI376T, corresponding to G6PD Canton. Another son was also identified to have a C to T nucleotide change at 1311st nucleotide 01 the G6PD gene (CI311T, corresponding to a Silent mutation. Their father was normal, but their mother obsorved to have the heleromutation 01 G1376T (G6PD Canton and C1311T (a Silent mutation.
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International Nuclear Information System (INIS)
Guan Rui; Wang Wenxiong
2006-01-01
We investigated the effects of genotype (two different clones) and multigenerational Cd-exposure history on Cd toxicity, individual fitness, and biokinetics in populations of a freshwater cladoceran Daphnia magna. The adults of the tolerant (T) clone had longer mean-survival-time than the sensitive (S) clone in both control groups (without Cd-exposure) and continuous Cd-exposure groups, but the two clones showed comparable resistances to acute Cd stress in the recovery groups. The body concentration of metallothionein (MT) played a critical role in handling Cd stress, which mainly accounted for the significant difference between the two clones in terms of survival distribution. High comparability of these two clones in individual fitness parameters and biokinetics suggested that these parameters are unlikely driven by genetic variation. For each specific clone, continuous Cd-exposure inhibited the animal growth, elevated the MT induction, and increased the Cd uptake rate (ingestion rate, assimilation efficiency from dietary phase, and uptake rate from dissolved phase), all of which enhanced the weight-specific Cd accumulation in daphnids' bodies. The strong dependence of biokinetic parameters on environmental factors (e.g., food concentrations, pH, dissolved or dietary metal concentration, and metal exposure histories) rather than on genotypes implied the great potential of using biokinetics in inter-lab comparisons and environmental risk assessments
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Guan, Rui; Wang, Wen-Xiong
2006-03-10
We investigated the effects of genotype (two different clones) and multigenerational Cd-exposure history on Cd toxicity, individual fitness, and biokinetics in populations of a freshwater cladoceran Daphnia magna. The adults of the tolerant (T) clone had longer mean-survival-time than the sensitive (S) clone in both control groups (without Cd-exposure) and continuous Cd-exposure groups, but the two clones showed comparable resistances to acute Cd stress in the recovery groups. The body concentration of metallothionein (MT) played a critical role in handling Cd stress, which mainly accounted for the significant difference between the two clones in terms of survival distribution. High comparability of these two clones in individual fitness parameters and biokinetics suggested that these parameters are unlikely driven by genetic variation. For each specific clone, continuous Cd-exposure inhibited the animal growth, elevated the MT induction, and increased the Cd uptake rate (ingestion rate, assimilation efficiency from dietary phase, and uptake rate from dissolved phase), all of which enhanced the weight-specific Cd accumulation in daphnids' bodies. The strong dependence of biokinetic parameters on environmental factors (e.g., food concentrations, pH, dissolved or dietary metal concentration, and metal exposure histories) rather than on genotypes implied the great potential of using biokinetics in inter-lab comparisons and environmental risk assessments.
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Kullar, Peter J; Gomez-Duran, Aurora; Gammage, Payam A; Garone, Caterina; Minczuk, Michal; Golder, Zoe; Wilson, Janet; Montoya, Julio; Häkli, Sanna; Kärppä, Mikko; Horvath, Rita; Majamaa, Kari; Chinnery, Patrick F
2018-01-01
The m.1555A>G mtDNA variant causes maternally inherited deafness, but the reasons for the highly variable clinical penetrance are not known. Exome sequencing identified a heterozygous start loss mutation in SSBP1, encoding the single stranded binding protein 1 (SSBP1), segregating with hearing loss in a multi-generational family transmitting m.1555A>G, associated with mtDNA depletion and multiple deletions in skeletal muscle. The SSBP1 mutation reduced steady state SSBP1 levels leading to a perturbation of mtDNA metabolism, likely compounding the intra-mitochondrial translation defect due to m.1555A>G in a tissue-specific manner. This family demonstrates the importance of rare trans-acting genetic nuclear modifiers in the clinical expression of mtDNA disease. © The Author (2017). Published by Oxford University Press on behalf of the Guarantors of Brain.
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Male-to-male transmission in extended pedigrees with multiple cases of autism
Energy Technology Data Exchange (ETDEWEB)
Hallmayer, J.; Spiker, D.; Lotspeich, L. [Stanford Univ., CA (United States)] [and others
1996-02-16
Despite strong genetic influences in autism, the true mode of inheritance remains unknown. Sex differences in autism have been described in both singleton and multiplex families: boys outnumber girls by 3 or 4 to 1, and so a sex-linked mode of transmission must also be considered. The key characteristic of X-linkage is that all sons of affected men are unaffected (no male-to-male transmission). In the present study, which is part of an ongoing linkage project in autism, we describe 77 multiplex autism families, 11 of who are affected cousin or half-sibling families. By using these families, it is possible to trace the path of genetic transmission and observe whether the hypothesis of X-linkage is tenable. Of 11 extended pedigrees from 77 multiplex families, six show male-to-male transmission; in these families, X-linkage can be excluded as the genetic basis for their autism. The data from the other five families are compatible with either an autosomal or an X-linked mode of transmission. The key point to emerge, then, is that autism cannot be exclusively an X-linked disorder; there must be an autosomal mode of transmission at least in some families. Thus we must consider the alternative hypotheses that autism is either entirely autosomal, or it is genetically heterogeneous, involving at least one autosomal locus with gender-specific expression, as well as a possible locus on the X-chromosome. 28 refs., 1 fig.
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Mitochondrial DNA sequence characteristics modulate the size of the genetic bottleneck.
Wilson, Ian J; Carling, Phillipa J; Alston, Charlotte L; Floros, Vasileios I; Pyle, Angela; Hudson, Gavin; Sallevelt, Suzanne C E H; Lamperti, Costanza; Carelli, Valerio; Bindoff, Laurence A; Samuels, David C; Wonnapinij, Passorn; Zeviani, Massimo; Taylor, Robert W; Smeets, Hubert J M; Horvath, Rita; Chinnery, Patrick F
2016-03-01
With a combined carrier frequency of 1:200, heteroplasmic mitochondrial DNA (mtDNA) mutations cause human disease in ∼1:5000 of the population. Rapid shifts in the level of heteroplasmy seen within a single generation contribute to the wide range in the severity of clinical phenotypes seen in families transmitting mtDNA disease, consistent with a genetic bottleneck during transmission. Although preliminary evidence from human pedigrees points towards a random drift process underlying the shifting heteroplasmy, some reports describe differences in segregation pattern between different mtDNA mutations. However, based on limited observations and with no direct comparisons, it is not clear whether these observations simply reflect pedigree ascertainment and publication bias. To address this issue, we studied 577 mother-child pairs transmitting the m.11778G>A, m.3460G>A, m.8344A>G, m.8993T>G/C and m.3243A>G mtDNA mutations. Our analysis controlled for inter-assay differences, inter-laboratory variation and ascertainment bias. We found no evidence of selection during transmission but show that different mtDNA mutations segregate at different rates in human pedigrees. m.8993T>G/C segregated significantly faster than m.11778G>A, m.8344A>G and m.3243A>G, consistent with a tighter mtDNA genetic bottleneck in m.8993T>G/C pedigrees. Our observations support the existence of different genetic bottlenecks primarily determined by the underlying mtDNA mutation, explaining the different inheritance patterns observed in human pedigrees transmitting pathogenic mtDNA mutations. © The Author 2016. Published by Oxford University Press.
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Madsen, Thomas; Braun, Danielle; Peng, Gang; Parmigiani, Giovanni; Trippa, Lorenzo
2018-06-25
The Elston-Stewart peeling algorithm enables estimation of an individual's probability of harboring germline risk alleles based on pedigree data, and serves as the computational backbone of important genetic counseling tools. However, it remains limited to the analysis of risk alleles at a small number of genetic loci because its computing time grows exponentially with the number of loci considered. We propose a novel, approximate version of this algorithm, dubbed the peeling and paring algorithm, which scales polynomially in the number of loci. This allows extending peeling-based models to include many genetic loci. The algorithm creates a trade-off between accuracy and speed, and allows the user to control this trade-off. We provide exact bounds on the approximation error and evaluate it in realistic simulations. Results show that the loss of accuracy due to the approximation is negligible in important applications. This algorithm will improve genetic counseling tools by increasing the number of pathogenic risk alleles that can be addressed. To illustrate we create an extended five genes version of BRCAPRO, a widely used model for estimating the carrier probabilities of BRCA1 and BRCA2 risk alleles and assess its computational properties. © 2018 WILEY PERIODICALS, INC.
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A colony of dog guides: analysis of the genetic variability assessed by pedigree data
Directory of Open Access Journals (Sweden)
Roberta Ciampolini
2010-01-01
Full Text Available The study presents the analysis of the genetic variability in a colony of dog guides. Three breeds, Labrador (L, Golden Retriever (GR, and German Shepherd (GS, were evaluated. Pedigrees data on 370 L, 260 GR, and 85 GS dogs bred for guide by the National Guide Dog School (SNCG of Scandicci (Florence, Italy were used. Data were available beginning from 1994. The average coefficient of coancestry and the mean F were 0.8% and 0.45% in GR, 0.7% and 0.38% in L, 1.0% and 0.49% in GS, respectively. The rate of increase in inbreeding was lower in L population (0.17 than in GR population (0.54, while in GS only the dogs with 5 e 7 traced generations resulted inbred. The results of this research point out that the genetic management of the dogs seems to be carefully and rationally monitored. Nevertheless, the population that may require a greater attention seems to be the GR, where a higher increase of the coefficient of inbreeding per generation is observed; therefore, the importation of germplasm from other working dogs is desirable in order to avoid in future an excessive increase of the inbreeding that could lead to adverse consequences for dogs health and fertility.
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The double pedigree: a method for studying culturally and genetically inherited behavior in tandem.
Directory of Open Access Journals (Sweden)
Etienne Danchin
Full Text Available Transgenerational sources of biological variation have been at the center of evolutionary studies ever since Darwin and Wallace identified natural selection. This is because evolution can only operate on traits whose variation is transmitted, i.e. traits that are heritable. The discovery of genetic inheritance has led to a semantic shift, resulting in the tendency to consider that only genes are inherited across generations. Today, however, concepts of heredity are being broadened again to integrate the accruing evidence of non-genetic inheritance, and many evolutionary biologists are calling for the inclusion of non-genetic inheritance into an inclusive evolutionary synthesis. Here, we focus on social heredity and its role in the inheritance of behavioral traits. We discuss quantitative genetics methods that might allow us to disentangle genetic and non-genetic transmission in natural populations with known pedigrees. We then propose an experimental design based on cross-fostering among animal cultures, environments and families that has the potential to partition inherited phenotypic variation into socially (i.e. culturally and genetically inherited components. This approach builds towards a new conceptual framework based on the use of an extended version of the animal model of quantitative genetics to integrate genetic and cultural components of behavioral inheritance.
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Corry, Justine; Green, Melissa; Roberts, Gloria; Fullerton, Janice M; Schofield, Peter R; Mitchell, Philip B
2017-10-06
Bipolar disorder (BD) and the anxiety disorders are highly comorbid. The present study sought to examine perfectionism and goal attainment values as potential mechanisms of known associations between anxiety, stress and BD symptomatology. Measures of perfectionism and goal attainment values were administered to 269 members of BD pedigrees, alongside measures of anxiety and stress, and BD mood symptoms. Regression analyses were used to determine whether perfectionism and goal attainment values were related to depressive and (hypo)manic symptoms; planned mediation models were then used to test the potential for perfectionism to mediate associations between anxiety/stress and BD symptoms. Self-oriented perfectionism was associated with chronic depressive symptoms; socially-prescribed perfectionism was associated with chronic (hypo)manic symptoms. Self-oriented perfectionism mediated relationships between anxiety/stress and chronic depressive symptoms even after controlling for chronic hypomanic symptoms. Similarly, socially-prescribed perfectionism mediated associations between anxiety/stress and chronic hypomanic symptoms after controlling for chronic depressive symptoms. Goal attainment beliefs were not uniquely associated with chronic depressive or (hypo)manic symptoms. Cognitive styles of perfectionism may explain the co-occurrence of anxiety and stress symptoms and BD symptoms. Psychological interventions for anxiety and stress symptoms in BD might therefore address perfectionism in attempt to reduce depression and (hypo)manic symptoms in addition to appropriate pharmacotherapy.
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Laffin, Jennifer J S; Raca, Gordana; Jackson, Craig A; Strand, Edythe A; Jakielski, Kathy J; Shriberg, Lawrence D
2012-11-01
The goal of this study was to identify new candidate genes and genomic copy-number variations associated with a rare, severe, and persistent speech disorder termed childhood apraxia of speech. Childhood apraxia of speech is the speech disorder segregating with a mutation in FOXP2 in a multigenerational London pedigree widely studied for its role in the development of speech-language in humans. A total of 24 participants who were suspected to have childhood apraxia of speech were assessed using a comprehensive protocol that samples speech in challenging contexts. All participants met clinical-research criteria for childhood apraxia of speech. Array comparative genomic hybridization analyses were completed using a customized 385K Nimblegen array (Roche Nimblegen, Madison, WI) with increased coverage of genes and regions previously associated with childhood apraxia of speech. A total of 16 copy-number variations with potential consequences for speech-language development were detected in 12 or half of the 24 participants. The copy-number variations occurred on 10 chromosomes, 3 of which had two to four candidate regions. Several participants were identified with copy-number variations in two to three regions. In addition, one participant had a heterozygous FOXP2 mutation and a copy-number variation on chromosome 2, and one participant had a 16p11.2 microdeletion and copy-number variations on chromosomes 13 and 14. Findings support the likelihood of heterogeneous genomic pathways associated with childhood apraxia of speech.
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Multi-generational drinking of bottled low mineral water impairs bone quality in female rats.
Directory of Open Access Journals (Sweden)
Zhiqun Qiu
Full Text Available Because of reproductions and hormone changes, females are more sensitive to bone mineral loss during their lifetime. Bottled water has become more popular in recent years, and a large number of products are low mineral water. However, research on the effects of drinking bottled low mineral water on bone health is sparse.To elucidate the skeletal effects of multi-generational bottled water drinking in female rats.Rats continuously drank tap water (TW, bottled natural water (bNW, bottled mineralized water (bMW, or bottled purified water (bPW for three generations.The maximum deflection, elastic deflection, and ultimate strain of the femoral diaphysis in the bNW, bMW, and bPW groups and the fracture strain in the bNW and bMW groups were significantly decreased. The tibiae calcium levels in both the bNW and bPW groups were significantly lower than that in the TW group. The tibiae and teeth magnesium levels in both the bNW and bPW groups were significantly lower than those in the TW group. The collagen turnover markers PICP (in both bNW and bPW groups were significantly lower than that in the TW group. In all three low mineral water groups, the 1,25-dihydroxy-vitamin D levels were significantly lower than those in the TW group.Long-term drinking of low mineral water may disturb bone metabolism and biochemical properties and therefore weaken biomechanical bone properties in females. Drinking tap water, which contains adequate minerals, was found to be better for bone health. To our knowledge, this is the first report on drinking bottled low mineral water and female bone quality on three generation model.
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Energy Technology Data Exchange (ETDEWEB)
Lin, Dolly; Hubbes, M.; Zsuffa, L. [Toronto Univ., ON (Canada). Faculty of Forestry; Tsarouhas, V.; Gullberg, U. [Swedish Univ. of Agricultural Sciences, Uppsala (Sweden). Dept. of Forest Genetics; Howe, G.; Hackett, W.; Gardner, G.; Furnier, G. [Minnesota Univ., St. Paul, MN (United States). Dept. of Forest Resources; Tuskan, G. [Oak Ridge National Lab., TN (United States)
1998-12-31
Molecular characterization of advanced-generation pedigrees and evaluation of cold tolerance are two aspects of Populus and Salix genetic improvement programmes worldwide that have traditionally received little emphasis. As such, chloroplast DNA markers were tested as a means of determining multi-generation parental contributions to hybrid progeny. Likewise, greenhouse, growth chamber and field studies were used to assess cold tolerance in Populus and Salix. Chloroplast DNA markers did not reveal size polymorphisms among four tested Populus species, but did produce sequence polymorphisms between P. maximowiczii and P. trichocarpa. Additional crosses between multiple genotypes from each species are being used to evaluate the utility of the detected polymorphism for ascertaining parentage within interspecific crosses. Short-day, cold tolerance greenhouse studies revealed that bud set date and frost damage are moderately heritable and genetically correlated in Populus. The relationship between greenhouse and field studies suggests that factors other than short days contribute to cold tolerance in Populus. In Salix, response to artificial fall conditioning varied among full-sibling families, with the fastest growing family displaying the greatest amount of cold tolerance 26 refs, 3 tabs
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International Nuclear Information System (INIS)
Middeldorp, Anneke; Wijnen, Juul T; Wezel, Tom van; Jagmohan-Changur, Shantie; Helmer, Quinta; Klift, Heleen M van der; Tops, Carli MJ; Vasen, Hans FA; Devilee, Peter; Morreau, Hans; Houwing-Duistermaat, Jeanine J
2007-01-01
The apparent dominant model of colorectal cancer (CRC) inheritance in several large families, without mutations in known CRC susceptibility genes, suggests the presence of so far unidentified genes with strong or moderate effect on the development of CRC. Linkage analysis could lead to identification of susceptibility genes in such families. In comparison to classical linkage analysis with multi-allelic markers, single nucleotide polymorphism (SNP) arrays have increased information content and can be processed with higher throughput. Therefore, SNP arrays can be excellent tools for linkage analysis. However, the vast number of SNPs on the SNP arrays, combined with large informative pedigrees (e.g. >35–40 bits), presents us with a computational complexity that is challenging for existing statistical packages or even exceeds their capacity. We therefore setup a procedure for linkage analysis in large pedigrees and validated the method by genotyping using SNP arrays of a colorectal cancer family with a known MLH1 germ line mutation. Quality control of the genotype data was performed in Alohomora, Mega2 and SimWalk2, with removal of uninformative SNPs, Mendelian inconsistencies and Mendelian consistent errors, respectively. Linkage disequilibrium was measured by SNPLINK and Merlin. Parametric linkage analysis using two flanking markers was performed using MENDEL. For multipoint parametric linkage analysis and haplotype analysis, SimWalk2 was used. On chromosome 3, in the MLH1-region, a LOD score of 1.9 was found by parametric linkage analysis using two flanking markers. On chromosome 11 a small region with LOD 1.1 was also detected. Upon linkage disequilibrium removal, multipoint linkage analysis yielded a LOD score of 2.1 in the MLH1 region, whereas the LOD score dropped to negative values in the region on chromosome 11. Subsequent haplotype analysis in the MLH1 region perfectly matched the mutation status of the family members. We developed a workflow for linkage
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Novel pedigree analysis implicates DNA repair and chromatin remodeling in multiple myeloma risk.
Waller, Rosalie G; Darlington, Todd M; Wei, Xiaomu; Madsen, Michael J; Thomas, Alun; Curtin, Karen; Coon, Hilary; Rajamanickam, Venkatesh; Musinsky, Justin; Jayabalan, David; Atanackovic, Djordje; Rajkumar, S Vincent; Kumar, Shaji; Slager, Susan; Middha, Mridu; Galia, Perrine; Demangel, Delphine; Salama, Mohamed; Joseph, Vijai; McKay, James; Offit, Kenneth; Klein, Robert J; Lipkin, Steven M; Dumontet, Charles; Vachon, Celine M; Camp, Nicola J
2018-02-01
The high-risk pedigree (HRP) design is an established strategy to discover rare, highly-penetrant, Mendelian-like causal variants. Its success, however, in complex traits has been modest, largely due to challenges of genetic heterogeneity and complex inheritance models. We describe a HRP strategy that addresses intra-familial heterogeneity, and identifies inherited segments important for mapping regulatory risk. We apply this new Shared Genomic Segment (SGS) method in 11 extended, Utah, multiple myeloma (MM) HRPs, and subsequent exome sequencing in SGS regions of interest in 1063 MM / MGUS (monoclonal gammopathy of undetermined significance-a precursor to MM) cases and 964 controls from a jointly-called collaborative resource, including cases from the initial 11 HRPs. One genome-wide significant 1.8 Mb shared segment was found at 6q16. Exome sequencing in this region revealed predicted deleterious variants in USP45 (p.Gln691* and p.Gln621Glu), a gene known to influence DNA repair through endonuclease regulation. Additionally, a 1.2 Mb segment at 1p36.11 is inherited in two Utah HRPs, with coding variants identified in ARID1A (p.Ser90Gly and p.Met890Val), a key gene in the SWI/SNF chromatin remodeling complex. Our results provide compelling statistical and genetic evidence for segregating risk variants for MM. In addition, we demonstrate a novel strategy to use large HRPs for risk-variant discovery more generally in complex traits.
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Novel pedigree analysis implicates DNA repair and chromatin remodeling in multiple myeloma risk.
Directory of Open Access Journals (Sweden)
Rosalie G Waller
2018-02-01
Full Text Available The high-risk pedigree (HRP design is an established strategy to discover rare, highly-penetrant, Mendelian-like causal variants. Its success, however, in complex traits has been modest, largely due to challenges of genetic heterogeneity and complex inheritance models. We describe a HRP strategy that addresses intra-familial heterogeneity, and identifies inherited segments important for mapping regulatory risk. We apply this new Shared Genomic Segment (SGS method in 11 extended, Utah, multiple myeloma (MM HRPs, and subsequent exome sequencing in SGS regions of interest in 1063 MM / MGUS (monoclonal gammopathy of undetermined significance-a precursor to MM cases and 964 controls from a jointly-called collaborative resource, including cases from the initial 11 HRPs. One genome-wide significant 1.8 Mb shared segment was found at 6q16. Exome sequencing in this region revealed predicted deleterious variants in USP45 (p.Gln691* and p.Gln621Glu, a gene known to influence DNA repair through endonuclease regulation. Additionally, a 1.2 Mb segment at 1p36.11 is inherited in two Utah HRPs, with coding variants identified in ARID1A (p.Ser90Gly and p.Met890Val, a key gene in the SWI/SNF chromatin remodeling complex. Our results provide compelling statistical and genetic evidence for segregating risk variants for MM. In addition, we demonstrate a novel strategy to use large HRPs for risk-variant discovery more generally in complex traits.
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Directory of Open Access Journals (Sweden)
Mojca Simčič
Full Text Available The aim of this study was to obtain unbiased estimates of the diversity parameters, the population history, and the degree of admixture in Cika cattle which represents the local admixed breeds at risk of extinction undergoing challenging conservation programs. Genetic analyses were performed on the genome-wide Single Nucleotide Polymorphism (SNP Illumina Bovine SNP50 array data of 76 Cika animals and 531 animals from 14 reference populations. To obtain unbiased estimates we used short haplotypes spanning four markers instead of single SNPs to avoid an ascertainment bias of the BovineSNP50 array. Genome-wide haplotypes combined with partial pedigree and type trait classification show the potential to improve identification of purebred animals with a low degree of admixture. Phylogenetic analyses demonstrated unique genetic identity of Cika animals. Genetic distance matrix presented by rooted Neighbour-Net suggested long and broad phylogenetic connection between Cika and Pinzgauer. Unsupervised clustering performed by the admixture analysis and two-dimensional presentation of the genetic distances between individuals also suggest Cika is a distinct breed despite being similar in appearance to Pinzgauer. Animals identified as the most purebred could be used as a nucleus for a recovery of the native genetic background in the current admixed population. The results show that local well-adapted strains, which have never been intensively managed and differentiated into specific breeds, exhibit large haplotype diversity. They suggest a conservation and recovery approach that does not rely exclusively on the search for the original native genetic background but rather on the identification and removal of common introgressed haplotypes would be more powerful. Successful implementation of such an approach should be based on combining phenotype, pedigree, and genome-wide haplotype data of the breed of interest and a spectrum of reference breeds which
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Energy Technology Data Exchange (ETDEWEB)
Griffith, A.J.; Burgess, D.L.; Kohrman, D.C.; Yu, J. [Univ. of Michigan, Ann Arbor, MI (United States)] [and others
1996-06-15
The transgene-induced mutation 9257 and the spontaneous mutation twirler cause craniofacial and inner ear malformations and are located on mouse chromosome 18 near the ataxia locus ax. To map the human homolog of 9257, a probe from the transgene insertion site was used to screen a human genomic library. Analysis of a cross-hybridizing human clone identified a 3-kb conserved sequence block that does not appear to contain protein coding sequence. Analysis of somatic cell hybrid panels assigned the human locus to 18q11. The polymorphic microsatellite markers D18S1001 and D18S1002 were isolated from the human locus and mapped by linkage analysis using the CEPH pedigrees. The 9257 locus maps close to the centromeres of human chromosome 18q and mouse chromosome 18 at the proximal end of a conserved linkage group. To evaluate the role of this locus in human craniofacial disorders, linkage to D18S1002 was tested in 11 families with autosomal dominant nonsyndromic cleft lip and palate and 3 families with autosomal dominant cleft palate only. Obligatory recombinants were observed in 8 of the families, and negative lod scores from the other families indicated that these disorders are not linked to the chromosome 18 loci. 23 refs., 4 figs., 2 tabs.
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Guo, Wei-Hong; Li, Qiang; Wei, Hong-Yan; Lu, Hong-Yan; Qu, Hui-Qi; Zhu, Mei
2016-10-01
Polyuria and polydipsia are the characteristics of congenital nephrogenic diabetes insipidus (CNDI). Approximately 90% of all patients with CNDI have X-linked hereditary disease, which is due to a mutation of the arginine vasopressin receptor 2 ( AVPR2) gene. This case report describes a 54-year-old male with polyuria and polydipsia and several male members of his pedigree who had the same symptoms. The proband was diagnosed with diabetes insipidus using a water-deprivation and arginine vasopressin stimulation test. Genomic DNA from the patient and his family members was extracted and the AVPR2 gene was sequenced. A novel missense mutation of a cytosine to guanine transition at position 972 (c.972C > G) was found, which resulted in the substitution of isoleucine for methionine at amino acid position 324 (p.I324M) in the seventh transmembrane domain of the protein. The proband's mother and daughter were heterozygous for this mutation. The novel mutation of the AVPR2 gene further broadens the phenotypic spectrum of the AVPR2 gene.
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Broad-scale recombination patterns underlying proper disjunction in humans.
Directory of Open Access Journals (Sweden)
Adi Fledel-Alon
2009-09-01
Full Text Available Although recombination is essential to the successful completion of human meiosis, it remains unclear how tightly the process is regulated and over what scale. To assess the nature and stringency of constraints on human recombination, we examined crossover patterns in transmissions to viable, non-trisomic offspring, using dense genotyping data collected in a large set of pedigrees. Our analysis supports a requirement for one chiasma per chromosome rather than per arm to ensure proper disjunction, with additional chiasmata occurring in proportion to physical length. The requirement is not absolute, however, as chromosome 21 seems to be frequently transmitted properly in the absence of a chiasma in females, a finding that raises the possibility of a back-up mechanism aiding in its correct segregation. We also found a set of double crossovers in surprisingly close proximity, as expected from a second pathway that is not subject to crossover interference. These findings point to multiple mechanisms that shape the distribution of crossovers, influencing proper disjunction in humans.
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Mortality and morbidity due to gastric dilatation-volvulus syndrome in pedigree dogs in the UK.
Evans, Katy M; Adams, Vicki J
2010-07-01
To estimate breed-specific risk of death due to, and prevalence of, gastric dilatation-volvulus (GDV) in UK pedigree dogs. Data were available on the reported cause of and age at death and occurrence of and age at diagnosis of disease from the 2004 purebred dog health survey. A total of 15,881 dogs of 165 breeds had died in the previous 10 years; GDV was the cause of death in 65 breeds. There were 36,006 live dogs of 169 breeds of which 48 breeds had experienced > or =1 episodes of GDV. Prevalence ratios were used to estimate breed-specific GDV mortality and morbidity risks. Gastric dilatation-volvulus was the cause of death for 389 dogs, representing 2.5% (95% CI: 2.2-2.7) of all deaths reported and the median age at death was 7.92 years. There were 253 episodes in 238 live dogs. The median age at first diagnosis was five years. Breeds at greatest risk of GDV mortality were the bloodhound, Grand Bleu de Gascogne, German longhaired pointer and Neapolitan mastiff. Breeds at greatest risk of GDV morbidity were the Grand Bleu de Gascogne, bloodhound, otterhound, Irish setter and Weimaraner. These results suggest that 16 breeds, mainly large/giant, are at increased risk of morbidity/mortality due to GDV.
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Miljkovic-Gacic, Iva; Wang, Xiaojing; Kammerer, Candace M; Bunker, Clareann H; Patrick, Alan L; Wheeler, Victor W; Kuller, Lewis H; Evans, Rhobert W; Zmuda, Joseph M
2008-06-01
Very few studies have comprehensively defined the genetic and environmental influences on body fat storage in the arms and legs and their association with diabetes, especially in families of African heritage. We analyzed body fat distribution by dual-energy x-ray absorptiometry (percentage total fat, percentage trunk fat, percentage arm fat, and percentage leg fat) and fasting serum glucose in 471 individuals (mean age, 43 years) from 8 multigenerational Afro-Caribbean families (mean family size = 51; 3535 relative pairs). Diabetes was inversely associated with percentage leg fat (P = .009) and, to some extent, positively associated with percentage arm fat independent of age, sex, and body size (P = .08), but not with anthropometric or dual-energy x-ray absorptiometric measures of total and central adiposity. Furthermore, percentage leg fat was inversely, whereas percentage arm fat was positively, associated with body mass index, waist circumference, and serum glucose (P Genetic correlation (rho(G)) between arm and leg fat was -0.61 (P genetic influences. This study provides new evidence for a strong genetic and sex contribution to upper and lower body fat, with relatively little covariation between these traits due to shared genes. Our findings also suggest that, in this population, leg fat is associated with diabetes independent of overall adiposity.
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Giraudo, Maeva; Dubé, Maxime; Lépine, Mélanie; Gagnon, Pierre; Douville, Mélanie; Houde, Magali
2017-09-01
Tris(2-butoxyethyl) phosphate (TBOEP) is an organophosphate ester used as substitute following the phase-out of brominated flamed retardants. Because of its high production volume and its use in a broad range of applications, this chemical is now frequently detected in the environment and biota. However, limited information is available on the long-term effects of TBOEP in aquatic organisms. In this study, Daphnia magna were exposed over three 21d generations to an environmentally relevant concentration of TBOEP (10μg/L) and effects were evaluated at the gene transcription, protein, and life-history (i.e., survival, reproduction and growth) levels. Chronic exposure to TBEOP did not impact survival or reproduction of D. magna but affected the growth output. The mean number of molts was also found to be lower in daphnids exposed to the chemical compared to control for a given generation, however there were no significant differences over the three generations. Molecular responses indicated significant differences in the transcription of genes related to growth, molting, ecdysteroid and juvenile hormone signaling, proteolysis, oxidative stress, and oxygen transport within generations. Levels of mRNA were also found to be significantly different for genes known to be involved in endocrine-mediated mechanisms such as reproduction and growth between generations F0, F1, and F2, indicating effects of parental exposure on offspring. Transcription results were supported by protein analyses with the significant decreased in catalase (CAT) activity in F1 generation, following the decreased transcription of cat in the parental generation. Taken together, these multi-biological level results suggest long-term potential endocrine disruption effects of TBOEP in D. magna exposed to an environmentally relevant concentration. This study highlights the importance of using chronic and multigenerational biological evaluation to assess risks of emerging chemicals. Crown Copyright
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[Essentials of pharmacophylogeny: knowledge pedigree, epistemology and paradigm shift].
Hao, Da-cheng; Xiao, Pei-gen; Liu, Li-wei; Peng, Yong; He, Chun-nian
2015-09-01
Chinese materia medica resource (CMM resource) is the foundation of the development of traditional Chinese medicine. In the study of sustainable utilization of CMM resource, adopting innovative theory and method to find new CMM resource is one of hotspots and always highlighted. Pharmacophylogeny interrogates the phylogenetic relationship of medicinal organisms (especially medicinal plants), as well as the intrinsic correlation of morphological taxonomy, molecular phylogeny, chemical constituents, and therapeutic efficacy (ethnopharmacology and pharmacological activity). This new discipline may have the power to change the way we utilize medicinal plant resources and develop plant-based drugs. Phylogenomics is the crossing of evolutionary biology and genomics, in which genome data are utilized for evolutionary reconstructions. Phylogenomics can be integrated into the flow chart of drug discovery and development, and extends the field of pharmacophylogeny at the omic level, thus the concept of pharmacophylogenomics could be redefined in the context of plant pharmaceutical resources. This contribution gives a brief discourse of knowledge pedigree of pharmacophylogeny, epistemology and paradigm shift, highlighting the theoretical and practical values of pharmacophylogenomics. Many medicinally important tribes and genera, such as Clematis, Pulsatilla, Anemone, Cimicifugeae, Nigella, Delphinieae, Adonideae, Aquilegia, Thalictrum, and Coptis, belong to Ranunculaceae family. Compared to other plant families, Ranunculaceae has the most species that are recorded in China Pharmacopoeia (CP) 2010. However, many Ranunculaceae species, e. g., those that are closely related to CP species, as well as those endemic to China, have not been investigated in depth, and their phylogenetic relationship and potential in medicinal use remain elusive. As such, it is proposed to select Ranunculaceae to exemplify the utility of pharmacophylogenomics and to elaborate the new concept
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Shevah, Orit; Laron, Zvi
2006-08-01
Out of the 63 patients with Laron Syndrome ( LS) followed in our clinic we were able to perform a genetic analysis on 43 patients belonging to 28 families. Twenty-seven patients were Jews, eight were Arabs, one was Druze, and six were Caucasians from countries other then Israel. Consanguinity was found in 11 families. Molecular analysis of the growth hormone receptor gene was performed in 32 patients and 32 family members. From the study of the pedigrees, as well as the GH receptor gene analysis, we confirmed an earlier report from our group that LS is a recessively inherited disease. One patient with a classical phenotype of LS had a non-classical pattern of inheritance: R43X heterozygosity together with a heterozygous polymorphism G168G; a condition which needs further exploration.
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Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis.
Ma, Li; O'Connell, Jeffrey R; VanRaden, Paul M; Shen, Botong; Padhi, Abinash; Sun, Chuanyu; Bickhart, Derek M; Cole, John B; Null, Daniel J; Liu, George E; Da, Yang; Wiggans, George R
2015-11-01
Meiotic recombination is an essential biological process that generates genetic diversity and ensures proper segregation of chromosomes during meiosis. From a large USDA dairy cattle pedigree with over half a million genotyped animals, we extracted 186,927 three-generation families, identified over 8.5 million maternal and paternal recombination events, and constructed sex-specific recombination maps for 59,309 autosomal SNPs. The recombination map spans for 25.5 Morgans in males and 23.2 Morgans in females, for a total studied region of 2,516 Mb (986 kb/cM in males and 1,085 kb/cM in females). The male map is 10% longer than the female map and the sex difference is most pronounced in the subtelomeric regions. We identified 1,792 male and 1,885 female putative recombination hotspots, with 720 hotspots shared between sexes. These hotspots encompass 3% of the genome but account for 25% of the genome-wide recombination events in both sexes. During the past forty years, males showed a decreasing trend in recombination rate that coincided with the artificial selection for milk production. Sex-specific GWAS analyses identified PRDM9 and CPLX1 to have significant effects on genome-wide recombination rate in both sexes. Two novel loci, NEK9 and REC114, were associated with recombination rate in both sexes, whereas three loci, MSH4, SMC3 and CEP55, affected recombination rate in females only. Among the multiple PRDM9 paralogues on the bovine genome, our GWAS of recombination hotspot usage together with linkage analysis identified the PRDM9 paralogue on chromosome 1 to be associated in the U.S. Holstein data. Given the largest sample size ever reported for such studies, our results reveal new insights into the understanding of cattle and mammalian recombination.
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Bailey, Drew H.; Walker, Robert S.; Blomquist, Gregory E.; Hill, Kim R.; Hurtado, A. Magdalena; Geary, David C.
2013-01-01
The current study assessed the heritability of personality in a traditional natural-fertility population, the Ache of eastern Paraguay. Self-reports (n = 110) and other-reports (n = 66) on the commonly used Big Five Personality Inventory (i.e., extraversion, agreeableness, conscientiousness, neuroticism, openness) were collected. Self-reports did not support the Five Factor Model developed with Western samples, and did not correlate with other-reports for three of the five measured personality factors. Heritability was assessed using factors that were consistent across self- and other-reports and factors assessed using other-reports that showed reliabilities similar to those found in Western samples. Analyses of these items in combination with a multi-generation pedigree (n = 2,132) revealed heritability estimates similar to those found in most Western samples, although we were not able to separately estimate the influence of the common environment on these traits. We also assessed relations between personality and reproductive success (RS), allowing for a test of several mechanisms that might be maintaining heritable variation in personality. Phenotypic analyses, based largely on other-reports, revealed that extraverted men had higher RS than other men, but no other dimensions of personality predicted RS in either sex. Mothers with more agreeable children had more children, and parents mated assortatively on personality. Of the evolutionary processes proposed to maintain variation in personality, assortative mating, selective neutrality, and temporal variation in selection pressures received the most support. However, the current study does not rule out other processes affecting the evolution and maintenance of individual differences in human personality. PMID:23527163
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Docosahexaenoic Acid (DHA: An Ancient Nutrient for the Modern Human Brain
Directory of Open Access Journals (Sweden)
Joanne Bradbury
2011-05-01
Full Text Available Modern humans have evolved with a staple source of preformed docosahexaenoic acid (DHA in the diet. An important turning point in human evolution was the discovery of high-quality, easily digested nutrients from coastal seafood and inland freshwater sources. Multi-generational exploitation of seafood by shore-based dwellers coincided with the rapid expansion of grey matter in the cerebral cortex, which characterizes the modern human brain. The DHA molecule has unique structural properties that appear to provide optimal conditions for a wide range of cell membrane functions. This has particular implications for grey matter, which is membrane-rich tissue. An important metabolic role for DHA has recently been identified as the precursor for resolvins and protectins. The rudimentary source of DHA is marine algae; therefore it is found concentrated in fish and marine oils. Unlike the photosynthetic cells in algae and higher plants, mammalian cells lack the specific enzymes required for the de novo synthesis of alpha-linolenic acid (ALA, the precursor for all omega-3 fatty acid syntheses. Endogenous synthesis of DHA from ALA in humans is much lower and more limited than previously assumed. The excessive consumption of omega-6 fatty acids in the modern Western diet further displaces DHA from membrane phospholipids. An emerging body of research is exploring a unique role for DHA in neurodevelopment and the prevention of neuropsychiatric and neurodegenerative disorders. DHA is increasingly being added back into the food supply as fish oil or algal oil supplementation.
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Docosahexaenoic acid (DHA): an ancient nutrient for the modern human brain.
Bradbury, Joanne
2011-05-01
Modern humans have evolved with a staple source of preformed docosahexaenoic acid (DHA) in the diet. An important turning point in human evolution was the discovery of high-quality, easily digested nutrients from coastal seafood and inland freshwater sources. Multi-generational exploitation of seafood by shore-based dwellers coincided with the rapid expansion of grey matter in the cerebral cortex, which characterizes the modern human brain. The DHA molecule has unique structural properties that appear to provide optimal conditions for a wide range of cell membrane functions. This has particular implications for grey matter, which is membrane-rich tissue. An important metabolic role for DHA has recently been identified as the precursor for resolvins and protectins. The rudimentary source of DHA is marine algae; therefore it is found concentrated in fish and marine oils. Unlike the photosynthetic cells in algae and higher plants, mammalian cells lack the specific enzymes required for the de novo synthesis of alpha-linolenic acid (ALA), the precursor for all omega-3 fatty acid syntheses. Endogenous synthesis of DHA from ALA in humans is much lower and more limited than previously assumed. The excessive consumption of omega-6 fatty acids in the modern Western diet further displaces DHA from membrane phospholipids. An emerging body of research is exploring a unique role for DHA in neurodevelopment and the prevention of neuropsychiatric and neurodegenerative disorders. DHA is increasingly being added back into the food supply as fish oil or algal oil supplementation.
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NIMH Repository and Genomics Resources (RGR)
U.S. Department of Health & Human Services — The NIMH Repository and Genomics Resource (RGR) stores biosamples, genetic, pedigree and clinical data collected in designated NIMH-funded human subject studies. The...
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Directory of Open Access Journals (Sweden)
Dong Hua Cao
2014-09-01
Full Text Available OBJECTIVE: Hemophilia B is caused by coagulation defects in the factor IX gene located in Xq27.1 on the X chromosome. A wide range of mutations, showing extensive molecular heterogeneity, have been described in hemophilia B patients. Our study was aimed at genetic analysis and prenatal diagnosis of hemophilia B in order to further elucidate the pathogenesis of the hemophilia B pedigree in China. METHODS: Polymerase chain reaction amplification and direct sequencing of all the coding regions was conducted in hemophilia B patients and carriers. Prenatal diagnosis of the proband was conducted at 20 weeks. RESULTS: We identified the novel point mutation 10.389 A>G, located upstream of the intron 3 acceptor site in hemophilia B patients. The fetus of the proband’s cousin was identified as a carrier. CONCLUSION: Our identification of a novel mutation in the F9 gene associated with hemophilia B provides novel insight into the pathogenesis of this genetically inherited disorder and also represents the basis of prenatal diagnosis.
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CHARACTERIZATION OF ENU-INDUCED MUTATIONS IN RED BLOOD CELL STRUCTURAL PROTEINS
Directory of Open Access Journals (Sweden)
Katrina Kildey
2013-03-01
Full Text Available Murine models with modified gene function as a result of N-ethyl-N-nitrosourea (ENU mutagenesis have been used to study phenotypes resulting from genetic change. This study investigated genetic factors associated with red blood cell (RBC physiology and structural integrity that may impact on blood component storage and transfusion outcome. Forward and reverse genetic approaches were employed with pedigrees of ENU-treated mice using a homozygous recessive breeding strategy. In a “forward genetic” approach, pedigree selection was based upon identification of an altered phenotype followed by exome sequencing to identify a causative mutation. In a second strategy, a “reverse genetic” approach based on selection of pedigrees with mutations in genes of interest was utilised and, following breeding to homozygosity, phenotype assessed. Thirty-three pedigrees were screened by the forward genetic approach. One pedigree demonstrated reticulocytosis, microcytic anaemia and thrombocytosis. Exome sequencing revealed a novel single nucleotide variation (SNV in Ank1 encoding the RBC structural protein ankyrin-1 and the pedigree was designated Ank1EX34. The reticulocytosis and microcytic anaemia observed in the Ank1EX34 pedigree were similar to clinical features of hereditary spherocytosis in humans. For the reverse genetic approach three pedigrees with different point mutations in Spnb1 encoding RBC protein spectrin-1β, and one pedigree with a mutation in Epb4.1, encoding band 4.1 were selected for study. When bred to homozygosity two of the spectrin-1β pedigrees (a, b demonstrated increased RBC count, haemoglobin (Hb and haematocrit (HCT. The third Spnb1 mutation (spectrin-1β c and mutation in Epb4.1 (band 4.1 did not significantly affect the haematological phenotype, despite these two mutations having a PolyPhen score predicting the mutation may be damaging. Exome sequencing allows rapid identification of causative mutations and development of
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Calderón, R; Morales, B; Peña, J A; Delgado, J
1995-10-01
Pedigree structures of 161 uncle/niece-aunt/nephew and 4420 first cousin consanguineous marriages registered during the 19th and 20th centuries in two large and very different Spanish regions have been analysed and their genetic consequences evaluated. The frequencies of the different pedigree subtypes within each degree of relationship were quite similar in both populations despite significant heterogeneity in inbreeding patterns. The mean X-linked inbreeding coefficient (Fx) for each type of cousin mating was calculated and compared to that expected for autosomal genes (F). The effect of genealogical structure on the Fx/F ratio was compared to different cultural populations worldwide. Preferentiality and avoidance of close consanguinity along with specific types of pedigrees are discussed on the basis of premarital migration and sociocultural rules still deeply rooted in certain human groups. By admitting that the observed Fx coefficient is usually higher than F in most human populations some remarks have been made in terms of population genetic risk.
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Kuo, Hsiao-Che; Hsu, Hao-Hsuan; Chua, Chee Shin; Wang, Ting-Yu; Chen, Young-Mao; Chen, Tzong-Yueh
2014-01-01
Most giant groupers in the market are derived from inbred stock. Inbreeding can cause trait depression, compromising the animals’ fitness and disease resistance, obligating farmers to apply increased amounts of drugs. In order to solve this problem, a pedigree classification method is needed. Here, microsatellite and mitochondrial DNA were used as genetic markers to analyze the genetic relationships among giant grouper broodstocks. The 776-bp fragment of high polymorphic mitochondrial D-loop sequence was selected for measuring sibling relatedness. In a sample of 118 giant groupers, 42 haplotypes were categorized, with nucleotide diversity (π) of 0.00773 and haplotype diversity (HD) of 0.983. Furthermore, microsatellites were used for investigation of parentage. Six out of 33 microsatellite loci were selected as markers based on having a high number of alleles and compliance with Hardy-Weinberg equilibrium. Microsatellite profiles based on these loci provide high variability with low combined non-exclusion probability, permitting practical use in aquaculture. The method described here could be used to improve grouper broodstock management and lower the chances of inbreeding. This approach is expected to lead to production of higher quality groupers with higher disease resistance, thereby reducing the need for drug application. PMID:24796300
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Watson-Lazowski, Alexander; Lin, Yunan; Miglietta, Franco; Edwards, Richard J; Chapman, Mark A; Taylor, Gail
2016-11-01
Atmospheric carbon dioxide (CO 2 ) directly determines the rate of plant photosynthesis and indirectly effects plant productivity and fitness and may therefore act as a selective pressure driving evolution, but evidence to support this contention is sparse. Using Plantago lanceolata L. seed collected from a naturally high CO 2 spring and adjacent ambient CO 2 control site, we investigated multigenerational response to future, elevated atmospheric CO 2 . Plants were grown in either ambient or elevated CO 2 (700 μmol mol -1 ), enabling for the first time, characterization of the functional and population genomics of plant acclimation and adaptation to elevated CO 2 . This revealed that spring and control plants differed significantly in phenotypic plasticity for traits underpinning fitness including above-ground biomass, leaf size, epidermal cell size and number and stomatal density and index. Gene expression responses to elevated CO 2 (acclimation) were modest [33-131 genes differentially expressed (DE)], whilst those between control and spring plants (adaptation) were considerably larger (689-853 DE genes). In contrast, population genomic analysis showed that genetic differentiation between spring and control plants was close to zero, with no fixed differences, suggesting that plants are adapted to their native CO 2 environment at the level of gene expression. An unusual phenotype of increased stomatal index in spring but not control plants in elevated CO 2 correlated with altered expression of stomatal patterning genes between spring and control plants for three loci (YODA, CDKB1;1 and SCRM2) and between ambient and elevated CO 2 for four loci (ER, YODA, MYB88 and BCA1). We propose that the two positive regulators of stomatal number (SCRM2) and CDKB1;1 when upregulated act as key controllers of stomatal adaptation to elevated CO 2 . Combined with significant transcriptome reprogramming of photosynthetic and dark respiration and enhanced growth in spring plants
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Identification of four novel mutations of the WFS1 gene in Iranian Wolfram syndrome pedigrees.
Ghahraman, Martha; Abbaszadegan, Mohammad Reza; Vakili, Rahim; Hosseini, Sousan; Fardi Golyan, Fatemeh; Ghaemi, Nosrat; Forghanifard, Mohammad Mahdi
2016-12-01
Wolfram syndrome is a rare neurodegenerative disorder with an autosomal recessive pattern of inheritance characterized by various clinical manifestations. The related gene, WFS1, encodes a transmembrane glycoprotein, named wolframin. Genetic analyses demonstrated that mutations in this gene are associated with WS type 1. Our aim in this study was to sequence WFS1 coding region in Iranian Wolfram syndrome pedigrees. Genomic DNA was extracted from peripheral blood of 12 WS patients and their healthy parents. Exons 2-8 and the exon-intron junctions of WFS1 were sequenced. DNA sequences were compared to the reference using Sequencher software. Molecular analysis of WFS1 revealed six different mutations. Four novel and two previously reported mutations were identified. One novel mutation, c.1379_1381del, is predicted to produce an aberrant protein. A second novel mutation, c.1384G > T, encodes a truncated protein. Novel mutation, c.1097-1107dup (11 bp), causes a frameshift which results in a premature stop codon. We screened for the novel missense mutation, c.1010C > T, in 100 control alleles. This mutation was not found in any of the healthy controls. Our study increased the spectrum of WFS1 mutations and supported the role of WFS1 in susceptibility to WS. We hope that these findings open new horizons to future molecular investigations which may help to prevent and treat this devastating disease.
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Danchin-Burge, C; Leroy, G; Brochard, M; Moureaux, S; Verrier, E
2012-06-01
A pedigree analysis was performed on eight French dairy cattle breeds to assess their change in genetic variability since a first analysis completed in 1996. The Holstein, Normande and Montbéliarde breeds are selected internationally with over hundreds of thousands cows registered in the performance recording system. Three breeds are internationally selected but with limited numbers of cows in France (Brown Swiss, French Simmental and French Red Pied). The last two remaining breeds (Abondance and Tarentaise) are raised at regional level. The effective numbers of ancestors of cows born between 2004 and 2007 varied between 15 (Abondance and Tarentaise) and 51 (French Red Pied). The effective population sizes (classical approach) varied between 53 (Abondance) and 197 (French Red Pied). This article also compares the genetic variability of the ex situ (collections of the French National Cryobank) and in situ populations. The results were commented in regard to the recent history of gene flows in the different breeds as well as the existence of more or less stringent bottlenecks. Our results showed that whatever the size of the breeds, their genetic diversity impoverished quite rapidly since 1996 and they all could be considered as quite poor from a genetic diversity point of view. It shows the need for setting up cryobanks as gene reservoirs as well as sustainable breeding programmes that include loss of genetic diversity as an integrated control parameter. © 2011 Blackwell Verlag GmbH.
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A novel nonsense mutation of the GPR143 gene identified in a Chinese pedigree with ocular albinism.
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Naihong Yan
Full Text Available BACKGROUND: The purpose of this study was to elucidate the molecular basis of ocular albinism type I in a Chinese pedigree. METHODOLOGY/PRINCIPAL FINDINGS: Complete ophthalmologic examinations were performed on 4 patients, 7 carriers and 17 unaffected individuals in this five-generation family. All coding exons of four-point-one (4.1, ezrin, radixin, moesin (FERM domain-containing 7 (FRMD7 and G protein-coupled receptor 143 (GPR143 genes were amplified by polymerase chain reaction (PCR, sequenced and compared with a reference database. Ocular albinism and nystagmus were found in all patients of this family. Macular hypoplasia was present in the patients including the proband. A novel nonsense hemizygous mutation c.807T>A in the GPR143 gene was identified in four patients and the heterozygous mutation was found in seven asymptomatic individuals. This mutation is a substitution of tyrosine for adenine which leads to a premature stop codon at position 269 (p.Y269X of GPR143. CONCLUSIONS/SIGNIFICANCE: This is the first report that p.Y269X mutation of GPR143 gene is responsible for the pathogenesis of familial ocular albinism. These results expand the mutation spectrum of GPR143, and demonstrate the clinical characteristics of ocular albinism type I in Chinese population.
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International Nuclear Information System (INIS)
Livshits, Gregory; Cohen, Zvi; Higla, Orabi; Yakovenko, Konstantin
2001-01-01
The present study used computed tomography imaging to evaluate the extent and pattern of the intergenerational transmission of spinal disc degeneration disease (DDD) in complex pedigrees. Contribution of a number of the potential covariates was also studied using univariate and multivariate logistic regression analysis, as well as two types of complex segregation analysis models. Among 161 individuals studied, DDD was diagnosed in 60 individuals. The number of protruded discs varied from 1 to 4, mostly in lumbar or lumbosacral regions. The average age at onset of the disease was similar for both women (36.0 years) and men (34.8 years). The proportion of the individuals affected by the DDD status of their parents ranged from 10% in families of two healthy parents to 55.5% of two affected parents (p < 0.01). The results of the logistic regression analyses and complex segregation analysis were qualitatively the same: DDD status of parents, age and smoking were the main risk factors for disc herniation in the Arabic families we examined. All analyses showed a predominating role of the family history as a risk factor for DDD in offsprings. It showed, for example, four times higher risk at age 50 for individuals with two affected parents vs. those who have two non-affected parents. However, the results of models-fitting genetic analysis, did not confirm a monogenic Mendelian pattern of inheritance
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Two novel mutations in the PPIB gene cause a rare pedigree of osteogenesis imperfecta type IX.
Jiang, Yu; Pan, Jingxin; Guo, Dongwei; Zhang, Wei; Xie, Jie; Fang, Zishui; Guo, Chunmiao; Fang, Qun; Jiang, Weiying; Guo, Yibin
2017-06-01
Osteogenesis imperfecta (OI) is a rare genetic skeletal disorder characterized by increased bone fragility and vulnerability to fractures. PPIB is identified as a candidate gene for OI-IX, here we detect two pathogenic mutations in PPIB and analyze the genotype-phenotype correlation in a Chinese family with OI. Next-generation sequencing (NGS) was used to screen the whole exome of the parents of proband. Screening of variation frequency, evolutionary conservation comparisons, pathogenicity evaluation, and protein structure prediction were conducted to assess the pathogenicity of the novel mutations. Sanger sequencing was used to confirm the candidate variants. RTQ-PCR was used to analyze the PPIB gene expression. All mutant genes screened out by NGS were excluded except PPIB. Two novel heterozygous PPIB mutations (father, c.25A>G; mother, c.509G>A) were identified in relation to osteogenesis imperfecta type IX. Both mutations were predicted to be pathogenic by bioinformatics analysis and RTQ-PCR analysis revealed downregulated PPIB expression in the two carriers. We report a rare pedigree with an autosomal recessive osteogenesis imperfecta type IX (OI-IX) caused by two novel PPIB mutations identified for the first time in China. The current study expands our knowledge of PPIB mutations and their associated phenotypes, and provides new information on the genetic defects associated with this disease for clinical diagnosis. Copyright © 2017 Elsevier B.V. All rights reserved.
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Ahram, D.F.; Grozdanic, S.D.; Kecova, H.; Henkes, A.; Collin, R.W.J.; Kuehn, M.H.
2015-01-01
Several dog breeds are susceptible to developing primary angle closure glaucoma (PACG), which suggests a genetic basis for the disease. We have identified a four-generation Basset Hound pedigree with characteristic autosomal recessive PACG that closely recapitulates PACG in humans. Our aim is to utilize gene mapping and whole exome sequencing approaches to identify PACG-causing sequence variants in the Basset. Extensive clinical phenotyping of all pedigree members was conducted. SNP-chip geno...
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Post, Robert M; Altshuler, Lori L; Kupka, Ralph; McElroy, Susan L; Frye, Mark A; Rowe, Michael; Grunze, Heinz; Suppes, Trisha; Keck, Paul E; Nolen, Willem A
2017-01-01
Patients with bipolar disorder from the US have more early-onset illness and a greater familial loading for psychiatric problems than those from the Netherlands or Germany (abbreviated here as Europe). We hypothesized that these regional differences in illness burden would extend to the patients siblings. Outpatients with bipolar disorder gave consent for participation in a treatment outcome network and for filling out detailed questionnaires. This included a family history of unipolar depression, bipolar disorder, suicide attempt, alcohol abuse/dependence, drug abuse/dependence, and "other" illness elicited for the patients' grandparents, parents, spouses, offspring, and siblings. Problems in the siblings were examined as a function of parental and grandparental problems and the patients' adverse illness characteristics or poor prognosis factors (PPFs). Each problem in the siblings was significantly (pUS than in those from Europe. In the US, problems in the parents and grandparents were almost uniformly associated with the same problems in the siblings, and sibling problems were related to the number of PPFs observed in the patients. Family history was based on patient report. Increased familial loading for psychiatric problems extends through 4 generations of patients with bipolar disorder from the US compared to Europe, and appears to "breed true" into the siblings of the patients. In addition to early onset, a variety of PPFs are associated with the burden of psychiatric problems in the patients' siblings and offspring. Greater attention to the multigenerational prevalence of illness in patients from the US is indicated. Copyright © 2016 Elsevier B.V. All rights reserved.
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Goebel, Katie; Merner, Nancy D
2017-05-01
Canines are excellent models for cancer studies due to their similar physiology and genomic sequence to humans, companion status and limited intra-breed heterogeneity. Due to their affliction to mammary cancers, canines can serve as powerful genetic models of hereditary breast cancers. Variants within known human breast cancer susceptibility genes only explain a fraction of familial cases. Thus, further discovery is necessary but such efforts have been thwarted by genetic heterogeneity. Reducing heterogeneity is key, and studying isolated human populations have helped in the endeavour. An alternative is to study dog pedigrees, since artificial selection has resulted in extreme homogeneity. Identifying the genetic predisposition to canine mammary tumours can translate to human discoveries - a strategy currently underutilized. To explore this potential, we reviewed published canine mammary tumour genetic studies and proposed benefits of next generation sequencing canine cohorts to facilitate moving beyond incremental advances.
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Carr, Vaughan J; Harris, Felicity; Raudino, Alessandra; Luo, Luming; Kariuki, Maina; Liu, Enwu; Tzoumakis, Stacy; Smith, Maxwell; Holbrook, Allyson; Bore, Miles; Brinkman, Sally; Lenroot, Rhoshel; Dix, Katherine; Dean, Kimberlie; Laurens, Kristin R; Green, Melissa J
2016-02-11
The initial aim of this multiagency, multigenerational record linkage study is to identify childhood profiles of developmental vulnerability and resilience, and to identify the determinants of these profiles. The eventual aim is to identify risk and protective factors for later childhood-onset and adolescent-onset mental health problems, and other adverse social outcomes, using subsequent waves of record linkage. The research will assist in informing the development of public policy and intervention guidelines to help prevent or mitigate adverse long-term health and social outcomes. The study comprises a population cohort of 87,026 children in the Australian State of New South Wales (NSW). The cohort was defined by entry into the first year of full-time schooling in NSW in 2009, at which time class teachers completed the Australian Early Development Census (AEDC) on each child (with 99.7% coverage in NSW). The AEDC data have been linked to the children's birth, health, school and child protection records for the period from birth to school entry, and to the health and criminal records of their parents, as well as mortality databases. Descriptive data summarising sex, geographic and socioeconomic distributions, and linkage rates for the various administrative databases are presented. Child data are summarised, and the mental health and criminal records data of the children's parents are provided. In 2015, at age 11 years, a self-report mental health survey was administered to the cohort in collaboration with government, independent and Catholic primary school sectors. A second record linkage, spanning birth to age 11 years, will be undertaken to link this survey data with the aforementioned administrative databases. This will enable a further identification of putative risk and protective factors for adverse mental health and other outcomes in adolescence, which can then be tested in subsequent record linkages. Published by the BMJ Publishing Group Limited. For
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Kos, Mark Z; Carless, Melanie A; Peralta, Juan; Curran, Joanne E; Quillen, Ellen E; Almeida, Marcio; Blackburn, August; Blondell, Lucy; Roalf, David R; Pogue-Geile, Michael F; Gur, Ruben C; Göring, Harald H H; Nimgaonkar, Vishwajit L; Gur, Raquel E; Almasy, Laura
2017-12-01
Schizophrenia is a serious mental illness, involving disruptions in thought and behavior, with a worldwide prevalence of about one percent. Although highly heritable, much of the genetic liability of schizophrenia is yet to be explained. We searched for susceptibility loci in multiplex, multigenerational families affected by schizophrenia, targeting protein-altering variation with in silico predicted functional effects. Exome sequencing was performed on 136 samples from eight European-American families, including 23 individuals diagnosed with schizophrenia or schizoaffective disorder. In total, 11,878 non-synonymous variants from 6,396 genes were tested for their association with schizophrenia spectrum disorders. Pathway enrichment analyses were conducted on gene-based test results, protein-protein interaction (PPI) networks, and epistatic effects. Using a significance threshold of FDR < 0.1, association was detected for rs10941112 (p = 2.1 × 10 -5 ; q-value = 0.073) in AMACR, a gene involved in fatty acid metabolism and previously implicated in schizophrenia, with significant cis effects on gene expression (p = 5.5 × 10 -4 ), including brain tissue data from the Genotype-Tissue Expression project (minimum p = 6.0 × 10 -5 ). A second SNP, rs10378 located in TMEM176A, also shows risk effects in the exome data (p = 2.8 × 10 -5 ; q-value = 0.073). PPIs among our top gene-based association results (p < 0.05; n = 359 genes) reveal significant enrichment of genes involved in NCAM-mediated neurite outgrowth (p = 3.0 × 10 -5 ), while exome-wide SNP-SNP interaction effects for rs10941112 and rs10378 indicate a potential role for kinase-mediated signaling involved in memory and learning. In conclusion, these association results implicate AMACR and TMEM176A in schizophrenia risk, whose effects may be modulated by genes involved in synaptic plasticity and neurocognitive performance. © 2017 Wiley Periodicals, Inc.
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Directory of Open Access Journals (Sweden)
Hsiao-Che Kuo
2014-04-01
Full Text Available Most giant groupers in the market are derived from inbred stock. Inbreeding can cause trait depression, compromising the animals’ fitness and disease resistance, obligating farmers to apply increased amounts of drugs. In order to solve this problem, a pedigree classification method is needed. Here, microsatellite and mitochondrial DNA were used as genetic markers to analyze the genetic relationships among giant grouper broodstocks. The 776-bp fragment of high polymorphic mitochondrial D-loop sequence was selected for measuring sibling relatedness. In a sample of 118 giant groupers, 42 haplotypes were categorized, with nucleotide diversity (π of 0.00773 and haplotype diversity (HD of 0.983. Furthermore, microsatellites were used for investigation of parentage. Six out of 33 microsatellite loci were selected as markers based on having a high number of alleles and compliance with Hardy-Weinberg equilibrium. Microsatellite profiles based on these loci provide high variability with low combined non-exclusion probability, permitting practical use in aquaculture. The method described here could be used to improve grouper broodstock management and lower the chances of inbreeding. This approach is expected to lead to production of higher quality groupers with higher disease resistance, thereby reducing the need for drug application.
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Directory of Open Access Journals (Sweden)
Saleha S
2016-06-01
Full Text Available Clinical anophthalmia is a rare inherited disease of the eye and phenotype refers to the absence of ocular tissue in the orbit of eye. Patients may have unilateral or bilateral anophthalmia, and generally have short palpebral fissures and small orbits. Anophthalmia may be isolated or associated with a broader syndrome and may have genetic or environmental causes. However, genetic cause has been defined in only a small proportion of cases, therefore, a consanguineous Pakistani family of the Pashtoon ethnic group, with isolated clinical anophthalmia was investigated using linkage mapping. A family pedigree was created to trace the possible mode of inheritance of the disease. Blood samples were collected from affected as well as normal members of this family, and screened for disease-associated mutations. This family was analyzed for linkage to all the known loci of clinical anophthalmia, using microsatellite short tandem repeat (STR markers. Direct sequencing was performed to find out disease-associated mutations in the candidate gene. This family with isolated clinical anophthalmia, was mapped to the SOX2 gene that is located at chromosome 3q26.3-q27. However, on exonic and regulatory regions mutation screening of the SOX2 gene, the disease-associated mutation was not identified. It showed that another gene responsible for development of the eye might be present at chromosome 3q26.3-q27 and needs to be identified and screened for the disease-associated mutation in this family.
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Ajmal, M; Zafar, S; Hameed, A
2016-01-01
ABSTRACT Clinical anophthalmia is a rare inherited disease of the eye and phenotype refers to the absence of ocular tissue in the orbit of eye. Patients may have unilateral or bilateral anophthalmia, and generally have short palpebral fissures and small orbits. Anophthalmia may be isolated or associated with a broader syndrome and may have genetic or environmental causes. However, genetic cause has been defined in only a small proportion of cases, therefore, a consanguineous Pakistani family of the Pashtoon ethnic group, with isolated clinical anophthalmia was investigated using linkage mapping. A family pedigree was created to trace the possible mode of inheritance of the disease. Blood samples were collected from affected as well as normal members of this family, and screened for disease-associated mutations. This family was analyzed for linkage to all the known loci of clinical anophthalmia, using microsatellite short tandem repeat (STR) markers. Direct sequencing was performed to find out disease-associated mutations in the candidate gene. This family with isolated clinical anophthalmia, was mapped to the SOX2 gene that is located at chromosome 3q26.3-q27. However, on exonic and regulatory regions mutation screening of the SOX2 gene, the disease-associated mutation was not identified. It showed that another gene responsible for development of the eye might be present at chromosome 3q26.3-q27 and needs to be identified and screened for the disease-associated mutation in this family. PMID:27785411
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A locus for isolated cataract on human Xp.
Francis, P J; Berry, V; Hardcastle, A J; Maher, E R; Moore, A T; Bhattacharya, S S
2002-02-01
To genetically map the gene causing isolated X linked cataract in a large European pedigree. Using the patient registers at Birmingham Women's Hospital, UK, we identified and examined 23 members of a four generation family with nuclear cataract. Four of six affected males also had complex congenital heart disease. Pedigree data were collated and leucocyte DNA extracted from venous blood. Linkage analysis by PCR based microsatellite marker genotyping was used to identify the disease locus and mutations within candidate genes screened by direct sequencing. The disease locus was genetically refined to chromosome Xp22, within a 3 cM linkage interval flanked by markers DXS9902 and DXS999 (Zmax=3.64 at theta=0 for marker DXS8036). This is the first report of a locus for isolated inherited cataract on the X chromosome. The disease interval lies within the Nance-Horan locus suggesting allelic heterogeneity. The apparent association with congenital cardiac anomalies suggests a possible new oculocardiac syndrome.
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Haplotypes in the APOA1-C3-A4-A5 gene cluster affect plasma lipids in both humans and baboons
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Wang, Qian-fei; Liu, Xin; O' Connell, Jeff; Peng, Ze; Krauss, Ronald M.; Rainwater, David L.; VandeBerg, John L.; Rubin, Edward M.; Cheng, Jan-Fang; Pennacchio, Len A.
2003-09-15
Genetic studies in non-human primates serve as a potential strategy for identifying genomic intervals where polymorphisms impact upon human disease-related phenotypes. It remains unclear, however, whether independently arising polymorphisms in orthologous regions of non-human primates leads to similar variation in a quantitative trait found in both species. To explore this paradigm, we studied a baboon apolipoprotein gene cluster (APOA1/C3/A4/A5) for which the human gene orthologs have well established roles in influencing plasma HDL-cholesterol and triglyceride concentrations. Our extensive polymorphism analysis of this 68 kb gene cluster in 96 pedigreed baboons identified several haplotype blocks each with limited diversity, consistent with haplotype findings in humans. To determine whether baboons, like humans, also have particular haplotypes associated with lipid phenotypes, we genotyped 634 well characterized baboons using 16 haplotype tagging SNPs. Genetic analysis of single SNPs, as well as haplotypes, revealed an association of APOA5 and APOC3 variants with HDL cholesterol and triglyceride concentrations, respectively. Thus, independent variation in orthologous genomic intervals does associate with similar quantitative lipid traits in both species, supporting the possibility of uncovering human QTL genes in a highly controlled non-human primate model.
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Mutations in LRRC50 predispose zebrafish and humans to seminomas.
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Sander G Basten
2013-04-01
Full Text Available Seminoma is a subclass of human testicular germ cell tumors (TGCT, the most frequently observed cancer in young men with a rising incidence. Here we describe the identification of a novel gene predisposing specifically to seminoma formation in a vertebrate model organism. Zebrafish carrying a heterozygous nonsense mutation in Leucine-Rich Repeat Containing protein 50 (lrrc50 also called dnaaf1, associated previously with ciliary function, are found to be highly susceptible to the formation of seminomas. Genotyping of these zebrafish tumors shows loss of heterozygosity (LOH of the wild-type lrrc50 allele in 44.4% of tumor samples, correlating with tumor progression. In humans we identified heterozygous germline LRRC50 mutations in two different pedigrees with a family history of seminomas, resulting in a nonsense Arg488* change and a missense Thr590Met change, which show reduced expression of the wild-type allele in seminomas. Zebrafish in vivo complementation studies indicate the Thr590Met to be a loss-of-function mutation. Moreover, we show that a pathogenic Gln307Glu change is significantly enriched in individuals with seminoma tumors (13% of our cohort. Together, our study introduces an animal model for seminoma and suggests LRRC50 to be a novel tumor suppressor implicated in human seminoma pathogenesis.
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Visions of human futures in space and SETI
Wright, Jason T.; Oman-Reagan, Michael P.
2018-04-01
We discuss how visions for the futures of humanity in space and SETI are intertwined, and are shaped by prior work in the fields and by science fiction. This appears in the language used in the fields, and in the sometimes implicit assumptions made in discussions of them. We give examples from articulations of the so-called Fermi Paradox, discussions of the settlement of the Solar System (in the near future) and the Galaxy (in the far future), and METI. We argue that science fiction, especially the campy variety, is a significant contributor to the `giggle factor' that hinders serious discussion and funding for SETI and Solar System settlement projects. We argue that humanity's long-term future in space will be shaped by our short-term visions for who goes there and how. Because of the way they entered the fields, we recommend avoiding the term `colony' and its cognates when discussing the settlement of space, as well as other terms with similar pedigrees. We offer examples of science fiction and other writing that broaden and challenge our visions of human futures in space and SETI. In an appendix, we use an analogy with the well-funded and relatively uncontroversial searches for the dark matter particle to argue that SETI's lack of funding in the national science portfolio is primarily a problem of perception, not inherent merit.
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Schür, Remmelt; Sjouwerman, Rachel; Service, Susan K.; Araya, Carmen; Araya, Xinia; Bejarano, Julio; Knowles, Emma; Gomez-Makhinson, Juliana; Lopez, Maria C.; Aldana, Ileana; Teshiba, Terri M.; Abaryan, Zvart; Al-Sharif, Noor B.; Navarro, Linda; Tishler, Todd A.; Altshuler, Lori; Bartzokis, George; Escobar, Javier I.; Glahn, David C.; Thompson, Paul M.; Lopez-Jaramillo, Carlos; Macaya, Gabriel; Molina, Julio; Reus, Victor I.; Sabatti, Chiara; Cantor, Rita M.; Freimer, Nelson B.; Bearden, Carrie E.
2015-01-01
Recent theories regarding the pathophysiology of bipolar disorder suggest contributions of both neurodevelopmental and neurodegenerative processes. While structural neuroimaging studies indicate disease-associated neuroanatomical alterations, the behavioural correlates of these alterations have not been well characterized. Here, we investigated multi-generational families genetically enriched for bipolar disorder to: (i) characterize neurobehavioural correlates of neuroanatomical measures implicated in the pathophysiology of bipolar disorder; (ii) identify brain–behaviour associations that differ between diagnostic groups; (iii) identify neurocognitive traits that show evidence of accelerated ageing specifically in subjects with bipolar disorder; and (iv) identify brain–behaviour correlations that differ across the age span. Structural neuroimages and multi-dimensional assessments of temperament and neurocognition were acquired from 527 (153 bipolar disorder and 374 non-bipolar disorder) adults aged 18–87 years in 26 families with heavy genetic loading for bipolar disorder. We used linear regression models to identify significant brain–behaviour associations and test whether brain–behaviour relationships differed: (i) between diagnostic groups; and (ii) as a function of age. We found that total cortical and ventricular volume had the greatest number of significant behavioural associations, and included correlations with measures from multiple cognitive domains, particularly declarative and working memory and executive function. Cortical thickness measures, in contrast, showed more specific associations with declarative memory, letter fluency and processing speed tasks. While the majority of brain–behaviour relationships were similar across diagnostic groups, increased cortical thickness in ventrolateral prefrontal and parietal cortical regions was associated with better declarative memory only in bipolar disorder subjects, and not in non
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Toghiani, S; Aggrey, S E; Rekaya, R
2016-07-01
Availability of high-density single nucleotide polymorphism (SNP) genotyping platforms provided unprecedented opportunities to enhance breeding programmes in livestock, poultry and plant species, and to better understand the genetic basis of complex traits. Using this genomic information, genomic breeding values (GEBVs), which are more accurate than conventional breeding values. The superiority of genomic selection is possible only when high-density SNP panels are used to track genes and QTLs affecting the trait. Unfortunately, even with the continuous decrease in genotyping costs, only a small fraction of the population has been genotyped with these high-density panels. It is often the case that a larger portion of the population is genotyped with low-density and low-cost SNP panels and then imputed to a higher density. Accuracy of SNP genotype imputation tends to be high when minimum requirements are met. Nevertheless, a certain rate of genotype imputation errors is unavoidable. Thus, it is reasonable to assume that the accuracy of GEBVs will be affected by imputation errors; especially, their cumulative effects over time. To evaluate the impact of multi-generational selection on the accuracy of SNP genotypes imputation and the reliability of resulting GEBVs, a simulation was carried out under varying updating of the reference population, distance between the reference and testing sets, and the approach used for the estimation of GEBVs. Using fixed reference populations, imputation accuracy decayed by about 0.5% per generation. In fact, after 25 generations, the accuracy was only 7% lower than the first generation. When the reference population was updated by either 1% or 5% of the top animals in the previous generations, decay of imputation accuracy was substantially reduced. These results indicate that low-density panels are useful, especially when the generational interval between reference and testing population is small. As the generational interval
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Human subcortical brain asymmetries in 15,847 people worldwide reveal effects of age and sex.
Guadalupe, Tulio; Mathias, Samuel R; vanErp, Theo G M; Whelan, Christopher D; Zwiers, Marcel P; Abe, Yoshinari; Abramovic, Lucija; Agartz, Ingrid; Andreassen, Ole A; Arias-Vásquez, Alejandro; Aribisala, Benjamin S; Armstrong, Nicola J; Arolt, Volker; Artiges, Eric; Ayesa-Arriola, Rosa; Baboyan, Vatche G; Banaschewski, Tobias; Barker, Gareth; Bastin, Mark E; Baune, Bernhard T; Blangero, John; Bokde, Arun L W; Boedhoe, Premika S W; Bose, Anushree; Brem, Silvia; Brodaty, Henry; Bromberg, Uli; Brooks, Samantha; Büchel, Christian; Buitelaar, Jan; Calhoun, Vince D; Cannon, Dara M; Cattrell, Anna; Cheng, Yuqi; Conrod, Patricia J; Conzelmann, Annette; Corvin, Aiden; Crespo-Facorro, Benedicto; Crivello, Fabrice; Dannlowski, Udo; de Zubicaray, Greig I; de Zwarte, Sonja M C; Deary, Ian J; Desrivières, Sylvane; Doan, Nhat Trung; Donohoe, Gary; Dørum, Erlend S; Ehrlich, Stefan; Espeseth, Thomas; Fernández, Guillén; Flor, Herta; Fouche, Jean-Paul; Frouin, Vincent; Fukunaga, Masaki; Gallinat, Jürgen; Garavan, Hugh; Gill, Michael; Suarez, Andrea Gonzalez; Gowland, Penny; Grabe, Hans J; Grotegerd, Dominik; Gruber, Oliver; Hagenaars, Saskia; Hashimoto, Ryota; Hauser, Tobias U; Heinz, Andreas; Hibar, Derrek P; Hoekstra, Pieter J; Hoogman, Martine; Howells, Fleur M; Hu, Hao; Hulshoff Pol, Hilleke E; Huyser, Chaim; Ittermann, Bernd; Jahanshad, Neda; Jönsson, Erik G; Jurk, Sarah; Kahn, Rene S; Kelly, Sinead; Kraemer, Bernd; Kugel, Harald; Kwon, Jun Soo; Lemaitre, Herve; Lesch, Klaus-Peter; Lochner, Christine; Luciano, Michelle; Marquand, Andre F; Martin, Nicholas G; Martínez-Zalacaín, Ignacio; Martinot, Jean-Luc; Mataix-Cols, David; Mather, Karen; McDonald, Colm; McMahon, Katie L; Medland, Sarah E; Menchón, José M; Morris, Derek W; Mothersill, Omar; Maniega, Susana Munoz; Mwangi, Benson; Nakamae, Takashi; Nakao, Tomohiro; Narayanaswaamy, Janardhanan C; Nees, Frauke; Nordvik, Jan E; Onnink, A Marten H; Opel, Nils; Ophoff, Roel; Paillère Martinot, Marie-Laure; Papadopoulos Orfanos, Dimitri; Pauli, Paul; Paus, Tomáš; Poustka, Luise; Reddy, Janardhan Yc; Renteria, Miguel E; Roiz-Santiáñez, Roberto; Roos, Annerine; Royle, Natalie A; Sachdev, Perminder; Sánchez-Juan, Pascual; Schmaal, Lianne; Schumann, Gunter; Shumskaya, Elena; Smolka, Michael N; Soares, Jair C; Soriano-Mas, Carles; Stein, Dan J; Strike, Lachlan T; Toro, Roberto; Turner, Jessica A; Tzourio-Mazoyer, Nathalie; Uhlmann, Anne; Hernández, Maria Valdés; van den Heuvel, Odile A; van der Meer, Dennis; van Haren, Neeltje E M; Veltman, Dick J; Venkatasubramanian, Ganesan; Vetter, Nora C; Vuletic, Daniella; Walitza, Susanne; Walter, Henrik; Walton, Esther; Wang, Zhen; Wardlaw, Joanna; Wen, Wei; Westlye, Lars T; Whelan, Robert; Wittfeld, Katharina; Wolfers, Thomas; Wright, Margaret J; Xu, Jian; Xu, Xiufeng; Yun, Je-Yeon; Zhao, JingJing; Franke, Barbara; Thompson, Paul M; Glahn, David C; Mazoyer, Bernard; Fisher, Simon E; Francks, Clyde
2017-10-01
The two hemispheres of the human brain differ functionally and structurally. Despite over a century of research, the extent to which brain asymmetry is influenced by sex, handedness, age, and genetic factors is still controversial. Here we present the largest ever analysis of subcortical brain asymmetries, in a harmonized multi-site study using meta-analysis methods. Volumetric asymmetry of seven subcortical structures was assessed in 15,847 MRI scans from 52 datasets worldwide. There were sex differences in the asymmetry of the globus pallidus and putamen. Heritability estimates, derived from 1170 subjects belonging to 71 extended pedigrees, revealed that additive genetic factors influenced the asymmetry of these two structures and that of the hippocampus and thalamus. Handedness had no detectable effect on subcortical asymmetries, even in this unprecedented sample size, but the asymmetry of the putamen varied with age. Genetic drivers of asymmetry in the hippocampus, thalamus and basal ganglia may affect variability in human cognition, including susceptibility to psychiatric disorders.
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Sexually antagonistic selection in human male homosexuality.
Directory of Open Access Journals (Sweden)
Andrea Camperio Ciani
Full Text Available Several lines of evidence indicate the existence of genetic factors influencing male homosexuality and bisexuality. In spite of its relatively low frequency, the stable permanence in all human populations of this apparently detrimental trait constitutes a puzzling 'Darwinian paradox'. Furthermore, several studies have pointed out relevant asymmetries in the distribution of both male homosexuality and of female fecundity in the parental lines of homosexual vs. heterosexual males. A number of hypotheses have attempted to give an evolutionary explanation for the long-standing persistence of this trait, and for its asymmetric distribution in family lines; however a satisfactory understanding of the population genetics of male homosexuality is lacking at present. We perform a systematic mathematical analysis of the propagation and equilibrium of the putative genetic factors for male homosexuality in the population, based on the selection equation for one or two diallelic loci and Bayesian statistics for pedigree investigation. We show that only the two-locus genetic model with at least one locus on the X chromosome, and in which gene expression is sexually antagonistic (increasing female fitness but decreasing male fitness, accounts for all known empirical data. Our results help clarify the basic evolutionary dynamics of male homosexuality, establishing this as a clearly ascertained sexually antagonistic human trait.
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Kamada, Fumiaki; Kure, Shigeo; Kudo, Takayuki; Suzuki, Yoichi; Oshima, Takeshi; Ichinohe, Akiko; Kojima, Kanako; Niihori, Tetsuya; Kanno, Junko; Narumi, Yoko; Narisawa, Ayumi; Kato, Kumi; Aoki, Yoko; Ikeda, Katsuhisa; Kobayashi, Toshimitsu; Matsubara, Yoichi
2006-01-01
Autosomal-dominant, nonsyndromic hearing impairment is clinically and genetically heterogeneous. We encountered a large Japanese pedigree in which nonsyndromic hearing loss was inherited in an autosomal-dominant fashion. A genome-wide linkage study indicated linkage to the DFNA2 locus on chromosome 1p34. Mutational analysis of KCNQ4 encoding a potassium channel revealed a novel one-base deletion in exon 1, c.211delC, which generated a profoundly truncated protein without transmembrane domains (p.Q71fsX138). Previously, six missense mutations and one 13-base deletion, c.211_223del, had been reported in KCNQ4. Patients with the KCNQ4 missense mutations had younger-onset and more profound hearing loss than patients with the 211_223del mutation. In our current study, 12 individuals with the c.211delC mutation manifested late-onset and pure high-frequency hearing loss. Our results support the genotype-phenotype correlation that the KCNQ4 deletions are associated with later-onset and milder hearing impairment than the missense mutations. The phenotypic difference may be caused by the difference in pathogenic mechanisms: haploinsufficiency in deletions and dominant-negative effect in missense mutations.
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Heidaritabar, M; Vereijken, A; Muir, W M; Meuwissen, T; Cheng, H; Megens, H-J; Groenen, M A M; Bastiaansen, J W M
2014-12-01
Genomic selection (GS) is a DNA-based method of selecting for quantitative traits in animal and plant breeding, and offers a potentially superior alternative to traditional breeding methods that rely on pedigree and phenotype information. Using a 60 K SNP chip with markers spaced throughout the entire chicken genome, we compared the impact of GS and traditional BLUP (best linear unbiased prediction) selection methods applied side-by-side in three different lines of egg-laying chickens. Differences were demonstrated between methods, both at the level and genomic distribution of allele frequency changes. In all three lines, the average allele frequency changes were larger with GS, 0.056 0.064 and 0.066, compared with BLUP, 0.044, 0.045 and 0.036 for lines B1, B2 and W1, respectively. With BLUP, 35 selected regions (empirical P selected regions were identified. Empirical thresholds for local allele frequency changes were determined from gene dropping, and differed considerably between GS (0.167-0.198) and BLUP (0.105-0.126). Between lines, the genomic regions with large changes in allele frequencies showed limited overlap. Our results show that GS applies selection pressure much more locally than BLUP, resulting in larger allele frequency changes. With these results, novel insights into the nature of selection on quantitative traits have been gained and important questions regarding the long-term impact of GS are raised. The rapid changes to a part of the genetic architecture, while another part may not be selected, at least in the short term, require careful consideration, especially when selection occurs before phenotypes are observed.
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Ambeskovic, Mirela; Soltanpour, Nasrin; Falkenberg, Erin A; Zucchi, Fabiola C R; Kolb, Bryan; Metz, Gerlinde A S
2017-03-01
In a continuously stressful environment, the effects of recurrent prenatal stress (PS) accumulate across generations and generate new behavioral traits in the absence of genetic variation. Here, we investigated if PS or multigenerational PS across 4 generations differentially affect behavioral traits, laterality, and hemispheric dominance in male and female rats. Using skilled reaching and skilled walking tasks, 3 findings support the formation of new behavioral traits and shifted laterality by multigenerational stress. First, while PS in the F1 generation did not alter paw preference, multigenerational stress in the F4 generation shifted paw preference to favor left-handedness only in males. Second, multigenerational stress impaired skilled reaching and skilled walking movement abilities in males, while improving these abilities in females beyond the levels of controls. Third, the shift toward left-handedness in multigenerationally stressed males was accompanied by increased dendritic complexity and greater spine density in the right parietal cortex. Thus, cumulative multigenerational stress generates sexually dimorphic left-handedness and dominance shift toward the right hemisphere in males. These findings explain the origins of apparently heritable behavioral traits and handedness in the absence of DNA sequence variations while proposing epigenetic mechanisms. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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Bolos, A.M.; Goldman, D.; Brown, G.L. (National Institute on Alcohol Abuse and Alcoholism, Bethesda, MD (USA)); Lucas-Derse, S.; Ramsburg, M. (Program Resources Inc., Frederick, MD (USA))
1990-12-26
Using the dopamine D{sub 2} receptor clone {lambda}hD2G1, Blum et al recently found that the D{sub 2}/Taq 1 allele (A1) was present in 69{percent} of 35 deceased alcoholics but in only 20{percent} of an equal number of controls. To assess this association further, the authors evaluated the D{sub 2}/Taq 1 polymorphism and a single-strand conformation polymorphism detected by polymerase chain reaction and nondenaturing gel electrophoresis (PCR-SSCP) of the 3{prime} noncoding region of the D{sub 2} receptor gene. They studied 40 unrelated white alcoholics, 127 racially matched controls, and two white pedigrees. The Schedule for Affective Disorders and Schizophrenia-Lifetime Version (SADS-L) clinical diagnostic interviews were rated blindly by two clinicians. Alcoholics were subtyped according to age of onset, severity, presence of antisocial personality, and family history. No significant differences in either D{sub 2}/Taq 1 or PCR-SSCP allele frequencies were observed between alcoholics, subpopulations of alcoholics, or controls. The PCR-SSCP polymorphism provided independent information against linkage at the D{sub 2} receptor locus. This study does not support a widespread or consistent association between the D{sub 2} receptor gene and alcoholism.
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International Nuclear Information System (INIS)
Zha Jinmiao; Sun Liwei; Zhou Yiqi; Spear, Philip A.; Ma, Mei; Wang Zijian
2008-01-01
17α-Ethinylestradiol (EE 2 ) is a synthetic estrogen used primarily in birth control pills and in hormone replacement therapy. Owing to its occurrence in surface waters at concentrations frequently greater than 1 ng/l and its projected future use, EE 2 is expected to pose a significant risk to aquatic organisms. This study was conducted to obtain long-term exposure data necessary for the establishment of water quality criteria and to investigate mechanisms associated with toxic effects. In a multigeneration experiment, Chinese rare minnows (Gobiocypris rarus) were constantly exposed to environmentally relevant concentrations of the synthetic estrogen EE 2 . Mortality, deformities, reproductive parameters, plasma vitellogenin and histopathology were assessed. The results showed that, in the F 0 generation, all endpoints were significantly affected at concentrations higher than 0.2 ng/l EE 2 . No F 1 phenotypic males developed to maturity at 0.2 ng/l and, when adult females of this exposure group were crossed with unexposed males, no F 2 fertile eggs were produced. Kidney histopathology and ultrastructure suggest anomalies possibly associated with increased vitellogenin accumulation. We concluded that the reproduction of the F 1 minnows was completely inhibited at the lowest concentration tested, 0.2 ng/l EE 2 , a concentration frequently detected in surface waters. Growth effects may be related to increased energy requirements including the energy used in VTG synthesis. Reproductive effects are presumably associated with male feminization and the occurrence of testis-ova in males; however, ovarian degeneration observed in females may also have contributed to reproductive failure
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Personality Polygenes, Positive Affect, and Life Satisfaction
Weiss, Alexander; Baselmans, Bart M. L.; Hofer, Edith; Yang, Jingyun; Okbay, Aysu; Lind, Penelope A.; Miller, Mike B.; Nolte, Ilja M.; Zhao, Wei; Hagenaars, Saskia P.; Hottenga, Jouke-Jan; Matteson, Lindsay K.; Snieder, Harold; Faul, Jessica D.; Hartman, Catharina A.; Boyle, Patricia A.; Tiemeier, Henning; Mosing, Miriam A.; Pattie, Alison; Davies, Gail; Liewald, David C.; Schmidt, Reinhold; De Jager, Philip L.; Heath, Andrew C.; Jokela, Markus; Starr, John M.; Oldehinkel, Albertine J.; Johannesson, Magnus; Cesarini, David; Hofman, Albert; Harris, Sarah E.; Smith, Jennifer A.; Keltikangas-Jaervinen, Liisa; Pulkki-Raback, Laura; Schmidt, Helena; Smith, Jacqui; Iacono, William G.; McGue, Matt; Bennett, David A.; Pedersen, Nancy L.; Magnusson, Patrik K. E.; Deary, Ian J.; Martin, Nicholas G.; Boomsma, Dorret I.; Bartels, Meike; Luciano, Michelle
2016-01-01
Approximately half of the variation in wellbeing measures overlaps with variation in personality traits. Studies of non-human primate pedigrees and human twins suggest that this is due to common genetic influences. We tested whether personality polygenic scores for the NEO Five-Factor Inventory
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Personality Polygenes, Positive Affect, and Life Satisfaction.
Weiss, A.; Baselmans, B.M.L.; Hofer, E.; Yang, J.; Okbay, A.; Lind, P.A.; Miller, M.B.; Nolte, I.M.; Zhao, W.; Hagenaars, S.P.; Hottenga, J.J.; Matteson, L.K.; Snieder, H.; Faul, J.D.; Hartman, C.A.; Boyle, P.A.; Tiemeier, H.; Mosing, M.A.; Pattie, A.; Davies, G.; Liewald, D.C.; Schmidt, R.; Jager, P.L.; Heath, A.C.; Jokela, M; Starr, J.M.; Oldehinkel, A.J.; Johannesson, M.; Cesarini, D.; Hofman, A.; Harris, S.E.; Smith, J.A.; Keltikangas-Järvinen, L.; Pulkki-Råback, L.; Schmidt, H.; Smith, J; Iacono, W.G.; McGue, M.; Bennett, D.A.; Pedersen, N.L.; Magnusson, P.K.E.; Deary, I.J.; Martin, N.G.; Boomsma, D.I.; Bartels, M.; Luciano, M.
2016-01-01
Approximately half of the variation in wellbeing measures overlaps with variation in personality traits. Studies of non-human primate pedigrees and human twins suggest that this is due to common genetic influences. We tested whether personality polygenic scores for the NEO Five-Factor Inventory
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Identification of 17 hearing impaired mouse strains in the TMGC ENU-mutagenesis screen
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Kermany, Mohammad [St. Jude Children' s Research Hospital; Parker, Lisan [St. Jude Children' s Research Hospital; Guo, Yun-Kai [St. Jude Children' s Research Hospital; Miller, Darla R [ORNL; Swanson, Douglas J [ORNL; Yoo, Tai-June [Neuroscience Institute, Memphis, TN; Goldowitz, Daniel [University of Tennessee Health Science Center, Memphis; Zuo, Jian [St. Jude Children' s Research Hospital
2006-01-01
The Tennessee Mouse Genome Consortium (TMGC) employed an N-ethyl-N-nitrosourea (ENU)-mutagenesis scheme to identify mouse recessive mutants with hearing phenotypes. We employed auditory brainstem responses (ABR) to click and 8, 16, and 32 kHz stimuli and screened 285 pedigrees (1819 mice of 8-11 weeks old in various mixed genetic backgrounds) each bred to carry a homozygous ENU-induced mutation. To define mutant pedigrees, we measured P12 mice per pedigree in P2 generations and used a criterion where the mean ABR threshold per pedigree was two standard deviations above the mean of all offspring from the same parental strain. We thus identified 17 mutant pedigrees (6%), all exhibiting hearing loss at high frequencies (P16 kHz) with an average threshold elevation of 30-35 dB SPL. Interestingly, four mutants showed sex-biased hearing loss and six mutants displayed wide range frequency hearing loss. Temporal bone histology revealed that six of the first nine mutants displayed cochlear morphological defects: degeneration of spiral ganglia, spiral ligament fibrocytes or inner hair cells (but not outer hair cells) mostly in basal turns. In contrast to other ENU-mutagenesis auditory screens, our screen identified high-frequency, mild and sex-biased hearing defects. Further characterization of these 17 mouse models will advance our understanding of presbycusis and noise-induced hearing loss in humans.
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Sajjadi, Amir; Åkesson Castillo, Lars Christian Felipe; Sun, Bicen
2012-01-01
Introduction: A population that can live and work longer has resulted in a wider range of generations being active in the workplace simultaneously and the diverse multi-generational work environment is a new challenge for human resource management. The most recent generation that is entering the job market is Generation Y, which is also referred to as Millennials. Currently, organizations and Human Resource departments are facing the issue of Generation Y entering the workforce and the issue ...
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Fears, Scott C; Schür, Remmelt; Sjouwerman, Rachel; Service, Susan K; Araya, Carmen; Araya, Xinia; Bejarano, Julio; Knowles, Emma; Gomez-Makhinson, Juliana; Lopez, Maria C; Aldana, Ileana; Teshiba, Terri M; Abaryan, Zvart; Al-Sharif, Noor B; Navarro, Linda; Tishler, Todd A; Altshuler, Lori; Bartzokis, George; Escobar, Javier I; Glahn, David C; Thompson, Paul M; Lopez-Jaramillo, Carlos; Macaya, Gabriel; Molina, Julio; Reus, Victor I; Sabatti, Chiara; Cantor, Rita M; Freimer, Nelson B; Bearden, Carrie E
2015-07-01
Recent theories regarding the pathophysiology of bipolar disorder suggest contributions of both neurodevelopmental and neurodegenerative processes. While structural neuroimaging studies indicate disease-associated neuroanatomical alterations, the behavioural correlates of these alterations have not been well characterized. Here, we investigated multi-generational families genetically enriched for bipolar disorder to: (i) characterize neurobehavioural correlates of neuroanatomical measures implicated in the pathophysiology of bipolar disorder; (ii) identify brain-behaviour associations that differ between diagnostic groups; (iii) identify neurocognitive traits that show evidence of accelerated ageing specifically in subjects with bipolar disorder; and (iv) identify brain-behaviour correlations that differ across the age span. Structural neuroimages and multi-dimensional assessments of temperament and neurocognition were acquired from 527 (153 bipolar disorder and 374 non-bipolar disorder) adults aged 18-87 years in 26 families with heavy genetic loading for bipolar disorder. We used linear regression models to identify significant brain-behaviour associations and test whether brain-behaviour relationships differed: (i) between diagnostic groups; and (ii) as a function of age. We found that total cortical and ventricular volume had the greatest number of significant behavioural associations, and included correlations with measures from multiple cognitive domains, particularly declarative and working memory and executive function. Cortical thickness measures, in contrast, showed more specific associations with declarative memory, letter fluency and processing speed tasks. While the majority of brain-behaviour relationships were similar across diagnostic groups, increased cortical thickness in ventrolateral prefrontal and parietal cortical regions was associated with better declarative memory only in bipolar disorder subjects, and not in non-bipolar disorder family
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Recombination in the human Pseudoautosomal region PAR1.
Directory of Open Access Journals (Sweden)
Anjali G Hinch
2014-07-01
Full Text Available The pseudoautosomal region (PAR is a short region of homology between the mammalian X and Y chromosomes, which has undergone rapid evolution. A crossover in the PAR is essential for the proper disjunction of X and Y chromosomes in male meiosis, and PAR deletion results in male sterility. This leads the human PAR with the obligatory crossover, PAR1, to having an exceptionally high male crossover rate, which is 17-fold higher than the genome-wide average. However, the mechanism by which this obligatory crossover occurs remains unknown, as does the fine-scale positioning of crossovers across this region. Recent research in mice has suggested that crossovers in PAR may be mediated independently of the protein PRDM9, which localises virtually all crossovers in the autosomes. To investigate recombination in this region, we construct the most fine-scale genetic map containing directly observed crossovers to date using African-American pedigrees. We leverage recombination rates inferred from the breakdown of linkage disequilibrium in human populations and investigate the signatures of DNA evolution due to recombination. Further, we identify direct PRDM9 binding sites using ChIP-seq in human cells. Using these independent lines of evidence, we show that, in contrast with mouse, PRDM9 does localise peaks of recombination in the human PAR1. We find that recombination is a far more rapid and intense driver of sequence evolution in PAR1 than it is on the autosomes. We also show that PAR1 hotspot activities differ significantly among human populations. Finally, we find evidence that PAR1 hotspot positions have changed between human and chimpanzee, with no evidence of sharing among the hottest hotspots. We anticipate that the genetic maps built and validated in this work will aid research on this vital and fascinating region of the genome.
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Boattini, A; Sarno, S; Pedrini, P; Medoro, C; Carta, M; Tucci, S; Ferri, G; Alù, M; Luiselli, D; Pettener, D
2015-02-01
Social and cultural factors had a critical role in determining the genetic structure of Europe. Therefore, socially stratified populations may help to focus on specific episodes of European demographic history. In this study, we use uniparental markers to analyse the genetic structure of Partecipanza in San Giovanni in Persiceto (Northern Italy), a peculiar institution whose origins date back to the Middle Ages and whose members form the patrilineal descent of a group of founder families. From a maternal point of view (mtDNA), Partecipanza is genetically homogeneous with the rest of the population. However, we observed a significant differentiation for Y-chromosomes. In addition, by comparing 17 Y-STR profiles with deep-rooted paternal pedigrees, we estimated a Y-STR mutation rate equal to 3.90 * 10(-3) mutations per STR per generation and an average generation duration time of 33.38 years. When we used these values for tentative dating, we estimated 1300-600 years ago for the origins of the Partecipanza. These results, together with a peculiar Y-chromosomal composition and historical evidence, suggest that Germanic populations (Lombards in particular) settled in the area during the Migration Period (400-800 AD, approximately) and may have had an important role in the foundation of this community.
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Vogt, Christian; Hess, Maren; Nowak, Carsten; Diogo, João Barateiro; Oehlmann, Jörg; Oetken, Matthias
2010-10-01
So far only a few studies have been performed to assess the effects of dynamic pollutant exposure on life-history parameters of invertebrates. In a previous multi-generation approach with the midge Chironomus riparius we tested if a chronic tributyltin pre-exposure alters the ability of a population to cope with subsequent cadmium stress. In the experiment two separate chironomid populations were exposed via sediments to different TBT-concentrations (4.46 and 8.93 μg Sn/kg dw) for several generations, followed by subsequent cadmium exposure (1.2 mg Cd/kg dw) for three generations. While the TBT-exposure to 4.46 μg Sn/kg dw had only small effects on the development and reproduction of C. riparius the higher TBT-concentration of 8.93 μg Sn/kg dw led to negative effects on life-history traits. Therefore, a higher adverse effect of the higher TBT-concentration and thus a higher susceptibility to other stressors could be assumed. Within, this paper only the results of the second stressor experiment were presented; clear effects of Cd on development and reproduction of C. riparius were determined independent of the pre-exposure scenario. While no differences in Cd-sensitivity were found between the population without pre-exposure to TBT and the population pre-exposed to the low TBT-concentration (4.46 μg Sn/kg dw), the pre-exposure of midges to the higher TBT-concentration (8.93 μg Sn/kg dw) resulted in a significantly higher susceptibility to subsequent Cd-stress. These results document that the exposure history may influence the reaction to altered chemical stress. Our findings are relevant to understand and predict the evolutionary fate of populations in rapidly changing, human-impacted environments. However, the fact that chemical-induced reduced genetic diversity, which is not necessarily linked to genetic adaptation, leads to a reduced fitness under altered stress conditions, is to our knowledge a novel finding.
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Directory of Open Access Journals (Sweden)
Kwi Hye Kim
Full Text Available Fibroblasts from patients with Type I bipolar disorder (BPD and their unaffected siblings were obtained from an Old Order Amish pedigree with a high incidence of BPD and reprogrammed to induced pluripotent stem cells (iPSCs. Established iPSCs were subsequently differentiated into neuroprogenitors (NPs and then to neurons. Transcriptomic microarray analysis was conducted on RNA samples from iPSCs, NPs and neurons matured in culture for either 2 weeks (termed early neurons, E or 4 weeks (termed late neurons, L. Global RNA profiling indicated that BPD and control iPSCs differentiated into NPs and neurons at a similar rate, enabling studies of differentially expressed genes in neurons from controls and BPD cases. Significant disease-associated differences in gene expression were observed only in L neurons. Specifically, 328 genes were differentially expressed between BPD and control L neurons including GAD1, glutamate decarboxylase 1 (2.5 fold and SCN4B, the voltage gated type IV sodium channel beta subunit (-14.6 fold. Quantitative RT-PCR confirmed the up-regulation of GAD1 in BPD compared to control L neurons. Gene Ontology, GeneGo and Ingenuity Pathway Analysis of differentially regulated genes in L neurons suggest that alterations in RNA biosynthesis and metabolism, protein trafficking as well as receptor signaling pathways may play an important role in the pathophysiology of BPD.
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Variation in human recombination rates and its genetic determinants.
Directory of Open Access Journals (Sweden)
Adi Fledel-Alon
Full Text Available Despite the fundamental role of crossing-over in the pairing and segregation of chromosomes during human meiosis, the rates and placements of events vary markedly among individuals. Characterizing this variation and identifying its determinants are essential steps in our understanding of the human recombination process and its evolution.Using three large sets of European-American pedigrees, we examined variation in five recombination phenotypes that capture distinct aspects of crossing-over patterns. We found that the mean recombination rate in males and females and the historical hotspot usage are significantly heritable and are uncorrelated with one another. We then conducted a genome-wide association study in order to identify loci that influence them. We replicated associations of RNF212 with the mean rate in males and in females as well as the association of Inversion 17q21.31 with the female mean rate. We also replicated the association of PRDM9 with historical hotspot usage, finding that it explains most of the genetic variance in this phenotype. In addition, we identified a set of new candidate regions for further validation.These findings suggest that variation at broad and fine scales is largely separable and that, beyond three known loci, there is no evidence for common variation with large effects on recombination phenotypes.
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Directory of Open Access Journals (Sweden)
Yubin Wang
2016-06-01
Full Text Available A CAPN1 missense mutation in Parson Russell Terrier dogs is associated with spinocerebellar ataxia. We now report that homozygous or heterozygous CAPN1-null mutations in humans result in cerebellar ataxia and limb spasticity in four independent pedigrees. Calpain-1 knockout (KO mice also exhibit a mild form of ataxia due to abnormal cerebellar development, including enhanced neuronal apoptosis, decreased number of cerebellar granule cells, and altered synaptic transmission. Enhanced apoptosis is due to absence of calpain-1-mediated cleavage of PH domain and leucine-rich repeat protein phosphatase 1 (PHLPP1, which results in inhibition of the Akt pro-survival pathway in developing granule cells. Injection of neonatal mice with the indirect Akt activator, bisperoxovanadium, or crossing calpain-1 KO mice with PHLPP1 KO mice prevented increased postnatal cerebellar granule cell apoptosis and restored granule cell density and motor coordination in adult mice. Thus, mutations in CAPN1 are an additional cause of ataxia in mammals, including humans.
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Energy Technology Data Exchange (ETDEWEB)
Strand, R.; Cox, T.L.; Sjoreen, A.; Alvic, D.
1989-06-01
The National Center for Toxicological Research (NCTR) is the basic research arm of the US Food and Drug Administration (FDA). The NCTR has upgraded and standardized its computer operations on Digital Equipment Corporation VAX minicomputers using Software AG's ADABAS data base management system for all research applications. The NCTR is currently performing a large study to improve the functionality of the animal husbandry systems and applications called Breeding/Multigeneration Support System (BMSS). When functional, it will operate on VAX equipment using the ADABAS data base management system, TDMS, and COBOL. Oak Ridge National Laboratory (ORNL) is supporting NCTR in the design, prototyping, and software engineering of the BMSS. This document summarizes the internal design elements that include data structures, file structures, and system attributes that were required to facilitate the decision support requirements defined in the external design work. Prototype pseudocode then was developed for the recommended system attributes and file and data structures. Finally, ORNL described the processing requirements including the initial access of the BMSS, integration of the existing INLIFE system and the STUDY DEFINITION system under development, data system initialization and maintenance, and BMSS testing and verification. This document describes ORNL's recommendations for the internal design of the BMSS. ORNL will provide research support to NCTR in the additional phases of systems life cycle development for BMSS. ORNL has prepared this document according to NCTR's Standard Operating Procedures for Systems Development. 6 figs., 5 tabs.
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Rong, Weining; Chen, Xuejuan; Li, Huiping; Liu, Yani; Sheng, Xunlun
2014-06-01
To detect the disease-causing genes of 10 retinitis pigmentosa pedigrees by using exon combined target region capture sequencing chip. Pedigree investigation study. From October 2010 to December 2013, 10 RP pedigrees were recruited for this study in Ningxia Eye Hospital. All the patients and family members received complete ophthalmic examinations. DNA was abstracted from patients, family members and controls. Using exon combined target region capture sequencing chip to screen the candidate disease-causing mutations. Polymerase chain reaction (PCR) and direct sequencing were used to confirm the disease-causing mutations. Seventy patients and 23 normal family members were recruited from 10 pedigrees. Among 10 RP pedigrees, 1 was autosomal dominant pedigrees and 9 were autosomal recessive pedigrees. 7 mutations related to 5 genes of 5 pedigrees were detected. A frameshift mutation on BBS7 gene was detected in No.2 pedigree, the patients of this pedigree combined with central obesity, polydactyly and mental handicap. No.2 pedigree was diagnosed as Bardet-Biedl syndrome finally. A missense mutation was detected in No.7 and No.10 pedigrees respectively. Because the patients suffered deafness meanwhile, the final diagnosis was Usher syndrome. A missense mutation on C3 gene related to age-related macular degeneration was also detected in No. 7 pedigrees. A nonsense mutation and a missense mutation on CRB1 gene were detected in No. 1 pedigree and a splicesite mutation on PROM1 gene was detected in No. 5 pedigree. Retinitis pigmentosa is a kind of genetic eye disease with diversity clinical phenotypes. Rapid and effective genetic diagnosis technology combined with clinical characteristics analysis is helpful to improve the level of clinical diagnosis of RP.
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Zhang, Qi-Jie; Xu, Liu-Qing; Wang, Chong; Hu, Wei; Wang, Ning; Chen, Wan-Jin
2016-12-01
Wilson's disease (WD) is an autosomal recessive inherited disorder of copper metabolism with excellent prognosis if treated timely. However, WD is usually prone to neglect and misdiagnosis at an early stage. We reported a rare WD pedigree, and the clinical features, laboratory tests, and gene mutations were analyzed in detail. The patient was a 17-year-old and 136-cm-tall girl who presented with limb weakness, combined with multi-organ disorders including blind eye, epilepsy, and hypopituitarism. Clinical tests showed a low serum ceruloplasmin level, high urinary copper excretion and Kayser-Fleischer (K-F) rings. She carried a compound heterozygous mutations in ATP7B gene (c.2828G>A and c.3884C>T). Her younger brother, as an asymptomatic patient, manifested with elevation of transaminases but without neurological and hepatic symptoms. They were diagnosed as WD finally. They were treated with sodium dimercaptosulphonate, supplemented with zinc gluconate, vitamin B6, vitamin C, as well as restriction of dietary copper. The urinary copper excretion and serum transaminase level decreased gradually. The abnormal signals in brainstem and basal ganglia were also remarkably decreased after 4-year of de-copper treatment. As to the patients with complicated clinical manifestations, the extrapyramidal symptom and basal ganglia signals should be concerned. The serum ceruloplasmin detection and ATP7B gene mutation screening are necessary.
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Elmhiri, G; Gloaguen, C; Grison, S; Kereselidze, D; Elie, C; Tack, K; Benderitter, M; Lestaevel, P; Legendre, A; Souidi, M
2018-01-05
An increased health problem in industrialised countries is the contemporary concern of public and scientific community as well. This has been attributed in part to accumulated environmental pollutants especially radioactive substances and the use of nuclear power plants worldwide. However, the outcome of chronic exposure to low doses of a radionuclide such as uranium remains unknown. Recently, a paradigm shift in the perception of risk of radiotoxicology has emerged through investigating the possibility of transmission of biological effects over generations, in particular by epigenetic pathways. These processes are known for their crucial roles associated with the development of several diseases. The current work investigates the epigenetic effect of chronic exposure to low doses of uranium and its inheritance across generations. Materials and Methods To test this proposition, a rodent multigenerational model, males and females, were exposed to a non-toxic concentration of uranium (40mgL -1 drinking water) for nine months. The uranium effects on were evaluated over three generations (F0, F1 and F2) by analysing the DNA methylation profile and DNMT genes expression in ovaries and testes tissues. Here we report a significant hypermethylation of testes DNA (p <0.005) whereas ovaries showed hypomethylated DNA (p <0.005). Interestingly, this DNA methylation profile was significantly maintained across generations F0, F1 and F2. Furthermore, qPCR results of both tissues imply a significant change in the expression of DNA methyltransferase genes (DNMT 1 and DNMT3a/b) as well. Altogether, our work demonstrates for the first time a sex-dependance and inheritance of epigenetic marks, DNA methylation, as a biological response to the exposure to low doses of uranium. However, it is not clear which type of reproductive cell type is more responsive in this context. Copyright © 2017 Elsevier B.V. All rights reserved.
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Austin, Melissa A
2002-04-01
Recent completion of the draft sequence of the human genome has been greeted with both excitement and skepticism, and the potential of this accomplishment for advancing public health has been tempered by ethical concerns about the protection of human subjects. This commentary explores ethical issues arising in human genome epidemiology by using a case study approach based on the ongoing Japanese American Family Study at the University of Washington in Seattle (1994-2003). Ethical issues encountered in designing the study, collecting the data, and reporting the study results are considered. When developing studies, investigators must consider whether to restrict the study to specific racial or ethnic groups and whether community involvement is appropriate. Once the study design is in place, further ethical issues emerge, including obtaining informed consent for DNA banking and protecting the privacy and confidentiality of family members. Finally, investigators must carefully consider whether to report genotype results to study participants and whether pedigrees illustrating the results of the study will be published. Overall, the promise of genomics for improving public health must be pursued based on the fundamental ethical principles of respect for persons, beneficence, and justice.
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Quantifying inbreeding avoidance through extra-pair reproduction.
Reid, Jane M; Arcese, Peter; Keller, Lukas F; Germain, Ryan R; Duthie, A Bradley; Losdat, Sylvain; Wolak, Matthew E; Nietlisbach, Pirmin
2015-01-01
Extra-pair reproduction is widely hypothesized to allow females to avoid inbreeding with related socially paired males. Consequently, numerous field studies have tested the key predictions that extra-pair offspring are less inbred than females' alternative within-pair offspring, and that the probability of extra-pair reproduction increases with a female's relatedness to her socially paired male. However, such studies rarely measure inbreeding or relatedness sufficiently precisely to detect subtle effects, or consider biases stemming from failure to observe inbred offspring that die during early development. Analyses of multigenerational song sparrow (Melospiza melodia) pedigree data showed that most females had opportunity to increase or decrease the coefficient of inbreeding of their offspring through extra-pair reproduction with neighboring males. In practice, observed extra-pair offspring had lower inbreeding coefficients than females' within-pair offspring on average, while the probability of extra-pair reproduction increased substantially with the coefficient of kinship between a female and her socially paired male. However, simulations showed that such effects could simply reflect bias stemming from inbreeding depression in early offspring survival. The null hypothesis that extra-pair reproduction is random with respect to kinship therefore cannot be definitively rejected in song sparrows, and existing general evidence that females avoid inbreeding through extra-pair reproduction requires reevaluation given such biases. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.
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Extra Molting and Selection on Nymphal Growth in the Desert Locust.
Directory of Open Access Journals (Sweden)
Benjamin Pélissié
Full Text Available In insects, extra-molting has been viewed as a compensatory mechanism for nymphal growth that contributes to optimize body weight for successful reproduction. However, little is known on the capacity of extra-molting to evolve in natural populations, which limits our understanding of how selection acts on nymphal growth. We used a multi-generational pedigree, individual monitoring and quantitative genetics models to investigate the evolution of extra-molting and its impact on nymphal growth in a solitarious population of the desert locust, Schistocerca gregaria. Growth compensation via extra-molting was observed for 46% of the females, whose adult weight exceeded by 4% that of other females, at a cost of a 22% longer development time. We found a null heritability for body weight threshold only, and the highest and a strongly female-biased heritability for extra molting. Our genetic estimates show that (1 directional selection can act on growth rate, development time and extra-molting to optimize body weight threshold, the target of stabilizing selection, (2 extra-molting can evolve in natural populations, and (3 a genetic conflict, due to sexually antagonistic selection on extra-molting, might prevent its fixation. Finally, we discuss how antagonistic selection between solitarious and gregarious environments and/or genetic correlations between growth and phase traits might also impact the evolution of extra-molting in locusts.
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Leading and Managing Disparate Generations in Cross-Cultural Learning Organizations
Mujtaba, Bahaudin; Thomas, Gimol
2005-01-01
The enclosed literature focuses on learning about the various generations of the workforce and techniques that employers can utilize to organize collaborative teams in today's multigenerational and multicultural workplaces. Trainers and teachers can use this material to provide effective skills for managers that deal with a multi-generation of…
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Directory of Open Access Journals (Sweden)
Janković Snežana
2010-01-01
Full Text Available Relationships among quantitative traits of wheat were analyzed in parents and their F3, F4 and F5 hybrids. Three female parents (Briscard, Carifen 12 and Rescler were crossed with two male parents (Francuska and PKB-Prelivka. Same crosses were repeated 4 years, from 1996 to 1999. Hybrids were obtained via pedigree and bulk selection. In year 2000 the field experiments were set up with all parental and hybrid material, at the Institute 'PKB INI Agroekonomik', in Padinska Skela, near Belgrade. Six traits were measured: plant height, spike length, number of spikelets per spike, number of grains per spike, 1000 grain weight and grain weight per spike. In parental genotypes, it was found grain mass per spike was in significant and positive correlation with 1000 grain mass and number of grains per spike. As in parents, correlation between grain mass per spike and 1000 grain weight was almost functional in F3, F4 and F5 hybrids. However, correlation between grain mass per spike and number of grains per spike was negative or slight positive in hybrid descendents, what is surprising because it is oppositely to the parents. Similar values of correlation coefficients were found in both applied methods of selection. This fact shows correlations change between generations. Grain mass per spike depends on a 1000 grain mass in both, parental and hybrid generations. Stable relationship between traits could be use for selection of high yielding genotypes.
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DEFF Research Database (Denmark)
Nolsøe, R L; Kelly, J A; Pociot, F
2005-01-01
Systemic lupus erythematosus (SLE) is an autoimmune disorder characterized by production of autoantibodies against intracellular antigens and tissue injury. Defective apoptosis of activated immune cells leads to the development of autoantibodies in SLE. FasL initiated apoptosis is central...... for peripheral tolerance. Fas deficiencies in humans and mice predispose toward systemic autoimmunity. SLE is conferred by many genes. The genetic effects may be concentrated by familial clustering or by stratifying of subphenotypes. We have tested polymorphisms and haplotypes in FAS and FASL for association...... to SLE or subphenotypes in 126 multiplex American SLE pedigrees and found association of the FAS codon214 AC(C/T) as well as the FAS-670G>A'-codon214 AC(C/T)' haplotype to thrombocytopenia in SLE. Furthermore we have functionally characterized the FAS/FASL promoter polymorphisms associated with SLE...
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Meiotic gene-conversion rate and tract length variation in the human genome.
Padhukasahasram, Badri; Rannala, Bruce
2013-02-27
Meiotic recombination occurs in the form of two different mechanisms called crossing-over and gene-conversion and both processes have an important role in shaping genetic variation in populations. Although variation in crossing-over rates has been studied extensively using sperm-typing experiments, pedigree studies and population genetic approaches, our knowledge of variation in gene-conversion parameters (ie, rates and mean tract lengths) remains far from complete. To explore variability in population gene-conversion rates and its relationship to crossing-over rate variation patterns, we have developed and validated using coalescent simulations a comprehensive Bayesian full-likelihood method that can jointly infer crossing-over and gene-conversion rates as well as tract lengths from population genomic data under general variable rate models with recombination hotspots. Here, we apply this new method to SNP data from multiple human populations and attempt to characterize for the first time the fine-scale variation in gene-conversion parameters along the human genome. We find that the estimated ratio of gene-conversion to crossing-over rates varies considerably across genomic regions as well as between populations. However, there is a great degree of uncertainty associated with such estimates. We also find substantial evidence for variation in the mean conversion tract length. The estimated tract lengths did not show any negative relationship with the local heterozygosity levels in our analysis.European Journal of Human Genetics advance online publication, 27 February 2013; doi:10.1038/ejhg.2013.30.
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Novel human neuronal tau model exhibiting neurofibrillary tangles and transcellular propagation.
Reilly, Patrick; Winston, Charisse N; Baron, Kelsey R; Trejo, Margarita; Rockenstein, Edward M; Akers, Johnny C; Kfoury, Najla; Diamond, Marc; Masliah, Eliezer; Rissman, Robert A; Yuan, Shauna H
2017-10-01
Tauopathies are a class of neurodegenerative diseases, including Alzheimer's disease, frontotemporal dementia and progressive supranuclear palsy, which are associated with the pathological aggregation of tau protein into neurofibrillary tangles (NFT). Studies have characterized tau as a "prion-like" protein given its ability to form distinct, stable amyloid conformations capable of transcellular and multigenerational propagation in clonal fashion. It has been proposed that progression of tauopathy could be due to the prion-like propagation of tau, suggesting the possibility that end-stage pathologies, like NFT formation, may require an instigating event such as tau seeding. To investigate this, we applied a novel human induced pluripotent stem cell (hiPSC) system we have developed to serve as a human neuronal model. We introduced the tau repeat domain (tau-RD) with P301L and V337M (tau-RD-LM) mutations into hiPSC-derived neurons and observed expression of tau-RD at levels similar to total tau in postmortem AD brains. Tau aggregation occurred without the addition of recombinant tau fibrils. The conditioned media from tau-RD cultures contained tau-RD seeds, which were capable of inducing aggregate formation in homotypic mode in non-transduced recipient neuronal cultures. The resultant NFTs were thioflavin-positive, silver stain-positive, and assumed fibrillary appearance on transmission electron microscopy (TEM) with immunogold, which revealed paired helical filament 1 (PHF1)-positive NFTs, representing possible recruitment of endogenous tau in the aggregates. Functionally, expression of tau-RD caused neurotoxicity that manifested as axon retraction, synaptic density reduction, and enlargement of lysosomes. The results of our hiPSC study were reinforced by the observation that Tau-RD-LM is excreted in exosomes, which mediated the transfer of human tau to wild-type mouse neurons in vivo. Our hiPSC human neuronal system provides a model for further studies of tau
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Directory of Open Access Journals (Sweden)
Dina F Ahram
Full Text Available Several dog breeds are susceptible to developing primary angle closure glaucoma (PACG, which suggests a genetic basis for the disease. We have identified a four-generation Basset Hound pedigree with characteristic autosomal recessive PACG that closely recapitulates PACG in humans. Our aim is to utilize gene mapping and whole exome sequencing approaches to identify PACG-causing sequence variants in the Basset. Extensive clinical phenotyping of all pedigree members was conducted. SNP-chip genotyping was carried out in 9 affected and 15 unaffected pedigree members. Two-point and multipoint linkage analyses of genome-wide SNP data were performed using Superlink-Online SNP-1.1 and a locus was mapped to chromosome 19q with a maximum LOD score of 3.24. The locus contains 12 Ensemble predicted canine genes and is syntenic to a region on chromosome 2 in the human genome. Using exome-sequencing analysis, a possibly damaging, non-synonymous variant in the gene Nebulin (NEB was found to segregate with PACG which alters a phylogenetically conserved Lysine residue. The association of this variants with PACG was confirmed in a secondary cohort of unrelated Basset Hounds (p = 3.4 × 10-4, OR = 15.3 for homozygosity. Nebulin, a protein that promotes the contractile function of sarcomeres, was found to be prominently expressed in the ciliary muscles of the anterior segment. Our findings may provide insight into the molecular mechanisms that underlie PACG. The phenotypic similarities of disease presentation in dogs and humans may enable the translation of findings made in this study to patients with PACG.
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Ahram, Dina F; Grozdanic, Sinisa D; Kecova, Helga; Henkes, Arjen; Collin, Rob W J; Kuehn, Markus H
2015-01-01
Several dog breeds are susceptible to developing primary angle closure glaucoma (PACG), which suggests a genetic basis for the disease. We have identified a four-generation Basset Hound pedigree with characteristic autosomal recessive PACG that closely recapitulates PACG in humans. Our aim is to utilize gene mapping and whole exome sequencing approaches to identify PACG-causing sequence variants in the Basset. Extensive clinical phenotyping of all pedigree members was conducted. SNP-chip genotyping was carried out in 9 affected and 15 unaffected pedigree members. Two-point and multipoint linkage analyses of genome-wide SNP data were performed using Superlink-Online SNP-1.1 and a locus was mapped to chromosome 19q with a maximum LOD score of 3.24. The locus contains 12 Ensemble predicted canine genes and is syntenic to a region on chromosome 2 in the human genome. Using exome-sequencing analysis, a possibly damaging, non-synonymous variant in the gene Nebulin (NEB) was found to segregate with PACG which alters a phylogenetically conserved Lysine residue. The association of this variants with PACG was confirmed in a secondary cohort of unrelated Basset Hounds (p = 3.4 × 10-4, OR = 15.3 for homozygosity). Nebulin, a protein that promotes the contractile function of sarcomeres, was found to be prominently expressed in the ciliary muscles of the anterior segment. Our findings may provide insight into the molecular mechanisms that underlie PACG. The phenotypic similarities of disease presentation in dogs and humans may enable the translation of findings made in this study to patients with PACG.
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Shaw, Liam; Ribeiro, Andre L R; Levine, Adam P; Pontikos, Nikolas; Balloux, Francois; Segal, Anthony W; Roberts, Adam P; Smith, Andrew M
2017-09-12
The human microbiome is affected by multiple factors, including the environment and host genetics. In this study, we analyzed the salivary microbiomes of an extended family of Ashkenazi Jewish individuals living in several cities and investigated associations with both shared household and host genetic similarities. We found that environmental effects dominated over genetic effects. While there was weak evidence of geographical structuring at the level of cities, we observed a large and significant effect of shared household on microbiome composition, supporting the role of the immediate shared environment in dictating the presence or absence of taxa. This effect was also seen when including adults who had grown up in the same household but moved out prior to the time of sampling, suggesting that the establishment of the salivary microbiome earlier in life may affect its long-term composition. We found weak associations between host genetic relatedness and microbiome dissimilarity when using family pedigrees as proxies for genetic similarity. However, this association disappeared when using more-accurate measures of kinship based on genome-wide genetic markers, indicating that the environment rather than host genetics is the dominant factor affecting the composition of the salivary microbiome in closely related individuals. Our results support the concept that there is a consistent core microbiome conserved across global scales but that small-scale effects due to a shared living environment significantly affect microbial community composition. IMPORTANCE Previous research shows that the salivary microbiomes of relatives are more similar than those of nonrelatives, but it remains difficult to distinguish the effects of relatedness and shared household environment. Furthermore, pedigree measures may not accurately measure host genetic similarity. In this study, we include genetic relatedness based on genome-wide single nucleotide polymorphisms (SNPs) (rather than
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SIX2 haploinsufficiency causes conductive hearing loss with ptosis in humans.
Guan, Jing; Wang, Dayong; Cao, Wenjian; Zhao, Yali; Du, Renqian; Yuan, Hu; Liu, Qiong; Lan, Lan; Zong, Liang; Yang, Ju; Yin, Zifang; Han, Bing; Zhang, Feng; Wang, Qiuju
2016-11-01
The ossicles represent one of the most fundamental morphological features in evolutionary biology of the mammalians. The mobile ossicular morphology abnormalities result in the severe conductive hearing loss. Development and patterning of the middle ear malformation depend on genetic and environmental causes. However, the genetic basis for the risk of congenital ossicle malformation is poorly understood. We show here nine affected individuals in a Chinese pedigree who had bilateral conductive hearing loss with ptosis. We performed whole-genome sequencing and array comparative genomic hybridization (CGH) analysis on DNA samples from the Chinese pedigree. We confirmed the presence of a novel 60 kb heterozygous deletion in size, encompassing SIX2 in our family. Mutation screening in 169 sporadic cases with external ear and middle ear malformations identified no pathogenic variant or polymorphism. We suggest SIX2 haploinsufficiency as a potential congenital factor could be attributed to developmental malformation of the middle ear ossicles and upper eyelid. To the best of our knowledge, this is the first report to provide a description of copy number variation in the SIX2 gene resulting in syndromic conductive hearing loss.
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Ahram, D.F.; Grozdanic, S.D.; Kecova, H.; Henkes, A.; Collin, R.W.J.; Kuehn, M.H.
2015-01-01
Several dog breeds are susceptible to developing primary angle closure glaucoma (PACG), which suggests a genetic basis for the disease. We have identified a four-generation Basset Hound pedigree with characteristic autosomal recessive PACG that closely recapitulates PACG in humans. Our aim is to
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Directory of Open Access Journals (Sweden)
Jane Ellen Simmons
2011-10-01
Full Text Available In complex mixture toxicology, there is growing emphasis on testing environmentally representative doses that improve the relevance of results for health risk assessment, but are typically much lower than those used in traditional toxicology studies. Traditional experimental designs with typical sample sizes may have insufficient statistical power to detect effects caused by environmentally relevant doses. Proper study design, with adequate statistical power, is critical to ensuring that experimental results are useful for environmental health risk assessment. Studies with environmentally realistic complex mixtures have practical constraints on sample concentration factor and sample volume as well as the number of animals that can be accommodated. This article describes methodology for calculation of statistical power for non-independent observations for a multigenerational rodent reproductive/developmental bioassay. The use of the methodology is illustrated using the U.S. EPA’s Four Lab study in which rodents were exposed to chlorinated water concentrates containing complex mixtures of drinking water disinfection by-products. Possible experimental designs included two single-block designs and a two-block design. Considering the possible study designs and constraints, a design of two blocks of 100 females with a 40:60 ratio of control:treated animals and a significance level of 0.05 yielded maximum prospective power (~90% to detect pup weight decreases, while providing the most power to detect increased prenatal loss.
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Dingus, Cheryl A.; Teuschler, Linda K.; Rice, Glenn E.; Simmons, Jane Ellen; Narotsky, Michael G.
2011-01-01
In complex mixture toxicology, there is growing emphasis on testing environmentally representative doses that improve the relevance of results for health risk assessment, but are typically much lower than those used in traditional toxicology studies. Traditional experimental designs with typical sample sizes may have insufficient statistical power to detect effects caused by environmentally relevant doses. Proper study design, with adequate statistical power, is critical to ensuring that experimental results are useful for environmental health risk assessment. Studies with environmentally realistic complex mixtures have practical constraints on sample concentration factor and sample volume as well as the number of animals that can be accommodated. This article describes methodology for calculation of statistical power for non-independent observations for a multigenerational rodent reproductive/developmental bioassay. The use of the methodology is illustrated using the U.S. EPA’s Four Lab study in which rodents were exposed to chlorinated water concentrates containing complex mixtures of drinking water disinfection by-products. Possible experimental designs included two single-block designs and a two-block design. Considering the possible study designs and constraints, a design of two blocks of 100 females with a 40:60 ratio of control:treated animals and a significance level of 0.05 yielded maximum prospective power (~90%) to detect pup weight decreases, while providing the most power to detect increased prenatal loss. PMID:22073030
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Multigenerational epigenetic adaptation of the hepatic wound-healing response.
Zeybel, Müjdat; Hardy, Timothy; Wong, Yi K; Mathers, John C; Fox, Christopher R; Gackowska, Agata; Oakley, Fiona; Burt, Alastair D; Wilson, Caroline L; Anstee, Quentin M; Barter, Matt J; Masson, Steven; Elsharkawy, Ahmed M; Mann, Derek A; Mann, Jelena
2012-09-01
We investigated whether ancestral liver damage leads to heritable reprogramming of hepatic wound healing in male rats. We found that a history of liver damage corresponds with transmission of an epigenetic suppressive adaptation of the fibrogenic component of wound healing to the male F1 and F2 generations. Underlying this adaptation was less generation of liver myofibroblasts, higher hepatic expression of the antifibrogenic factor peroxisome proliferator-activated receptor γ (PPAR-γ) and lower expression of the profibrogenic factor transforming growth factor β1 (TGF-β1) compared to rats without this adaptation. Remodeling of DNA methylation and histone acetylation underpinned these alterations in gene expression. Sperm from rats with liver fibrosis were enriched for the histone variant H2A.Z and trimethylation of histone H3 at Lys27 (H3K27me3) at PPAR-γ chromatin. These modifications to the sperm chromatin were transmittable by adaptive serum transfer from fibrotic rats to naive rats and similar modifications were induced in mesenchymal stem cells exposed to conditioned media from cultured rat or human myofibroblasts. Thus, it is probable that a myofibroblast-secreted soluble factor stimulates heritable epigenetic signatures in sperm so that the resulting offspring better adapt to future fibrogenic hepatic insults. Adding possible relevance to humans, we found that people with mild liver fibrosis have hypomethylation of the PPARG promoter compared to others with severe fibrosis.
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Santos, O.
2002-01-01
term, multi-generational biological studies with large sample sizes and appropriate controls.
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Energy Technology Data Exchange (ETDEWEB)
Goodman, A.B. [Columbia Univ. School of Public Health, New York, NY (United States)
1994-09-15
Among relatives of Ashkenazi schizophrenic probands the rate of amyotrophic lateral sclerosis was 3/1,000, compared to expected population rates of approximately 2/100,000. Relative risk of bleeding disorders, including hematologic cancers, was increased more than three-fold compared to controls. Co-occurrence of motor neuron disease and blood dyscrasias, accompanied by psychosis, has long been recognized. A virally-mediated autoimmune pathogenesis has been proposed. However, the familial co-occurrence of these three disease entities raises the possibility that the disease constellation be considered as a manifestation of a common underlying genetic defect. Such expansion of the spectrum of affectation might enhance the power of both candidate gene and linkage studies. Based on these findings, the loci suggested as candidate regions in schizophrenia include a potential hot spot on chromosome 21q21-q22, involving the superoxide dismutase and amyloid precursor protein genes. Alternatively, genes on other chromosomes involved in the expression, transcription, or regulation of these genes, or associated with the illnesses of high frequency in these pedigrees are suggested. Candidates include the choroid plexus transport protein, transthyretin at 18q11.2-q12.1; the t(14;18)(q22;21) characterizing B-cell lymphoma-2, the most common form of hematologic cancer; and the 14q24 locus of early onset Alzheimer`s disease, c-Fos, transforming growth factor beta 3, and heat shock protein A2. Expression of hematologic cancers and the suggested candidate genes are known to involve retinoid pathways, and retinoid disregulation has been proposed as a cause of schizophrenia. 67 refs., 2 figs., 1 tab.
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Linkage and related analyses of Barrett's esophagus and its associated adenocarcinomas.
Sun, Xiangqing; Elston, Robert; Falk, Gary W; Grady, William M; Faulx, Ashley; Mittal, Sumeet K; Canto, Marcia I; Shaheen, Nicholas J; Wang, Jean S; Iyer, Prasad G; Abrams, Julian A; Willis, Joseph E; Guda, Kishore; Markowitz, Sanford; Barnholtz-Sloan, Jill S; Chandar, Apoorva; Brock, Wendy; Chak, Amitabh
2016-07-01
Familial aggregation and segregation analysis studies have provided evidence of a genetic basis for esophageal adenocarcinoma (EAC) and its premalignant precursor, Barrett's esophagus (BE). We aim to demonstrate the utility of linkage analysis to identify the genomic regions that might contain the genetic variants that predispose individuals to this complex trait (BE and EAC). We genotyped 144 individuals in 42 multiplex pedigrees chosen from 1000 singly ascertained BE/EAC pedigrees, and performed both model-based and model-free linkage analyses, using S.A.G.E. and other software. Segregation models were fitted, from the data on both the 42 pedigrees and the 1000 pedigrees, to determine parameters for performing model-based linkage analysis. Model-based and model-free linkage analyses were conducted in two sets of pedigrees: the 42 pedigrees and a subset of 18 pedigrees with female affected members that are expected to be more genetically homogeneous. Genome-wide associations were also tested in these families. Linkage analyses on the 42 pedigrees identified several regions consistently suggestive of linkage by different linkage analysis methods on chromosomes 2q31, 12q23, and 4p14. A linkage on 15q26 is the only consistent linkage region identified in the 18 female-affected pedigrees, in which the linkage signal is higher than in the 42 pedigrees. Other tentative linkage signals are also reported. Our linkage study of BE/EAC pedigrees identified linkage regions on chromosomes 2, 4, 12, and 15, with some reported associations located within our linkage peaks. Our linkage results can help prioritize association tests to delineate the genetic determinants underlying susceptibility to BE and EAC.
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Lesuisse, J; Li, C; Schallier, S; Clímaco, W L S; Bautil, A; Everaert, N; Buyse, J
2018-05-01
Studies on mammals and poultry showed that maternal dietary treatments can alter the offspring performance. However, in contrast to rodent studies, little is known about multigenerational dietary manipulations in broiler breeders. The presented research aimed to investigate the effects of a reduction of 25% in the dietary crude protein (CP) level in the F0 generation on the body composition and reproductive performance of F1 broiler breeders. In the F0 generation, breeders were fed either a control (C) or reduced balanced protein (RP) diet, 25% reduction in crude protein and amino acids. Female F0-progeny of each treatment were fed a C or RP diet, resulting in 4 treatments in the F1 breeder generation: C/C, C/RP, RP/C, and RP/RP. The reproductive performance of breeders fed RP diets was negatively influenced by the dietary CP reduction in the F1 generation (P diets in the F0 generation showed a significantly reduced reproductive capacity compared to their control fed counterparts (P diets in the F1 generation were characterized by higher plasma T3 concentrations (P diets in the F0 generation needed lower feed allocations in the laying phase to maintain a similar body weight. Egg weight was reduced for the C/RP and RP/RP breeders. At 34 wk of age, eggs from C/RP and RP/RP breeders showed a reduced proportional albumen weight, whereas no effects on egg composition were found at 42 wk of age. It was concluded that prenatal protein undernutrition triggered hens to relocate more energy towards growth and maintenance and less towards reproductive capacity.
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Genetics of human body size and shape: body proportions and indices.
Livshits, Gregory; Roset, A; Yakovenko, K; Trofimov, S; Kobyliansky, E
2002-01-01
The study of the genetic component in morphological variables such as body height and weight, head and chest circumference, etc. has a rather long history. However, only a few studies investigated body proportions and configuration. The major aim of the present study was to evaluate the extent of the possible genetic effects on the inter-individual variation of a number of body configuration indices amenable to clear functional interpretation. Two ethnically different pedigree samples were used in the study: (1) Turkmenians (805 individuals) from Central Asia, and (2) Chuvasha (732 individuals) from the Volga riverside, Russian Federation. To achieve the aim of the present study we proposed three new indices, which were subjected to a statistical-genetic analysis using modified version of "FISHER" software. The proposed indices were: (1) an integral index of torso volume (IND#1), an index reflecting a predisposition of body proportions to maintain a balance in a vertical position (IND#2), and an index of skeletal extremities volume (IND#3). Additionally, the first two principal factors (PF1 and PF2) obtained on 19 measurements of body length and breadth were subjected to genetic analysis. Variance decomposition analysis that simultaneously assess the contribution of gender, age, additive genetic effects and effects of environment shared by the nuclear family members, was applied to fit variation of the above three indices, and PF1 and PF2. The raw familial correlation of all study traits and in both samples showed: (1) all marital correlations did not differ significantly from zero; (2) parent-offspring and sibling correlations were all positive and statistically significant. The parameter estimates obtained in variance analyses showed that from 40% to 75% of inter-individual variation of the studied traits (adjusted for age and sex) were attributable to genetic effects. For PF1 and PF2 in both samples, and for IND#2 (in Chuvasha pedigrees), significant common sib
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Human-assisted spread of a maladaptive behavior in a critically endangered bird.
Massaro, Melanie; Sainudiin, Raazesh; Merton, Don; Briskie, James V; Poole, Anthony M; Hale, Marie L
2013-01-01
Conservation management often focuses on counteracting the adverse effects of human activities on threatened populations. However, conservation measures may unintentionally relax selection by allowing the 'survival of the not-so-fit', increasing the risk of fixation of maladaptive traits. Here, we report such a case in the critically-endangered Chatham Island black robin (Petroica traversi) which, in 1980, was reduced to a single breeding pair. Following this bottleneck, some females were observed to lay eggs on the rims of their nests. Rim eggs left in place always failed to hatch. To expedite population recovery, rim eggs were repositioned inside nests, yielding viable hatchlings. Repositioning resulted in rapid growth of the black robin population, but by 1989 over 50% of all females were laying rim eggs. We used an exceptional, species-wide pedigree to consider both recessive and dominant models of inheritance over all plausible founder genotype combinations at a biallelic and possibly sex-linked locus. The pattern of rim laying is best fitted as an autosomal dominant Mendelian trait. Using a phenotype permutation test we could also reject the null hypothesis of non-heritability for this trait in favour of our best-fitting model of heritability. Data collected after intervention ceased shows that the frequency of rim laying has strongly declined, and that this trait is maladaptive. This episode yields an important lesson for conservation biology: fixation of maladaptive traits could render small threatened populations completely dependent on humans for reproduction, irreversibly compromising the long term viability of populations humanity seeks to conserve.
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Human-assisted spread of a maladaptive behavior in a critically endangered bird.
Directory of Open Access Journals (Sweden)
Melanie Massaro
Full Text Available Conservation management often focuses on counteracting the adverse effects of human activities on threatened populations. However, conservation measures may unintentionally relax selection by allowing the 'survival of the not-so-fit', increasing the risk of fixation of maladaptive traits. Here, we report such a case in the critically-endangered Chatham Island black robin (Petroica traversi which, in 1980, was reduced to a single breeding pair. Following this bottleneck, some females were observed to lay eggs on the rims of their nests. Rim eggs left in place always failed to hatch. To expedite population recovery, rim eggs were repositioned inside nests, yielding viable hatchlings. Repositioning resulted in rapid growth of the black robin population, but by 1989 over 50% of all females were laying rim eggs. We used an exceptional, species-wide pedigree to consider both recessive and dominant models of inheritance over all plausible founder genotype combinations at a biallelic and possibly sex-linked locus. The pattern of rim laying is best fitted as an autosomal dominant Mendelian trait. Using a phenotype permutation test we could also reject the null hypothesis of non-heritability for this trait in favour of our best-fitting model of heritability. Data collected after intervention ceased shows that the frequency of rim laying has strongly declined, and that this trait is maladaptive. This episode yields an important lesson for conservation biology: fixation of maladaptive traits could render small threatened populations completely dependent on humans for reproduction, irreversibly compromising the long term viability of populations humanity seeks to conserve.
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Directory of Open Access Journals (Sweden)
Trino Baptista
2015-06-01
Full Text Available Objective:Evidence points to a high prevalence of metabolic dysfunction in bipolar disorder (BD, but few studies have evaluated the relatives of subjects with BD. We conducted a cross-sectional study in an extended family of patients with BD type I.Methods:The available relatives of the same family were interviewed (DSM-IV-R and assessed in fasting conditions for body mass index, constituent variables of the metabolic syndrome (MS, leptin levels, insulin resistance index, and single nucleotide polymorphisms (SNPs for the leptin receptor and promoter and PPAR-γ2 genes. The frequency of MS was compared with that recorded in the local general population.Results:Ninety-three relatives of three adults with BD were evaluated (30 aged 18 years. The frequency of MS was similar to that of the general population. Significantly higher frequencies of abnormal glucose, total and low density cholesterol (LDL-c levels (all p < 0.05, waist circumference (p = 0.057, and leptin and insulin resistance values (in adults only were observed in the family. Adults with the QQ genotype of the leptin receptor displayed higher LDL-c levels than carriers of the R allele.Conclusions:The associations among BD consanguinity, familial hypercholesterolemia, and leptin receptor SNPs reported herein should be replicated and extended in other pedigrees.
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International Nuclear Information System (INIS)
Avner, P.; Amar, L.; Arnaud, D.; Hanauer, A.; Cambrou, J.
1987-01-01
Five probes localizing to the Xq26-Xqter region of the human X chromosome have been genetically mapped on the mouse X chromosome using an interspecific cross involving Mus spretus to a contiguous region lying proximally to the Tabby (Ta) locus. Pedigree and recombinational analysis establish the marker order as being Hprt-FIX-c11-G6PD-St14-1. The size of this contiguous region is such that the X-linked muscular dystrophy (mdx) mouse mutation probably maps within this segment. This in turn suggests that it is highly improbable that the mouse mdx locus represents a model for Duchenne muscular dystrophy (DMD). It is, however, compatible with the idea that this mutation may correspond in man to Emery Dreifuss muscular dystrophy. The high frequency of restriction fragment length polymorphisms found in this interspecific system for all the human cross-reacting probes examined up until now, using only a limited number of restriction enzymes, suggests that the Mus spretus mapping system may be of great potential value for establishing the linkage relationships existing in man when conserved chromosomal regions are concerned and human/mouse cross-reacting probes are available or can be obtained
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Analysis of the rdd locus in chicken: a model for human retinitis pigmentosa.
Burt, David W; Morrice, David R; Lester, Douglas H; Robertson, Graeme W; Mohamed, Moin D; Simmons, Ian; Downey, Louise M; Thaung, Caroline; Bridges, Leslie R; Paton, Ian R; Gentle, Mike; Smith, Jacqueline; Hocking, Paul M; Inglehearn, Chris F
2003-04-30
To identify the locus responsible for the blind mutation rdd (retinal dysplasia and degeneration) in chickens and to further characterise the rdd phenotype. The eyes of blind and sighted birds were subjected to ophthalmic, morphometric and histopathological examination to confirm and extend published observations. Electroretinography was used to determine age of onset. Birds were crossed to create pedigrees suitable for genetic mapping. DNA samples were obtained and subjected to a linkage search. Measurement of IOP, axial length, corneal diameter, and eye weight revealed no gross morphological changes in the rdd eye. However, on ophthalmic examination, rdd homozygotes have a sluggish pupillary response, atrophic pecten, and widespread pigmentary disturbance that becomes more pronounced with age. Older birds also have posterior subcapsular cataracts. At three weeks of age, homozygotes have a flat ERG indicating severe loss of visual function. Pathological examination shows thinning of the RPE, ONL, photoreceptors and INL, and attenuation of the ganglion cell layer. From 77 classified backcross progeny, 39 birds were blind and 38 sighted. The rdd mutation was shown to be sex-linked and not autosomal as previously described. Linkage analysis mapped the rdd locus to a small region of the chicken Z chromosome with homologies to human chromosomes 5q and 9p. Ophthalmic, histopathologic, and electrophysiological observations suggest rdd is similar to human recessive retinitis pigmentosa. Linkage mapping places rdd in a region homologous to human chromosomes 9p and 5q. Candidate disease genes or loci include PDE6A, WGN1, and USH2C. This is the first use of genetic mapping in a chicken model of human disease.
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Energy Technology Data Exchange (ETDEWEB)
Griffith, A.J.; Burgess, D.L.; Kohrman, D. [Univ. of MIchigan, Ann Arbor, MI (United States)] [and others
1994-09-01
The Twirler mutation (Tw) causing cleft palate {plus_minus} cleft lip, vestibular defects and obesity is located within 0.5 cM of an ataxia locus (ax) on mouse chromosome 18. We identified a transgene-induced insertional mutation with vestibular and craniofacial defects that appears to be a new allele of Twirler. Mouse DNA flanking the transgene insertion site was isolated from a cosmid library. An evolutionarily conserved, zoo blot positive cosmid subclone was used to probe a human {lambda} genomic library. From the sequence of a highly homologous human {lambda} clone, we designed STS primers and screened a human P1 library. DNA from two positive P1 clones was hybridized with simple sequence probes, and a (CTAT){sub 12} repeat was detected. Analysis of 62 CEPH parents with primers flanking the repeat identified six alleles containing 9 to 14 copies of the repeat, at frequencies of 0.17, 0.17, 0.17, 0.27, 0.15 and 0.07, respectively. The observed heterozygosity was 49/62 with a calculated PIC value of 0.76. This polymorphic microsatellite marker, designated Umi3, was mapped to the predicted conserved human linkage group by analysis of somatic cell hybrid panels. The anticipated short distance between Umi3 and the disease genes will facilitate detection of linkage in small families. We would like to type appropriate human pedigrees with Umi3 in order to identify patients with inherited disorders homologous to the mouse mutations Twirler and ataxia.
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Directory of Open Access Journals (Sweden)
Sarvi Sharifi
2012-08-01
Full Text Available Background: Over 60 Asian and European families with cortical myoclonic tremor and epilepsy have been reported under various names. Cerebellar changes may be part of the syndrome. In this study, we report the neuropathology findings in a new Dutch familial cortical myoclonic tremor with epilepsy case and review the literature on this syndrome.Methods: Neuropathological investigations were performed for a third case of the Dutch pedigree. In addition, we searched the literature for pedigrees meeting the criteria for benign familial myoclonic tremor and epilepsy.Results: Our third Dutch case showed cerebellar Purkinje cell changes and a normal cerebral cortex. The pedigrees described show phenotypical differences, cerebellar symptoms and cerebellar atrophy to a variable degree. Japanese pedigrees with linkage to chromosome 8q have been reported with milder disease features than members of Italian pedigrees with linkage to chromosome 2p. French pedigrees (5p possibly show even more severe and progressive disease, including cognitive changes and cerebellar features.Discussion: Currently, familial cortical myoclonic tremor is not listed by the International League Against Epilepsy, although it can be differentiated from other epileptic syndromes. Genetic heterogeneity and phenotypical differences between pedigrees exist. Cerebellar changes seem to be part of the syndrome in at least a number of pedigrees.
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Energy Technology Data Exchange (ETDEWEB)
Duggirala, R.; Stern, M.P.; Reinhart, L.J. [Univ. of Texas Health Science Center, San Antonio, TX (United States)] [and others
1996-09-01
Despite the evidence that human obesity has strong genetic determinants, efforts at identifying specific genes that influence human obesity have largely been unsuccessful. Using the sibship data obtained from 32 low-income Mexican American pedigrees ascertained on a type II diabetic proband and a multipoint variance-components method, we tested for linkage between various obesity-related traits plus associated metabolic traits and 15 markers on human chromosome 7. We found evidence for linkage between markers in the OB gene region and various traits, as follows: D7S514 and extremity skinfolds (LOD = 3.1), human carboxypeptidase A1 (HCPA1) and 32,33-split proinsulin level (LOD = 4.2), and HCPA1 and proinsulin level (LOD = 3.2). A putative susceptibility locus linked to the marker D7S514 explained 56% of the total phenotypic variation in extremity skinfolds. Variation at the HCPA1 locus explained 64% of phenotypic variation in proinsulin level and {approximately}73% of phenotypic variation in split proinsulin concentration, respectively. Weaker evidence for linkage to several other obesity-related traits (e.g., waist circumference, body-mass index, fat mass by bioimpedance, etc.) was observed for a genetic location, which is {approximately}15 cM telomeric to OB. In conclusion, our study reveals that the OB region plays a significant role in determining the phenotypic variation of both insulin precursors and obesity-related traits, at least in Mexican Americans. 66 refs., 3 figs., 4 tabs.
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Nkya, Theresia Estomih; Poupardin, Rodolphe; Laporte, Frederic; Akhouayri, Idir; Mosha, Franklin; Magesa, Stephen; Kisinza, William; David, Jean-Philippe
2014-10-16
Resistance of mosquitoes to insecticides is mainly attributed to their adaptation to vector control interventions. Although pesticides used in agriculture have been frequently mentioned as an additional force driving the selection of resistance, only a few studies were dedicated to validate this hypothesis and characterise the underlying mechanisms. While insecticide resistance is rising dramatically in Africa, deciphering how agriculture affects resistance is crucial for improving resistance management strategies. In this context, the multigenerational effect of agricultural pollutants on the selection of insecticide resistance was examined in Anopheles gambiae. An urban Tanzanian An. gambiae population displaying a low resistance level was used as a parental strain for a selection experiment across 20 generations. At each generation larvae were selected with a mixture containing pesticides and herbicides classically used in agriculture in Africa. The resistance levels of adults to deltamethrin, DDT and bendiocarb were compared between the selected and non-selected strains across the selection process together with the frequency of kdr mutations. A microarray approach was used for pinpointing transcription level variations selected by the agricultural pesticide mixture at the adult stage. A gradual increase of adult resistance to all insecticides was observed across the selection process. The frequency of the L1014S kdr mutation rose from 1.6% to 12.5% after 20 generations of selection. Microarray analysis identified 90 transcripts over-transcribed in the selected strain as compared to the parental and the non-selected strains. Genes encoding cuticle proteins, detoxification enzymes, proteins linked to neurotransmitter activity and transcription regulators were mainly affected. RT-qPCR transcription profiling of candidate genes across multiple generations supported their link with insecticide resistance. This study confirms the potency of agriculture in selecting
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Directory of Open Access Journals (Sweden)
Sivakumar Sukumaran
2017-02-01
Full Text Available Developing genomic selection (GS models is an important step in applying GS to accelerate the rate of genetic gain in grain yield in plant breeding. In this study, seven genomic prediction models under two cross-validation (CV scenarios were tested on 287 advanced elite spring wheat lines phenotyped for grain yield (GY, thousand-grain weight (GW, grain number (GN, and thermal time for flowering (TTF in 18 international environments (year-location combinations in major wheat-producing countries in 2010 and 2011. Prediction models with genomic and pedigree information included main effects and interaction with environments. Two random CV schemes were applied to predict a subset of lines that were not observed in any of the 18 environments (CV1, and a subset of lines that were not observed in a set of the environments, but were observed in other environments (CV2. Genomic prediction models, including genotype × environment (G×E interaction, had the highest average prediction ability under the CV1 scenario for GY (0.31, GN (0.32, GW (0.45, and TTF (0.27. For CV2, the average prediction ability of the model including the interaction terms was generally high for GY (0.38, GN (0.43, GW (0.63, and TTF (0.53. Wheat lines in site-year combinations in Mexico and India had relatively high prediction ability for GY and GW. Results indicated that prediction ability of lines not observed in certain environments could be relatively high for genomic selection when predicting G×E interaction in multi-environment trials.
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International Nuclear Information System (INIS)
Zhao Lidong; Wang Qiuju; Qian Yaping; Li Ronghua; Cao Juayng; Hart, Laura Christine; Zhai Suoqiang; Han Dongyi; Young Wieyen; Guan Minxin
2005-01-01
We report here the clinical, genetic, and molecular characterization of two Chinese pedigrees with aminoglycoside-induced and non-syndromic hearing impairment. Clinical evaluation revealed the variable phenotype of hearing impairment including audiometric configuration in these subjects. Penetrances of hearing loss in BJ105 and BJ106 pedigrees are 67% and 33%, respectively. In particular, three of 10 affected matrilineal relatives of BJ105 pedigree had aminoglycoside-induced hearing loss, while seven affected matrilineal relatives in BJ105 pedigree and six affected matrilineal relatives in BJ106 pedigree did not have a history of exposure to aminoglycosides. Sequence analysis of the complete mitochondrial genomes in these pedigrees showed the identical homoplasmic A1555G mutation and distinct sets of mtDNA variants belonging to haplogroups F3 and M7b. These variants showed no evolutionary conservation, implying that mitochondrial haplotype may not play a significant role in the phenotypic expression of the A1555G mutation in these Chinese pedigrees. However, aminoglycosides and nuclear backgrounds appear to be major modifier factors for the phenotypic manifestation of the A1555G mutation in these Chinese families
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The Siblings With Ischemic Stroke Study (SWISS Protocol
Directory of Open Access Journals (Sweden)
Hardy John
2002-02-01
Full Text Available Abstract Background Family history and twins studies suggest an inherited component to ischemic stroke risk. Candidate gene association studies have been performed but have limited capacity to identify novel risk factor genes. The Siblings With Ischemic Stroke Study (SWISS aims to conduct a genome-wide scan in sibling pairs concordant or discordant for ischemic stroke to identify novel genetic risk factors through linkage analysis. Methods Screening at multiple clinical centers identifies patients (probands with radiographically confirmed ischemic stroke and a family history of at least 1 living full sibling with stroke. After giving informed consent, without violating privacy among other family members, the proband invites siblings concordant and discordant for stroke to participate. Siblings then contact the study coordinating center. The diagnosis of ischemic stroke in potentially concordant siblings is confirmed by systematic centralized review of medical records. The stroke-free status of potentially discordant siblings is confirmed by validated structured telephone interview. Blood samples for DNA analysis are taken from concordant sibling pairs and, if applicable, from 1 discordant sibling. Epstein-Barr virus-transformed lymphoblastoid cell lines are created, and a scan of the human genome is planned. Discussion Conducting adequately powered genomics studies of stroke in humans is challenging because of the heterogeneity of the stroke phenotype and the difficulty of obtaining DNA samples from clinically well-characterized members of a cohort of stroke pedigrees. The multicentered design of this study is intended to efficiently assemble a cohort of ischemic stroke pedigrees without invoking community consent or using cold-calling of pedigree members.
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Cissé, Yasmine M; Russart, Kathryn L G; Nelson, Randy J
2017-09-01
Rates of major depressive disorder (MDD) have steadily increased over the past 50 years. Many factors have been implicated in the etiology of depressive disorders and environmental influences are being increasingly recognized. The increase in depression rates has coincided with increased artificial nighttime lighting. Exposure to light at night (LAN) has been associated with increased depressive-like behavior in rodents and decreased mood in humans. However, relatively little is known on the multigenerational effects of dLAN on affect. In this study, we exposed adult male and female Siberian hamsters (Phodopus sungorus) to either DARK (0lx) or dim LAN (5lx) for 9 weeks, then paired animals in a full factorial design; all animals were thereafter housed in dark nights. Offspring were gestated and reared in dark nights, then tested in adulthood for depressive-like behaviors and hippocampal expression of glucocorticoid (GR) and melatonin (MT1) receptor expression. Maternal exposure to dLAN decreased sucrose preference, time to first float bout in the Porsolt swim test, and GR expression in the hippocampus. Paternal exposure to dLAN increased time spent floating, and increased hippocampal GR expression. Overall, our results suggest that chronic exposure of parents to light at night has multigenerational effects on offspring depressive-like behavior. If these results pertain to humans, then our data suggest that LAN may contribute to the rapidly rising rates of major depressive disorder in industrialized and developing countries. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Energy Technology Data Exchange (ETDEWEB)
Sorrenson, Brie; Suetani, Rachel J. [Department of Biochemistry, University of Otago, Dunedin (New Zealand); Bickley, Vivienne M.; George, Peter M. [Clinical Biochemistry, Canterbury Health Laboratories, Christchurch (New Zealand); Williams, Michael J.A. [Department of Medicine, University of Otago, Dunedin (New Zealand); Scott, Russell S. [Lipid and Diabetes Research Group, Christchurch Hospital (New Zealand); McCormick, Sally P.A., E-mail: sally.mccormick@otago.ac.nz [Department of Biochemistry, University of Otago, Dunedin (New Zealand)
2011-06-10
Highlights: {yields} Characterisation of an ABCA1 truncation mutant, C978fsX988, in a pedigree with three ABCA1 mutations. {yields} Functional analysis of C978fsX988 in patient fibroblasts and HEK 293 cells shows no cholesterol efflux function. {yields} Allele-specific quantification shows C978fsX988 not expressed at mRNA level in fibroblasts. {yields} Unlike other ABCA1 truncations, C978fsX988 mutant shows no dominant negative effect at mRNA or protein level. -- Abstract: The ATP binding cassette transporter (ABCA1) A1 is a key determinant of circulating high density lipoprotein cholesterol (HDL-C) levels. Mutations in ABCA1 are a major genetic contributor to low HDL-C levels within the general population. Following the finding of three different ABCA1 mutations, p.C978fsX988, p.T1512M and p.N1800H in a subject with hypoalphalipoproteinemia, we aimed to establish whether the p.C978fsX988 truncation exerted a dominant negative effect on the full-length ABCA1 alleles within family members as has been reported for other ABCA1 truncations. Characterisation of the p.C978fsX988 mutant in transfected HEK 293 cells showed it to be expressed as a GFP fusion protein but lacking in cholesterol efflux function. This was in keeping with results from cholesterol efflux assays in the fibroblasts of p.C978fsX988 carriers which also showed impaired efflux. Allele- specific quantification of p.C978fsX988 mRNA and analysis of ABCA1 protein levels in the fibroblasts of p.C978fsX988 heterozygotes showed negligible levels of mRNA and protein expression. There was no evidence of a dominant negative effect on wildtype or p.N1800H protein levels. We conclude that in the case of the p.C978fsX988 truncated mutant a lack of expression precludes it from having a dominant negative effect.
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Allelic variation of the FRMD7 gene in congenital idiopathic nystagmus.
Self, James E; Shawkat, Fatima; Malpas, Crispin T; Thomas, N Simon; Harris, Christopher M; Hodgkins, Peter R; Chen, Xiaoli; Trump, Dorothy; Lotery, Andrew J
2007-09-01
To perform a genotype-phenotype correlation study in an X-linked congenital idiopathic nystagmus pedigree (pedigree 1) and to assess the allelic variance of the FRMD7 gene in congenital idiopathic nystagmus. Subjects from pedigree 1 underwent detailed clinical examination including nystagmology. Screening of FRMD7 was undertaken in pedigree 1 and in 37 other congenital idiopathic nystagmus probands and controls. Direct sequencing confirmed sequence changes. X-inactivation studies were performed in pedigree 1. The nystagmus phenotype was extremely variable in pedigree 1. We identified 2 FRMD7 mutations. However, 80% of X-linked families and 96% of simplex cases showed no mutations. X-inactivation studies demonstrated no clear causal link between skewing and variable penetrance. We confirm profound phenotypic variation in X-linked congenital idiopathic nystagmus pedigrees. We demonstrate that other congenital nystagmus genes exist besides FRMD7. We show that the role of X inactivation in variable penetrance is unclear in congenital idiopathic nystagmus. Clinical Relevance We demonstrate that phenotypic variation of nystagmus occurs in families with FRMD7 mutations. While FRMD7 mutations may be found in some cases of X-linked congenital idiopathic nystagmus, the diagnostic yield is low. X-inactivation assays are unhelpful as a test for carrier status for this disease.
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Curtis, Sarah W; Conneely, Karen N; Marder, Mary E; Terrell, Metrecia L; Marcus, Michele; Smith, Alicia K
2018-06-11
Endocrine-disrupting compounds (EDCs) are a broad class of chemicals present in many residential products that can disrupt hormone signaling and cause health problems in humans. Multigenerational cohorts, like the Michigan polybrominated biphenyl registry, are ideal for studying the effects of intergenerational exposure. Registry participants report hormone-related health problems, particularly in those exposed before puberty or those in the second generation exposed through placental transfer or breastfeeding. However, more research is needed to determine how EDCs cause health problems and the mechanisms underlying intergenerational exposure. Utilizing existing data in this registry, along with genetic and epigenetic approaches, could provide insight to how EDCs cause human disease and help to determine the risk to exposed populations and future generations.
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Zou, Xuan; Dong, Fangtian; Zhang, Shuying; Tian, Rong; Sui, Ruifang
2013-05-01
The familial transthyretin (TTR) amyloidosis (FTA) demonstrates variable penetrance of clinical features associated with mutations in the plasma thyroid hormone-binding protein TTR gene. The purpose of this study was to assess the ocular features, to analyze vitreous and serum vascular endothelial growth factor (VEGF) levels, and to identify the genetic defect in a Chinese family with TTR FTA. The pedigree of interest was a three-generation family with eleven members. The primary ocular signs were vitreous opacities, beginning from the third or fourth decade, accompanied by retinal vasculitis, hemorrhages, and widespread pinpoint deposits in the peripheral retina. Two patients underwent vitrectomy with marked improvement of visual acuity postoperatively. Vitreous and serum samples for VEGF were analyzed with an enzyme-linked immunosorbent assay (ELISA). Forty-eight healthy adult volunteers were enrolled as a control group for the analysis of serum VEGF. Eight subjects who underwent vitrectomy for a macular epiretinal membrane or macular hole were enrolled as control for the analysis of vitreous VEGF. Both serum and vitreous VEGF levels of patients were raised compared to that of controls. Venous blood was collected from family members and the genomic DNA was extracted. All exons and exon-intron boundaries of the TTR gene were sequenced. A previously-described pathogenic transversion in exon 2 (c.G106C, p.Ala36Pro) was identified. Within this family eight individuals were confirmed as affected. In conclusion, a Chinese family with TTR Ala36Pro associated FTA is characterized by early ocular involvement. Widespread pinpoint lesions indicate RPE lesions caused by TTR deposition. FTA is associated with increased VEGF levels, both in serum and vitreous. Copyright © 2013 Elsevier Ltd. All rights reserved.
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DEFF Research Database (Denmark)
Kadri, Naveen; Guldbrandtsen, Bernt; Sørensen, Peter
2014-01-01
Population structure is known to cause false-positive detection in association studies. We compared the power, precision, and type-I error rates of various association models in analyses of a simulated dataset with structure at the population (admixture from two populations; P) and family (K......) levels. We also compared type-I error rates among models in analyses of publicly available human and dog datasets. The models corrected for none, one, or both structure levels. Correction for K was performed with linear mixed models incorporating familial relationships estimated from pedigrees or genetic...... corrected for P. In contrast, correction for P alone in linear models was insufficient. The power and precision of linear mixed models with and without correction for P were similar. Furthermore, power, precision, and type-I error rate were comparable in linear mixed models incorporating pedigree...
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Cultural Transmission and Evolution of Melodic Structures in Multi-generational Signaling Games
DEFF Research Database (Denmark)
Lumaca, Massimo; Baggio, G.
2017-01-01
It has been proposed that languages evolve by adapting to the perceptual and cognitive constraints of the human brain, developing, in the course of cultural transmission, structural regularities that maximize or optimize learnability and ease of processing. To what extent would perceptual and cog...
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Strategies for MCMC computation in quantitative genetics
DEFF Research Database (Denmark)
Waagepetersen, Rasmus; Ibanez, Noelia; Sorensen, Daniel
2006-01-01
Given observations of a trait and a pedigree for a group of animals, the basic model in quantitative genetics is a linear mixed model with genetic random effects. The correlation matrix of the genetic random effects is determined by the pedigree and is typically very highdimensional but with a sp......Given observations of a trait and a pedigree for a group of animals, the basic model in quantitative genetics is a linear mixed model with genetic random effects. The correlation matrix of the genetic random effects is determined by the pedigree and is typically very highdimensional...
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Ariffin, Hany; Hainaut, Pierre; Puzio-Kuter, Anna; Choong, Soo Sin; Chan, Adelyne Sue Li; Tolkunov, Denis; Rajagopal, Gunaretnam; Kang, Wenfeng; Lim, Leon Li Wen; Krishnan, Shekhar; Chen, Kok-Siong; Achatz, Maria Isabel; Karsa, Mawar; Shamsani, Jannah; Levine, Arnold J; Chan, Chang S
2014-10-28
The Li-Fraumeni syndrome (LFS) and its variant form (LFL) is a familial predisposition to multiple forms of childhood, adolescent, and adult cancers associated with germ-line mutation in the TP53 tumor suppressor gene. Individual disparities in tumor patterns are compounded by acceleration of cancer onset with successive generations. It has been suggested that this apparent anticipation pattern may result from germ-line genomic instability in TP53 mutation carriers, causing increased DNA copy-number variations (CNVs) with successive generations. To address the genetic basis of phenotypic disparities of LFS/LFL, we performed whole-genome sequencing (WGS) of 13 subjects from two generations of an LFS kindred. Neither de novo CNV nor significant difference in total CNV was detected in relation with successive generations or with age at cancer onset. These observations were consistent with an experimental mouse model system showing that trp53 deficiency in the germ line of father or mother did not increase CNV occurrence in the offspring. On the other hand, individual records on 1,771 TP53 mutation carriers from 294 pedigrees were compiled to assess genetic anticipation patterns (International Agency for Research on Cancer TP53 database). No strictly defined anticipation pattern was observed. Rather, in multigeneration families, cancer onset was delayed in older compared with recent generations. These observations support an alternative model for apparent anticipation in which rare variants from noncarrier parents may attenuate constitutive resistance to tumorigenesis in the offspring of TP53 mutation carriers with late cancer onset.
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Directory of Open Access Journals (Sweden)
Matthew R Halley
Full Text Available We discovered variable modes of parental care in a breeding population of color-banded Veeries (Catharus fuscescens, a Nearctic-Neotropical migratory songbird, long thought to be socially monogamous, and performed a multi-locus DNA microsatellite analysis to estimate parentage and kinship in a sample of 37 adults and 21 offspring. We detected multiple mating in both sexes, and four modes of parental care that varied in frequency within and between years including multiple male feeders at some nests, and males attending multiple nests in the same season, each with a different female. Unlike other polygynandrous systems, genetic evidence indicates that multi-generational patterns of kinship occur among adult Veeries at our study site, and this was corroborated by the capture of an adult male in 2013 that had been banded as a nestling in 2011 at a nest attended by multiple male feeders. All genotyped adults (n = 37 were related to at least one other bird in the sample at the cousin level or greater (r ≥ 0.125, and 81% were related to at least one other bird at the half-sibling level or greater (r ≥ 0.25, range 0.25-0.60. Although our sample size is small, it appears that the kin structure is maintained by natal philopatry in both sexes, and that Veeries avoid mating with close genetic kin. At nests where all adult feeders were genotyped (n = 9, the male(s were unrelated to the female (mean r = -0.11 ± 0.15, whereas genetic data suggest close kinship (r = 0.254 between two male co-feeders at the nests of two females in 2011, and among three of four females that were mated to the same polygynous male in 2012. To our knowledge, this is the first evidence of polygynandry occurring among multiple generations of close genetic kin on the breeding ground of a Nearctic-Neotropical migratory songbird.
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The importance of identity-by-state information for the accuracy of genomic selection
Directory of Open Access Journals (Sweden)
Luan Tu
2012-08-01
Full Text Available Abstract Background It is commonly assumed that prediction of genome-wide breeding values in genomic selection is achieved by capitalizing on linkage disequilibrium between markers and QTL but also on genetic relationships. Here, we investigated the reliability of predicting genome-wide breeding values based on population-wide linkage disequilibrium information, based on identity-by-descent relationships within the known pedigree, and to what extent linkage disequilibrium information improves predictions based on identity-by-descent genomic relationship information. Methods The study was performed on milk, fat, and protein yield, using genotype data on 35 706 SNP and deregressed proofs of 1086 Italian Brown Swiss bulls. Genome-wide breeding values were predicted using a genomic identity-by-state relationship matrix and a genomic identity-by-descent relationship matrix (averaged over all marker loci. The identity-by-descent matrix was calculated by linkage analysis using one to five generations of pedigree data. Results We showed that genome-wide breeding values prediction based only on identity-by-descent genomic relationships within the known pedigree was as or more reliable than that based on identity-by-state, which implicitly also accounts for genomic relationships that occurred before the known pedigree. Furthermore, combining the two matrices did not improve the prediction compared to using identity-by-descent alone. Including different numbers of generations in the pedigree showed that most of the information in genome-wide breeding values prediction comes from animals with known common ancestors less than four generations back in the pedigree. Conclusions Our results show that, in pedigreed breeding populations, the accuracy of genome-wide breeding values obtained by identity-by-descent relationships was not improved by identity-by-state information. Although, in principle, genomic selection based on identity-by-state does not require
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A polymorphism of the beta sub 1 adrenergic receptor gene (BADR) detected with Bgl I
Energy Technology Data Exchange (ETDEWEB)
Berrettini, W H; Hoehe, M R [National Institute of Mental Health, Bethesda, MD (USA)
1988-08-11
A 2.4 kb clone was isolated from a human cDNA library. This clone contains 86 bp of the 5{prime} untranslated region and 900 bp of the 3{prime} untranslated region. BGL I digestion of human genomic DNA reveals a biallelic RFLP with bands at 6.2 (allele A) and 4.7 (B) kb. Evaluation of 46 North American caucasian subjects showed a frequency for allele A of .80 and for allele B of .20. Co-dominant inheritance was demonstrated in three pedigrees.
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ASPM mutations identified in patients with primary microcephaly and seizures
Shen, J; Eyaid, W; Mochida, G; Al-Moayyad, F; Bodell, A; Woods, C; Walsh, C
2005-01-01
Background: Human autosomal recessive primary microcephaly (MCPH) is a heterogeneous disorder with at least six genetic loci (MCPH1–6), with MCPH5, caused by ASPM mutation, being the most common. Despite the high prevalence of epilepsy in microcephaly patients, microcephaly with frequent seizures has been excluded from the ascertainment of MCPH. Here, we report a pedigree with multiple affected individuals with microcephaly and seizures.
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Directory of Open Access Journals (Sweden)
Robert D.S. Pitceathly
2013-06-01
Full Text Available The molecular basis of cytochrome c oxidase (COX, complex IV deficiency remains genetically undetermined in many cases. Homozygosity mapping and whole-exome sequencing were performed in a consanguineous pedigree with isolated COX deficiency linked to a Leigh syndrome neurological phenotype. Unexpectedly, affected individuals harbored homozygous splice donor site mutations in NDUFA4, a gene previously assigned to encode a mitochondrial respiratory chain complex I (NADH:ubiquinone oxidoreductase subunit. Western blot analysis of denaturing gels and immunocytochemistry revealed undetectable steady-state NDUFA4 protein levels, indicating that the mutation causes a loss-of-function effect in the homozygous state. Analysis of one- and two-dimensional blue-native polyacrylamide gels confirmed an interaction between NDUFA4 and the COX enzyme complex in control muscle, whereas the COX enzyme complex without NDUFA4 was detectable with no abnormal subassemblies in patient muscle. These observations support recent work in cell lines suggesting that NDUFA4 is an additional COX subunit and demonstrate that NDUFA4 mutations cause human disease. Our findings support reassignment of the NDUFA4 protein to complex IV and suggest that patients with unexplained COX deficiency should be screened for NDUFA4 mutations.
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Parrott, Joanne L; Bjerregaard, Poul; Brugger, Kristin E; Gray, L Earl; Iguchi, Taisen; Kadlec, Sarah M; Weltje, Lennart; Wheeler, James R
2017-03-01
Endocrine-disrupting substances (EDS) may have certain biological effects including delayed effects, multigenerational effects, and may display nonmonotonic dose-response (NMDR) relationships that require careful consideration when determining environmental hazards. Endocrine disrupting substances can have specific and profound effects when exposure occurs during sensitive windows of the life cycle (development, reproduction). This creates the potential for delayed effects that manifest when exposure has ceased, possibly in a different life stage. This potential underscores the need for testing in appropriate (sensitive) life stages and full life cycle designs. Such tests are available in the Organisation for Economic Co-operation and Development (OECD) tool box and should be used to derive endpoints that can be considered protective of all life stages. Similarly, the potential for effects to be manifest in subsequent generations (multigenerational effects) has also been raised as a potential issue in the derivation of appropriate endpoints for EDS. However, multigenerational studies showing increasing sensitivity of successive generations are uncommon. Indeed this is reflected in the design of new higher tier tests to assess endocrine active substances (EAS) that move to extended one-generation designs and away from multi-generational studies. The occurrence of NMDRs is also considered a limiting factor for reliable risk assessment of EDS. Evidence to date indicates NMDRs are more prevalent in in vitro and mechanistic data, not often translating to adverse apical endpoints that would be used in risk assessment. A series of steps to evaluate NMDRs in the context of endocrine hazard and risk assessment procedures is presented. If careful consideration of delayed, multigenerational effects and NMDRs is made, it is feasible to assess environmental endocrine hazards and derive robust apical endpoints for risk assessment procedures ensuring a high level of environmental
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2011-01-01
Background The genomic architecture of bud phenology and height growth remains poorly known in most forest trees. In non model species, QTL studies have shown limited application because most often QTL data could not be validated from one experiment to another. The aim of our study was to overcome this limitation by basing QTL detection on the construction of genetic maps highly-enriched in gene markers, and by assessing QTLs across pedigrees, years, and environments. Results Four saturated individual linkage maps representing two unrelated mapping populations of 260 and 500 clonally replicated progeny were assembled from 471 to 570 markers, including from 283 to 451 gene SNPs obtained using a multiplexed genotyping assay. Thence, a composite linkage map was assembled with 836 gene markers. For individual linkage maps, a total of 33 distinct quantitative trait loci (QTLs) were observed for bud flush, 52 for bud set, and 52 for height growth. For the composite map, the corresponding numbers of QTL clusters were 11, 13, and 10. About 20% of QTLs were replicated between the two mapping populations and nearly 50% revealed spatial and/or temporal stability. Three to four occurrences of overlapping QTLs between characters were noted, indicating regions with potential pleiotropic effects. Moreover, some of the genes involved in the QTLs were also underlined by recent genome scans or expression profile studies. Overall, the proportion of phenotypic variance explained by each QTL ranged from 3.0 to 16.4% for bud flush, from 2.7 to 22.2% for bud set, and from 2.5 to 10.5% for height growth. Up to 70% of the total character variance could be accounted for by QTLs for bud flush or bud set, and up to 59% for height growth. Conclusions This study provides a basic understanding of the genomic architecture related to bud flush, bud set, and height growth in a conifer species, and a useful indicator to compare with Angiosperms. It will serve as a basic reference to functional and
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Directory of Open Access Journals (Sweden)
Peter Muennig
2018-04-01
Full Text Available Introduction: After nearly a century-long trend toward single-family living arrangements, people in wealthy nations are increasingly living in multi-generational households. Multi-generational living arrangements can, in theory, increase psychological, social, and financial capital—factors associated with improvements in health and longevity. Methods: We conducted a survival analysis using the 2014 General Social Survey-National Death Index, a prospective multi-year survey. We explored whether single generational living arrangements were associated with a higher risk of mortality than multi-generational living arrangements. Results: We explored this association for different groups (e.g., the foreign-born and those with high self-reported stress in family relationships. Healthy subjects who live in two-generation households were found to have lower premature mortality (hazard ratio 0.9, 95% confidence interval = 0.82, 0.99. Otherwise, we found little evidence that living arrangements matter for the respondents’ risk of premature mortality. Conclusions: Healthy people living in two-generation households have longer survival than healthy people living on their own. Keywords: Immigrant Health, Survival, Social capital and health
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Towards sustainable groundwater use: Setting long-term goals, backcasting, and managing adaptively
Gleeson, T.; Alley, W.M.; Allen, D.M.; Sophocleous, M.A.; Zhou, Y.; Taniguchi, M.; Vandersteen, J.
2012-01-01
The sustainability of crucial earth resources, such as groundwater, is a critical issue. We consider groundwater sustainability a value-driven process of intra- and intergenerational equity that balances the environment, society, and economy. Synthesizing hydrogeological science and current sustainability concepts, we emphasize three sustainability approaches: setting multigenerational sustainability goals, backcasting, and managing adaptively. As most aquifer problems are long-term problems, we propose that multigenerational goals (50 to 100 years) for water quantity and quality that acknowledge the connections between groundwater, surface water, and ecosystems be set for many aquifers. The goals should be set by a watershed- or aquifer-based community in an inclusive and participatory manner. Policies for shorter time horizons should be developed by backcasting, and measures implemented through adaptive management to achieve the long-term goals. Two case histories illustrate the importance and complexity of a multigenerational perspective and adaptive management. These approaches could transform aquifer depletion and contamination to more sustainable groundwater use, providing groundwater for current and future generations while protecting ecological integrity and resilience. ?? 2011, The Author(s). Ground Water ?? 2011, National Ground Water Association.
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Novel gene function revealed by mouse mutagenesis screens for models of age-related disease.
Potter, Paul K; Bowl, Michael R; Jeyarajan, Prashanthini; Wisby, Laura; Blease, Andrew; Goldsworthy, Michelle E; Simon, Michelle M; Greenaway, Simon; Michel, Vincent; Barnard, Alun; Aguilar, Carlos; Agnew, Thomas; Banks, Gareth; Blake, Andrew; Chessum, Lauren; Dorning, Joanne; Falcone, Sara; Goosey, Laurence; Harris, Shelley; Haynes, Andy; Heise, Ines; Hillier, Rosie; Hough, Tertius; Hoslin, Angela; Hutchison, Marie; King, Ruairidh; Kumar, Saumya; Lad, Heena V; Law, Gemma; MacLaren, Robert E; Morse, Susan; Nicol, Thomas; Parker, Andrew; Pickford, Karen; Sethi, Siddharth; Starbuck, Becky; Stelma, Femke; Cheeseman, Michael; Cross, Sally H; Foster, Russell G; Jackson, Ian J; Peirson, Stuart N; Thakker, Rajesh V; Vincent, Tonia; Scudamore, Cheryl; Wells, Sara; El-Amraoui, Aziz; Petit, Christine; Acevedo-Arozena, Abraham; Nolan, Patrick M; Cox, Roger; Mallon, Anne-Marie; Brown, Steve D M
2016-08-18
Determining the genetic bases of age-related disease remains a major challenge requiring a spectrum of approaches from human and clinical genetics to the utilization of model organism studies. Here we report a large-scale genetic screen in mice employing a phenotype-driven discovery platform to identify mutations resulting in age-related disease, both late-onset and progressive. We have utilized N-ethyl-N-nitrosourea mutagenesis to generate pedigrees of mutagenized mice that were subject to recurrent screens for mutant phenotypes as the mice aged. In total, we identify 105 distinct mutant lines from 157 pedigrees analysed, out of which 27 are late-onset phenotypes across a range of physiological systems. Using whole-genome sequencing we uncover the underlying genes for 44 of these mutant phenotypes, including 12 late-onset phenotypes. These genes reveal a number of novel pathways involved with age-related disease. We illustrate our findings by the recovery and characterization of a novel mouse model of age-related hearing loss.
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Extensible Systems Dynamics Framework
National Research Council Canada - National Science Library
Brooks, Christopher; Lee, Edward A
2008-01-01
.... The Pedigree Management and Assessment Framework (PMAF) enables the publisher of information to record standard pedigree, such as information about the source, manner of collection, and the chain of modification of that information...
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Legarra, Andres; Christensen, Ole F; Vitezica, Zulma G; Aguilar, Ignacio; Misztal, Ignacy
2015-06-01
Recent use of genomic (marker-based) relationships shows that relationships exist within and across base population (breeds or lines). However, current treatment of pedigree relationships is unable to consider relationships within or across base populations, although such relationships must exist due to finite size of the ancestral population and connections between populations. This complicates the conciliation of both approaches and, in particular, combining pedigree with genomic relationships. We present a coherent theoretical framework to consider base population in pedigree relationships. We suggest a conceptual framework that considers each ancestral population as a finite-sized pool of gametes. This generates across-individual relationships and contrasts with the classical view which each population is considered as an infinite, unrelated pool. Several ancestral populations may be connected and therefore related. Each ancestral population can be represented as a "metafounder," a pseudo-individual included as founder of the pedigree and similar to an "unknown parent group." Metafounders have self- and across relationships according to a set of parameters, which measure ancestral relationships, i.e., homozygozities within populations and relationships across populations. These parameters can be estimated from existing pedigree and marker genotypes using maximum likelihood or a method based on summary statistics, for arbitrarily complex pedigrees. Equivalences of genetic variance and variance components between the classical and this new parameterization are shown. Segregation variance on crosses of populations is modeled. Efficient algorithms for computation of relationship matrices, their inverses, and inbreeding coefficients are presented. Use of metafounders leads to compatibility of genomic and pedigree relationship matrices and to simple computing algorithms. Examples and code are given. Copyright © 2015 by the Genetics Society of America.
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Genetic mapping of the female mimic morph locus in the ruff
2013-01-01
Background Ruffs (Aves: Philomachus pugnax) possess a genetic polymorphism for male mating behaviour resulting in three permanent alternative male reproductive morphs: (i) territorial ‘Independents’, (ii) non-territorial ‘Satellites’, and (iii) female-mimicking ‘Faeders’. Development into independent or satellite morphs has previously been shown to be due to a single-locus, two-allele autosomal Mendelian mode of inheritance at the Satellite locus. Here, we use linkage analysis to map the chromosomal location of the Faeder locus, which controls development into the Faeder morph, and draw further conclusions about candidate genes, assuming shared synteny with other birds. Results Segregation data on the Faeder locus were obtained from captive-bred pedigrees comprising 64 multi-generation families (N = 381). There was no evidence that the Faeder locus was linked to the Satellite locus, but it was linked with microsatellite marker Ppu020. Comparative mapping of ruff microsatellite markers against the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) genomes places the Ppu020 and Faeder loci on a region of chromosome 11 that includes the Melanocortin-1 receptor (MC1R) gene, which regulates colour polymorphisms in numerous birds and other vertebrates. Melanin-based colouration varies with life-history strategies in ruffs and other species, thus the MC1R gene is a strong candidate to play a role in alternative male morph determination. Conclusion Two unlinked loci appear to control behavioural development in ruffs. The Faeder locus is linked to Ppu020, which, assuming synteny, is located on avian chromosome 11. MC1R is a candidate gene involved in alternative male morph determination in ruffs. PMID:24256185
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Imputing amino acid polymorphisms in human leukocyte antigens.
Directory of Open Access Journals (Sweden)
Xiaoming Jia
Full Text Available DNA sequence variation within human leukocyte antigen (HLA genes mediate susceptibility to a wide range of human diseases. The complex genetic structure of the major histocompatibility complex (MHC makes it difficult, however, to collect genotyping data in large cohorts. Long-range linkage disequilibrium between HLA loci and SNP markers across the major histocompatibility complex (MHC region offers an alternative approach through imputation to interrogate HLA variation in existing GWAS data sets. Here we describe a computational strategy, SNP2HLA, to impute classical alleles and amino acid polymorphisms at class I (HLA-A, -B, -C and class II (-DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 loci. To characterize performance of SNP2HLA, we constructed two European ancestry reference panels, one based on data collected in HapMap-CEPH pedigrees (90 individuals and another based on data collected by the Type 1 Diabetes Genetics Consortium (T1DGC, 5,225 individuals. We imputed HLA alleles in an independent data set from the British 1958 Birth Cohort (N = 918 with gold standard four-digit HLA types and SNPs genotyped using the Affymetrix GeneChip 500 K and Illumina Immunochip microarrays. We demonstrate that the sample size of the reference panel, rather than SNP density of the genotyping platform, is critical to achieve high imputation accuracy. Using the larger T1DGC reference panel, the average accuracy at four-digit resolution is 94.7% using the low-density Affymetrix GeneChip 500 K, and 96.7% using the high-density Illumina Immunochip. For amino acid polymorphisms within HLA genes, we achieve 98.6% and 99.3% accuracy using the Affymetrix GeneChip 500 K and Illumina Immunochip, respectively. Finally, we demonstrate how imputation and association testing at amino acid resolution can facilitate fine-mapping of primary MHC association signals, giving a specific example from type 1 diabetes.
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Gonzalez-Rodriguez, Pablo; Cantu, Jessica; O'Neil, Derek; Seferovic, Maxim D; Goodspeed, Danielle M; Suter, Melissa A; Aagaard, Kjersti M
2016-05-01
The H19/IGF2 imprinted loci have attracted recent attention because of their role in cellular differentiation and proliferation, heritable gene regulation, and in utero or early postnatal growth and development. Expression from the imprinted H19/IGF2 locus involves a complex interplay of 3 means of epigenetic regulation: proper establishment of DNA methylation, promoter occupancy of CTCF, and expression of microRNA-675. We have demonstrated previously in a multigenerational rat model of intrauterine growth restriction the epigenetic heritability of adult metabolic syndrome in a F2 generation. We have further demonstrated abrogation of the F2 adult metabolic syndrome phenotype with essential nutrient supplementation of intermediates along the 1-carbon pathway and shown that alterations in the metabolome precede the adult onset of metabolic syndrome. The upstream molecular and epigenomic mediators underlying these observations, however, have yet to be elucidated fully. In the current study, we sought to characterize the impact of the intrauterine growth-restricted lineage and essential nutrient supplementation on both levels and molecular mediators of H19 and IGF2 gene expression in the F2 generation. F2 intrauterine growth-restricted and sham lineages were obtained by exposing P1 (grandmaternal) pregnant dams to bilateral uterine artery ligation or sham surgery at gestational day 19.5. F1 pups were allocated to the essential nutrient supplemented or control diet at postnatal day 21, and bred at 6-7 weeks of age. Hepatic tissues from the resultant F2 offspring at birth and at weaning (day 21) were obtained. Bisulfite modification and sequencing was employed for methylation analysis. H19 and IGF2 expression was measured by quantitative polymerase chain reaction. Promoter occupancy was quantified by the use of chromatin immunoprecipitation, or ChIP, against CTCF insulator proteins. Growth-restricted F2 on control diet demonstrated significant down-regulation in H19
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Directory of Open Access Journals (Sweden)
Naveen K Kadri
Full Text Available Population structure is known to cause false-positive detection in association studies. We compared the power, precision, and type-I error rates of various association models in analyses of a simulated dataset with structure at the population (admixture from two populations; P and family (K levels. We also compared type-I error rates among models in analyses of publicly available human and dog datasets. The models corrected for none, one, or both structure levels. Correction for K was performed with linear mixed models incorporating familial relationships estimated from pedigrees or genetic markers. Linear models that ignored K were also tested. Correction for P was performed using principal component or structured association analysis. In analyses of simulated and real data, linear mixed models that corrected for K were able to control for type-I error, regardless of whether they also corrected for P. In contrast, correction for P alone in linear models was insufficient. The power and precision of linear mixed models with and without correction for P were similar. Furthermore, power, precision, and type-I error rate were comparable in linear mixed models incorporating pedigree and genomic relationships. In summary, in association studies using samples with both P and K, ancestries estimated using principal components or structured assignment were not sufficient to correct type-I errors. In such cases type-I errors may be controlled by use of linear mixed models with relationships derived from either pedigree or from genetic markers.
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Clark, Samuel A; Hickey, John M; Daetwyler, Hans D; van der Werf, Julius H J
2012-02-09
The theory of genomic selection is based on the prediction of the effects of genetic markers in linkage disequilibrium with quantitative trait loci. However, genomic selection also relies on relationships between individuals to accurately predict genetic value. This study aimed to examine the importance of information on relatives versus that of unrelated or more distantly related individuals on the estimation of genomic breeding values. Simulated and real data were used to examine the effects of various degrees of relationship on the accuracy of genomic selection. Genomic Best Linear Unbiased Prediction (gBLUP) was compared to two pedigree based BLUP methods, one with a shallow one generation pedigree and the other with a deep ten generation pedigree. The accuracy of estimated breeding values for different groups of selection candidates that had varying degrees of relationships to a reference data set of 1750 animals was investigated. The gBLUP method predicted breeding values more accurately than BLUP. The most accurate breeding values were estimated using gBLUP for closely related animals. Similarly, the pedigree based BLUP methods were also accurate for closely related animals, however when the pedigree based BLUP methods were used to predict unrelated animals, the accuracy was close to zero. In contrast, gBLUP breeding values, for animals that had no pedigree relationship with animals in the reference data set, allowed substantial accuracy. An animal's relationship to the reference data set is an important factor for the accuracy of genomic predictions. Animals that share a close relationship to the reference data set had the highest accuracy from genomic predictions. However a baseline accuracy that is driven by the reference data set size and the overall population effective population size enables gBLUP to estimate a breeding value for unrelated animals within a population (breed), using information previously ignored by pedigree based BLUP methods.
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Genomic prediction of traits related to canine hip dysplasia
Directory of Open Access Journals (Sweden)
Enrique eSanchez-Molano
2015-03-01
Full Text Available Increased concern for the welfare of pedigree dogs has led to development of selection programs against inherited diseases. An example is canine hip dysplasia (CHD, which has a moderate heritability and a high prevalence in some large-sized breeds. To date, selection using phenotypes has led to only modest improvement, and alternative strategies such as genomic selection may prove more effective. The primary aims of this study were to compare the performance of pedigree- and genomic-based breeding against CHD in the UK Labrador retriever population and to evaluate the performance of different genomic selection methods. A sample of 1179 Labrador Retrievers evaluated for CHD according to the UK scoring method (hip score, HS was genotyped with the Illumina CanineHD BeadChip. Twelve functions of HS and its component traits were analyzed using different statistical methods (GBLUP, Bayes C and Single-Step methods, and results were compared with a pedigree-based approach (BLUP using cross-validation. Genomic methods resulted in similar or higher accuracies than pedigree-based methods with training sets of 944 individuals for all but the untransformed HS, suggesting that genomic selection is an effective strategy. GBLUP and Bayes C gave similar prediction accuracies for HS and related traits, indicating a polygenic architecture. This conclusion was also supported by the low accuracies obtained in additional GBLUP analyses performed using only the SNPs with highest test statistics, also indicating that marker-assisted selection would not be as effective as genomic selection. A Single-Step method that combines genomic and pedigree information also showed higher accuracy than GBLUP and Bayes C for the log-transformed HS, which is currently used for pedigree based evaluations in UK. In conclusion, genomic selection is a promising alternative to pedigree-based selection against CHD, requiring more phenotypes with genomic data to improve further the accuracy
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Persistence of accuracy of genomic estimated breeding values over generations in layer chickens
Directory of Open Access Journals (Sweden)
Fernando Rohan
2011-06-01
Full Text Available Abstract Background The predictive ability of genomic estimated breeding values (GEBV originates both from associations between high-density markers and QTL (Quantitative Trait Loci and from pedigree information. Thus, GEBV are expected to provide more persistent accuracy over successive generations than breeding values estimated using pedigree-based methods. The objective of this study was to evaluate the accuracy of GEBV in a closed population of layer chickens and to quantify their persistence over five successive generations using marker or pedigree information. Methods The training data consisted of 16 traits and 777 genotyped animals from two generations of a brown-egg layer breeding line, 295 of which had individual phenotype records, while others had phenotypes on 2,738 non-genotyped relatives, or similar data accumulated over up to five generations. Validation data included phenotyped and genotyped birds from five subsequent generations (on average 306 birds/generation. Birds were genotyped for 23,356 segregating SNP. Animal models using genomic or pedigree relationship matrices and Bayesian model averaging methods were used for training analyses. Accuracy was evaluated as the correlation between EBV and phenotype in validation divided by the square root of trait heritability. Results Pedigree relationships in outbred populations are reduced by 50% at each meiosis, therefore accuracy is expected to decrease by the square root of 0.5 every generation, as observed for pedigree-based EBV (Estimated Breeding Values. In contrast the GEBV accuracy was more persistent, although the drop in accuracy was substantial in the first generation. Traits that were considered to be influenced by fewer QTL and to have a higher heritability maintained a higher GEBV accuracy over generations. In conclusion, GEBV capture information beyond pedigree relationships, but retraining every generation is recommended for genomic selection in closed breeding
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Lesuisse, J; Schallier, S; Li, C; Bautil, A; Li, B; Leblois, J; Buyse, J; Everaert, N
2018-05-01
Several studies in mammals focused on the maternal programming of the metabolism by epigenetic mechanisms, while currently, the consequences of a maternal dietary treatment on the offspring performance of farm animals are of particular interest for commercial purpose. In the present study, we investigated if the zootechnical performance of the progeny was altered by a maternal dietary treatment, being a lower dietary crude protein (CP) of the grandparent and/or parent generation. The multigenerational effects of a reduced maternal CP content were investigated by reducing the dietary CP level by 25% in rearing and laying diets of pure line A breeders. The F0 generation breeders were fed either control (C) or reduced balanced protein (RP) diets. The F1 breeder generation was constructed by dividing the F0 female progeny again over a C or RP diet, resulting in 4 dietary treatments in the F1 generation: C/C, C/RP, RP/C, and RP/RP (letters indicating the diets in, respectively, F0 and F1 generations). The offspring performance was evaluated by a zootechnical and nitrogen retention trial on C and low-protein (LP) broiler diets. For the C broiler diet, the C/RP and RP/RP offspring were characterized by a higher BW from d 35 until d 42 compared to the C/C progeny, whereas the RP/C offspring had an intermediate BW that did not differ from the other groups. A tendency (P = 0.067) towards a better nitrogen retention was observed for the offspring of breeders that received the RP diets in F0 and/or F1 generation compared to the C/C progeny. For the LP broiler diet, the C/RP (P = 0.021) and RP/C (P = 0.001) offspring had a higher BW compared to the C/C progeny during the entire grow-out period. In addition, the C/RP offspring were characterized by a lower FCR from d 28 onwards (P = 0.021). In conclusion, dietary treatments imposed on mother hens can have direct effects on the next generation, as well as indirect effects on multiple generations.
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A sampling algorithm for segregation analysis
Directory of Open Access Journals (Sweden)
Henshall John
2001-11-01
Full Text Available Abstract Methods for detecting Quantitative Trait Loci (QTL without markers have generally used iterative peeling algorithms for determining genotype probabilities. These algorithms have considerable shortcomings in complex pedigrees. A Monte Carlo Markov chain (MCMC method which samples the pedigree of the whole population jointly is described. Simultaneous sampling of the pedigree was achieved by sampling descent graphs using the Metropolis-Hastings algorithm. A descent graph describes the inheritance state of each allele and provides pedigrees guaranteed to be consistent with Mendelian sampling. Sampling descent graphs overcomes most, if not all, of the limitations incurred by iterative peeling algorithms. The algorithm was able to find the QTL in most of the simulated populations. However, when the QTL was not modeled or found then its effect was ascribed to the polygenic component. No QTL were detected when they were not simulated.
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Energy Technology Data Exchange (ETDEWEB)
Hoeche, M.R.; Berrettini, W.H. (Clinical Neurogenetics Branch, Bethesda, MD (USA)); Regan, J.W. (Duke Univ. Medical Center, Durham, NC (USA))
1989-12-11
A 1.5 kb Eco RI cDNA fragment representing the human alpha2-C4 adrenergic receptor (AR) gene encoding the putative alpha2B-AR, containing approximately 1270 bp of the coding and 240 bp of the 3{prime}flanking region, inserted into pSP65, was used as a probe (p ADRA2RL2). This clone was obtained by screening a human kidney lambda GT10 cDNA library with the 0.95 kb Pst I restriction fragment derived from the coding block of the gene for the human platelet alpha2-AR. Hybridization of human genomic DNA digested with Bsu 36 I identifies a two allele polymorphism with bands at 12 kb and 5.8 kb. 20 unrelated North American caucasian subjects were evaluated with frequencies of: A allele, 0.45; B allele, 0.55, heterozygosity (obs), 0.5. This alpha2-AR gene has been mapped in a separation effort in 59 CEPH reference pedigrees to the tip of the short arm of chromosome 4 just proximal to GB (4p 16.3) reported to be linked to the Huntingston's disease gene. Codominant inheritance was observed in seven families with two and three generations, respectively. The number of meioses scored was 95.
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DEFF Research Database (Denmark)
Moltke, Ida; Albrechtsen, Anders; Hansen, Thomas V O
2011-01-01
genome containing disease-causing variants. However, IBD regions can be difficult to detect, especially in the common case where no pedigree information is available. In particular, all existing non-pedigree based methods can only infer IBD sharing between two individuals. Here, we present a new Markov...... Chain Monte Carlo method for detection of IBD regions, which does not rely on any pedigree information. It is based on a probabilistic model applicable to unphased SNP data. It can take inbreeding, allele frequencies, genotyping errors, and genomic distances into account. And most importantly, it can...
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Improving Genetic Evaluation of Litter Size Using a Single-step Model
DEFF Research Database (Denmark)
Guo, Xiangyu; Christensen, Ole Fredslund; Ostersen, Tage
A recently developed single-step method allows genetic evaluation based on information from phenotypes, pedigree and markers simultaneously. This paper compared reliabilities of predicted breeding values obtained from single-step method and the traditional pedigree-based method for two litter size...... traits, total number of piglets born (TNB), and litter size at five days after birth (Ls 5) in Danish Landrace and Yorkshire pigs. The results showed that the single-step method combining phenotypic and genotypic information provided more accurate predictions than the pedigree-based method, not only...
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Transformational leadership to promote cross-generational retention.
Lobo, Vanessa M
2010-05-01
As the current nursing shortage intensifies under the weight of an aging population, retention of front-line staff is becoming paramount. Studies have consistently demonstrated that the leadership style of nurse managers plays a significant role to this end. This paper describes some of the challenges that managers encounter in their dealings with the contemporary multigenerational workforce - including the baby boomers, generation X and generation Y (the "millennials"). A review of research findings suggests the insufficiency of a single leadership approach to nurse management compared to more tailored generational strategies. Application of the transformational leadership model provides the background and tenets from which solutions are proposed for multigenerational management.
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Putz, A M; Tiezzi, F; Maltecca, C; Gray, K A; Knauer, M T
2018-02-01
The objective of this study was to compare and determine the optimal validation method when comparing accuracy from single-step GBLUP (ssGBLUP) to traditional pedigree-based BLUP. Field data included six litter size traits. Simulated data included ten replicates designed to mimic the field data in order to determine the method that was closest to the true accuracy. Data were split into training and validation sets. The methods used were as follows: (i) theoretical accuracy derived from the prediction error variance (PEV) of the direct inverse (iLHS), (ii) approximated accuracies from the accf90(GS) program in the BLUPF90 family of programs (Approx), (iii) correlation between predictions and the single-step GEBVs from the full data set (GEBV Full ), (iv) correlation between predictions and the corrected phenotypes of females from the full data set (Y c ), (v) correlation from method iv divided by the square root of the heritability (Y ch ) and (vi) correlation between sire predictions and the average of their daughters' corrected phenotypes (Y cs ). Accuracies from iLHS increased from 0.27 to 0.37 (37%) in the Large White. Approximation accuracies were very consistent and close in absolute value (0.41 to 0.43). Both iLHS and Approx were much less variable than the corrected phenotype methods (ranging from 0.04 to 0.27). On average, simulated data showed an increase in accuracy from 0.34 to 0.44 (29%) using ssGBLUP. Both iLHS and Y ch approximated the increase well, 0.30 to 0.46 and 0.36 to 0.45, respectively. GEBV Full performed poorly in both data sets and is not recommended. Results suggest that for within-breed selection, theoretical accuracy using PEV was consistent and accurate. When direct inversion is infeasible to get the PEV, correlating predictions to the corrected phenotypes divided by the square root of heritability is adequate given a large enough validation data set. © 2017 Blackwell Verlag GmbH.
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Assessment of clam ruditapes philippinarum as Heavy metal bioindicators using NMR-based metabolomics
Energy Technology Data Exchange (ETDEWEB)
Liu, Xiaoli; Zhang, Linbao; You, Liping [Key Laboratory of Coastal Zone Environment Processes, CAS, Shandong Provincial Key Laboratory of Coastal Zone Environment Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai (China); The Graduate School of Chinese Academy of Sciences, Beijing (China); Yu, Junbao; Cong, Ming; Wang, Qing; Li, Fei; Li, Lianzhen; Zhao, Jianmin; Li, Chenghua; Wu, Huifeng [Key Laboratory of Coastal Zone Environment Processes, CAS, Shandong Provincial Key Laboratory of Coastal Zone Environment Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai (China)
2011-08-15
There are mainly distributed three pedigrees (White, Liangdao Red, and Zebra) of Manila clam Ruditapes philippinarum in Yantai population along the Bohai marine and coast. However, the biological differences to environmental stressors have been ignored in toxicology studies, which could lead to the distortion of biological interpretations of toxicological effects induced by environmental contaminants. In this study, we applied a system biology approach, metabolomics to compare the metabolic profiles in digestive gland from three pedigrees of clam and characterize and compare the metabolic responses induced by mercury in clam digestive gland tissues to determine a sensitive pedigree of clam as a preferable bioindicator for metal pollution monitoring and toxicology research. The most abundant metabolites, respectively, included branched-chain amino acids, alanine, and arginine in White samples, glutamate, dimethylglycine, and glycine in Zebra clams and acetylcholine, betaine, glucose, and glycogen in Liangdao Red clams. After 48 h exposure of 20 {mu}g L{sup -1} Hg{sup 2+}, the metabolic profiles from the three pedigrees of clams showed differentially significant changes in alanine, glutamate, succinate, taurine, hypotaurine, glycine, arginine, glucose, etc. Our findings indicate the toxicological effects of mercury exposure in Manila clams including the neurotoxicity, disturbances in energetic metabolisms and osmoregulation in the digestive glands and suggest that Liangdao Red pedigree of clam could be a preferable bioindicator for the metal pollution monitoring based on the more sensitive classes of metabolic changes from digestive glands compared with other two (White and Zebra) pedigrees of clams. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)
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DEFF Research Database (Denmark)
Torskarska, M; Marshall, T; Kowalczyk, R
2009-01-01
The European bison (Bison bonasus) has recovered successfully after a severe bottleneck about 90 years ago. Pedigree analysis indicates that over 80% of the genes in the contemporary population descend from just 2 founder individuals and the pedigree-based inbreeding coefficient averages almost 0...
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Choi, Taejeong; Lim, Dajeong; Park, Byoungho; Sharma, Aditi; Kim, Jong-Joo; Kim, Sidong; Lee, Seung Hwan
2017-07-01
Intramuscular fat is one of the meat quality traits that is considered in the selection strategies for Hanwoo (Korean cattle). Different methods are used to estimate the breeding value of selection candidates. In the present work we focused on accuracy of different genotype relationship matrices as described by forni and pedigree based relationship matrix. The data set included a total of 778 animals that were genotyped for BovineSNP50 BeadChip. Among these 778 animals, 72 animals were sires for 706 reference animals and were used as a validation dataset. Single trait animal model (best linear unbiased prediction and genomic best linear unbiased prediction) was used to estimate the breeding values from genomic and pedigree information. The diagonal elements for the pedigree based coefficients were slightly higher for the genomic relationship matrices (GRM) based coefficients while off diagonal elements were considerably low for GRM based coefficients. The accuracy of breeding value for the pedigree based relationship matrix (A) was 13% while for GRM (GOF, G05, and Yang) it was 0.37, 0.45, and 0.38, respectively. Accuracy of GRM was 1.5 times higher than A in this study. Therefore, genomic information will be more beneficial than pedigree information in the Hanwoo breeding program.
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Jannovar: a java library for exome annotation.
Jäger, Marten; Wang, Kai; Bauer, Sebastian; Smedley, Damian; Krawitz, Peter; Robinson, Peter N
2014-05-01
Transcript-based annotation and pedigree analysis are two basic steps in the computational analysis of whole-exome sequencing experiments in genetic diagnostics and disease-gene discovery projects. Here, we present Jannovar, a stand-alone Java application as well as a Java library designed to be used in larger software frameworks for exome and genome analysis. Jannovar uses an interval tree to identify all transcripts affected by a given variant, and provides Human Genome Variation Society-compliant annotations both for variants affecting coding sequences and splice junctions as well as untranslated regions and noncoding RNA transcripts. Jannovar can also perform family-based pedigree analysis with Variant Call Format (VCF) files with data from members of a family segregating a Mendelian disorder. Using a desktop computer, Jannovar requires a few seconds to annotate a typical VCF file with exome data. Jannovar is freely available under the BSD2 license. Source code as well as the Java application and library file can be downloaded from http://compbio.charite.de (with tutorial) and https://github.com/charite/jannovar. © 2014 WILEY PERIODICALS, INC.
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Directory of Open Access Journals (Sweden)
Qiujie Qian
Full Text Available Human serum albumin (HSA is an important biological preparation with a variety of biological functions in clinical applications. In this study, the mRNA of a fusion transposase derived from the pESNT-PBase plasmid and a pBHSA plasmid containing the HSA gene under the control of a fibroin light chain (FL promoter were co-injected into fertilized eggs. Fifty-six transgenic silkworm pedigrees expressing theexogenous recombinant HSA (rHSA in the posterior silk glands (PSGs with stable inheritance were successfully obtained. The SDS-PAGE and Western blot results confirmed that the rHSA was secreted into the transgenic silkworm cocoon, and the rHSA could be easily extracted with phosphate-buffered saline (PBS. In our research, the isolated highest amount rHSA constituted up to 29.1% of the total soluble protein of the cocoon shell, indicating that the transgenic silkworm produced an average of 17.4 μg/mg of rHSA in the cocoon shell. The production of soluble rHSA in the PSGs by means of generating transgenic silkworms is a novel approach, whereby a large amount of virus-free and functional HSA can be produced through the simple rearing of silkworms.
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Rusbridge, Clare; Knowler, Penny; Rouleau, Guy A; Minassian, Berge A; Rothuizen, Jan
2005-01-01
Inherited diseases commonly emerge within pedigree dog populations, often due to use of repeatedly bred carrier sire(s) within a small gene pool. Accurate family records are usually available making linkage analysis possible. However, there are many factors that are intrinsically difficult about collecting DNA and collating pedigree information from a large canine population. The keys to a successful DNA collection program include (1) the need to establish and maintain support from the pedigree breed clubs and pet owners; (2) committed individual(s) who can devote the considerable amount of time and energy to coordinating sample collection and communicating with breeders and clubs; and (3) providing means by which genotypic and phenotypic information can be easily collected and stored. In this article we described the clinical characteristics of inherited occipital hypoplasia/syringomyelia (Chiari type I malformation) in the cavalier King Charles spaniel and our experiences in establishing a pedigree and DNA database to study the disease.
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Population structure and genetic trends for indigenous African beef ...
African Journals Online (AJOL)
The aim of this study was to investigate population structure and genetic trends based on pedigree and performance records of five indigenous African beef cattle breeds (Afrikaner, Boran, Drakensberger, Nguni and Tuli) in South Africa. Pedigree completeness over six generations was higher than 88.5% in the first ...
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Developing and delivering food systems training programs for 21st century audiences
Directory of Open Access Journals (Sweden)
Troy Hahn
2016-04-01
Full Text Available Expectations for training programmes today are very different from expectations for training programmes in the past, because today’s audiences are not only multigenerational, but the younger generations learn in distinctly different ways from older, more traditional audiences. To meet the needs of these multigenerational audiences, the Auburn University Food Systems Institute (AUFSI has developed on-demand, online courses that offer a variety of ways for learners to interact with training materials. For example, a typical course may offer not only traditional text, but audio, video, simulations, and more. In addition, AUFSI has developed supporting educational tools such as interactive virtual tours and video games. This approach to creating courses is a response to the different levels of experiences of the generations as well as different expectations of how materials should be delivered. In order to be effective, training materials need to be designed to appeal to this multigenerational audience. Traditionalists (born before 1946 prefer face-to-face training programmes. Baby Boomers (born 1946-1964 are more accepting of technology. Generations X (born 1965-1980, Y (born 1981- 2000 and C (born after 2000, however, expect to receive training at their convenience, to have it delivered electronically, and to be entertained as well as educated.
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Knight, Stacey; Camp, Nicola J
2011-04-01
Current common wisdom posits that association analyses using family-based designs have inflated type 1 error rates (if relationships are ignored) and independent controls are more powerful than familial controls. We explore these suppositions. We show theoretically that family-based designs can have deflated type-error rates. Through simulation, we examine the validity and power of family designs for several scenarios: cases from randomly or selectively ascertained pedigrees; and familial or independent controls. Family structures considered are as follows: sibships, nuclear families, moderate-sized and extended pedigrees. Three methods were considered with the χ(2) test for trend: variance correction (VC), weighted (weights assigned to account for genetic similarity), and naïve (ignoring relatedness) as well as the Modified Quasi-likelihood Score (MQLS) test. Selectively ascertained pedigrees had similar levels of disease enrichment; random ascertainment had no such restriction. Data for 1,000 cases and 1,000 controls were created under the null and alternate models. The VC and MQLS methods were always valid. The naïve method was anti-conservative if independent controls were used and valid or conservative in designs with familial controls. The weighted association method was generally valid for independent controls, and was conservative for familial controls. With regard to power, independent controls were more powerful for small-to-moderate selectively ascertained pedigrees, but familial and independent controls were equivalent in the extended pedigrees and familial controls were consistently more powerful for all randomly ascertained pedigrees. These results suggest a more complex situation than previously assumed, which has important implications for study design and analysis. © 2011 Wiley-Liss, Inc.
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International Nuclear Information System (INIS)
Young Wieyen; Zhao Lidong; Qian Yaping; Wang Qiuju; Li Ning; Greinwald, John H.; Guan Minxin
2005-01-01
Mutations in mitochondrial DNA (mtDNA) have been found to be associated with sensorineural hearing loss. We report here the clinical, genetic, and molecular characterization of four Chinese pedigrees with aminoglycoside-induced and nonsyndromic hearing impairment. Clinical evaluation revealed the variable phenotype of hearing impairment including audiometric configuration in these subjects, although these subjects share some common features: bilateral and sensorineural hearing impairment. Strikingly, these Chinese pedigrees exhibited extremely low penetrance of hearing loss (5.2%, 4.8%, 4.2%, and 13.3%, respectively, and with an average 8% penetrance). In particular, four of all five affected matrilineal relatives of these pedigrees had aminoglycoside-induced hearing loss. Sequence analysis of the complete mitochondrial genomes in these pedigrees showed the distinct sets of mtDNA polymorphism, in addition to the identical homoplasmic A1555G mutation, associated with hearing impairment in many families from different genetic backgrounds. The fact that mtDNA of those pedigrees belonged to different haplogroups R9a, N9a, D4a, and D4 suggested that the A1555G mutation occurred sporadically and multiplied through evolution of the mtDNA in China. However, there was the absence of functionally significant mutations in tRNA and rRNAs or secondary LHON mutations in these Chinese families. These data imply that the nuclear background or/and mitochondrial haplotype may not play a significant role in the phenotypic expression of the A1555G mutation in these Chinese pedigrees. However, aminoglycoside appears to be a major modifier factor for the phenotypic manifestation of the A1555G mutation in these Chinese families
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Multi-generational stewardship of plutonium
International Nuclear Information System (INIS)
Pillay, K.K.S.
1997-01-01
The post-cold war era has greatly enhanced the interest in the long-term stewardship of plutonium. The management of excess plutonium from proposed nuclear weapons dismantlement has been the subject of numerous intellectual discussions during the past several years. In this context, issues relevant to long-term management of all plutonium as a valuable energy resource are also being examined. While there are differing views about the future role of plutonium in the economy, there is a recognition of the environmental and health related problems and proliferation potentials of weapons-grade plutonium. The long-term management of plutonium as an energy resource will require a new strategy to maintain stewardship for many generations to come
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X-ray sensitivity of fibroblasts from patients with hereditary retinoblastoma and their families.
Pledger, J. V.; Craft, A. W.; Bartlett, K.; Long, D. R.
1987-01-01
The in vitro response to X-irradiation of cultured human fibroblasts was studied using a colony forming assay. A comprehensive reference range was established, giving a median D0 value of 98.5 cGy with an interquartile range of 86.5-110.5 cGy. Cells from 3 retinoblastoma family pedigrees were studied and the cell survival after exposure to X-rays was compared between affected (11 samples) and unaffected (26 samples) family members. No significant differences in response to ionising radiation ...
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Frisell, Thomas; Pawitan, Yudi; Långström, Niklas
2012-01-01
Research has consistently found lower cognitive ability to be related to increased risk for violent and other antisocial behaviour. Since this association has remained when adjusting for childhood socioeconomic position, ethnicity, and parental characteristics, it is often assumed to be causal, potentially mediated through school adjustment problems and conduct disorder. Socioeconomic differences are notoriously difficult to quantify, however, and it is possible that the association between intelligence and delinquency suffer substantial residual confounding. We linked longitudinal Swedish total population registers to study the association of general cognitive ability (intelligence) at age 18 (the Conscript Register, 1980-1993) with the incidence proportion of violent criminal convictions (the Crime Register, 1973-2009), among all men born in Sweden 1961-1975 (N = 700,514). Using probit regression, we controlled for measured childhood socioeconomic variables, and further employed sibling comparisons (family pedigree data from the Multi-Generation Register) to adjust for shared familial characteristics. Cognitive ability in early adulthood was inversely associated to having been convicted of a violent crime (β = -0.19, 95% CI: -0.19; -0.18), the association remained when adjusting for childhood socioeconomic factors (β = -0.18, 95% CI: -0.18; -0.17). The association was somewhat lower within half-brothers raised apart (β = -0.16, 95% CI: -0.18; -0.14), within half-brothers raised together (β = -0.13, 95% CI: (-0.15; -0.11), and lower still in full-brother pairs (β = -0.10, 95% CI: -0.11; -0.09). The attenuation among half-brothers raised together and full brothers was too strong to be attributed solely to attenuation from measurement error. Our results suggest that the association between general cognitive ability and violent criminality is confounded partly by factors shared by brothers. However, most of the association remains even
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Detection of parent-of-origin effects for quantitative traits using ...
Indian Academy of Sciences (India)
However, these methods can only be applied to deal with nuclear families and thus are not suitable for extended pedigrees. ... In addition, the power comparison demonstrates that Q-PPAT() and Q-MCPPAT() for pedigree data are much more powerful than Q-PAT() only using two-generation nuclear families selected ...
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Genetic Testing for Inherited Heart Disease
... pedigree. A pedigree ( Figure 2 ) is a family tree that shows who has and who does not have the condition of interest. It is drawn to organize information about the medical history of family members, to illustrate who is affected, to identify the pattern of inheritance, and to identify who ...
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Inbreeding in the Danish populations of five Nordic sheep breeds
DEFF Research Database (Denmark)
Sørensen, Anders Christian; Norberg, Elise
2008-01-01
In Denmark there are small populations of five Nordic sheep breeds, two of which are Danish in origin. The purpose of this study was to estimate trends in inbreeding for these breeds. All five breeds have been recording pedigrees for decades, so pedigree completeness is adequate. The rate of inbr...
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Strategies for MCMC computation in quantitative genetics
DEFF Research Database (Denmark)
Waagepetersen, Rasmus; Ibánez, N.; Sorensen, Daniel
2006-01-01
Given observations of a trait and a pedigree for a group of animals, the basic model in quantitative genetics is a linear mixed model with genetic random effects. The correlation matrix of the genetic random effects is determined by the pedigree and is typically very highdimensional but with a sp...
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A genetic analysis of epistaxis as associated with EIPH in the ...
African Journals Online (AJOL)
Pedigree and race run data from Thoroughbreds racing in Southern Africa, covering the period 1986-2002 (63 146 horses in pedigree data-set and 778 532 race runs), were analysed in order to study genetic and environmental factors affecting the incidence of epistaxis as associated with \\"exercise-induced pulmonary ...
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The Fangshan/Family-based Ischemic Stroke Study In China (FISSIC protocol
Directory of Open Access Journals (Sweden)
Chen Dafang
2007-09-01
Full Text Available Abstract Background The exact etiology of ischemic stroke remains unclear, because multiple genetic predispositions and environmental risk factors may be involved, and their interactions dictate the complexity. Family-based studies provide unique features in design, while they are currently underrepresented for studies of ischemic stroke in developing countries. The Fangshan/Family-based Ischemic Stroke Study In China (FISSIC program aims to conduct a genetic pedigree study of ischemic stroke in rural communities of China. Methods/Design The pedigrees of ischemic stroke with clear documentation are recruited by using the proband-initiated contact method, based on the stroke registry in hospital and communities. Blood samples and detailed information of pedigrees are collected through the health care network in the rural area, and prospective follow-up of the pedigrees cohort is scheduled. Complementary strategies of both family-based design and matched case-spousal control design are used, and comprehensive statistical methods will be implemented to ascertain potential complex genetic and environmental factors and their interactions as well. Discussion This study is complementary to other genetic pedigree studies of ischemic stroke, such as the Siblings With Ischemic Stroke Study (SWISS, which are established in developed countries. We describe the protocol of this family-based genetic epidemiological study that may be used as a new practical guideline and research paradigm in developing countries and facilitate initiatives of stroke study for international collaborations.
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International Nuclear Information System (INIS)
Zhou Xiangtian; Wei Qiping; Yang Li; Tong Yi; Zhao Fuxin; Lu Chunjie; Qian Yaping; Sun Yanghong; Lu Fan; Qu Jia; Guan Minxin
2006-01-01
We report here the clinical, genetic, and molecular characterization of five Chinese families with Leber's hereditary optic neuropathy (LHON). Clinical and genetic evaluations revealed the variable severity and age-of-onset in visual impairment in these families. Strikingly, there were extremely low penetrances of visual impairment in these Chinese families. Sequence analysis of the complete mitochondrial genomes in these pedigrees showed the distinct sets of mtDNA polymorphism, in addition to the identical ND4 G11696A mutation associated with LHON. Indeed, this mutation is present in homoplasmy only in the maternal lineage of those pedigrees but not other members of these families. In fact, the occurrence of the G11696A mutation in these several genetically unrelated subjects affected by visual impairment strongly indicates that this mutation is involved in the pathogenesis of visual impairment. Furthermore, the N405D in the ND5 and G5820A in the tRNA Cys , showing high evolutional conservation, may contribute to the phenotypic expression of G11696A mutation in the WZ10 pedigree. However, there was the absence of functionally significant mtDNA mutations in other four Chinese pedigrees carrying the G11696A mutation. Therefore, nuclear modifier gene(s) or environmental factor(s) may play a role in the phenotypic expression of the LHON-associated G11696A mutation in these Chinese pedigrees
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Prevalence of genetic disorders in dog breeds: a literature review
Wirth, J.
2015-01-01
Genetic disorders are common in dogs and in the media it is reported that genetic disorders are more frequent in pedigree dogs than in look-a-likes or in mixed-breed dogs. Here, we consider pedigree dogs as purebred dogs (i.e. matching a breed-specific morphology) with a registered and certified
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Directory of Open Access Journals (Sweden)
Magdalena Kowalska
2008-06-01
Full Text Available Research was carried out in 2006 in three gminas (administrative boroughs of the Małopolska Province – Dębno, Wieliczka, and Zabierzów. 40 multigeneration rural families were selected in each gmina. Interviews were conducted with them on the basis of a questionnaire made up of three parts focused on the representatives of three genera-tions: grandparents, parents, and grandchildren. 360 people were surveyed in total. The results of the research, which are presented here, will try to provide an answer to the ques-tion of how critical a role tradition plays in the life of multigeneration rural families, and also to what extent they cherish the customs and habits which they have inherited from previous generations.
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Multi generations in the workforce: Building collaboration
Directory of Open Access Journals (Sweden)
Vasanthi Srinivasan
2012-03-01
Full Text Available Organisations the world over in today's rapid growth context are faced with the challenge of understanding a multi-generational workforce and devising policies and processes to build collaboration between them. In its first part, this article synthesises the literature on generational studies, with emphasis on the definition of generations and the characteristics of the generational cohorts. It emphasises that such studies are embedded in the socio-economic-cultural-context and India-specific scholarship must take into account the demographic and economic variations across the country. It then discusses the challenges of multi-generations in the Indian workforce, their impact on leadership styles and managerial practices, and the task of building inter-generational collaboration with an eminent panel of practitioners and researchers.
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FamSeq: a variant calling program for family-based sequencing data using graphics processing units.
Directory of Open Access Journals (Sweden)
Gang Peng
2014-10-01
Full Text Available Various algorithms have been developed for variant calling using next-generation sequencing data, and various methods have been applied to reduce the associated false positive and false negative rates. Few variant calling programs, however, utilize the pedigree information when the family-based sequencing data are available. Here, we present a program, FamSeq, which reduces both false positive and false negative rates by incorporating the pedigree information from the Mendelian genetic model into variant calling. To accommodate variations in data complexity, FamSeq consists of four distinct implementations of the Mendelian genetic model: the Bayesian network algorithm, a graphics processing unit version of the Bayesian network algorithm, the Elston-Stewart algorithm and the Markov chain Monte Carlo algorithm. To make the software efficient and applicable to large families, we parallelized the Bayesian network algorithm that copes with pedigrees with inbreeding loops without losing calculation precision on an NVIDIA graphics processing unit. In order to compare the difference in the four methods, we applied FamSeq to pedigree sequencing data with family sizes that varied from 7 to 12. When there is no inbreeding loop in the pedigree, the Elston-Stewart algorithm gives analytical results in a short time. If there are inbreeding loops in the pedigree, we recommend the Bayesian network method, which provides exact answers. To improve the computing speed of the Bayesian network method, we parallelized the computation on a graphics processing unit. This allowed the Bayesian network method to process the whole genome sequencing data of a family of 12 individuals within two days, which was a 10-fold time reduction compared to the time required for this computation on a central processing unit.
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POPULATION STUDIES OF CZECH HUCUL HORSES
Directory of Open Access Journals (Sweden)
Hana Vostrá Vydrová
2015-09-01
Full Text Available Population studies were carried out analysis Czech Hucul breed based on pedigree information of animals registered in the Studbook. Pedigree records collected from the year 1834 to 2013 comprised information on 9455 animals used in the analyses. The pedigree depth of the analysed individuals was up to 19 generations. The mean value of inbreeding coefficient was 5.35% (with maximum value 30%. The proportion of inbreed animals was high (98%. The average rate of inbreeding in the reference population was lower than 1%, and the respective estimates of effective population sizes were 54. The presented paper is indicating that genetic diversity in the Czech Hucul breeds is still relatively high and conservation programs should be continued.
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Webster, R J; Williams, A; Marchetti, F; Yauk, C L
2018-07-01
Mutations in germ cells pose potential genetic risks to offspring. However, de novo mutations are rare events that are spread across the genome and are difficult to detect. Thus, studies in this area have generally been under-powered, and no human germ cell mutagen has been identified. Whole Genome Sequencing (WGS) of human pedigrees has been proposed as an approach to overcome these technical and statistical challenges. WGS enables analysis of a much wider breadth of the genome than traditional approaches. Here, we performed power analyses to determine the feasibility of using WGS in human families to identify germ cell mutagens. Different statistical models were compared in the power analyses (ANOVA and multiple regression for one-child families, and mixed effect model sampling between two to four siblings per family). Assumptions were made based on parameters from the existing literature, such as the mutation-by-paternal age effect. We explored two scenarios: a constant effect due to an exposure that occurred in the past, and an accumulating effect where the exposure is continuing. Our analysis revealed the importance of modeling inter-family variability of the mutation-by-paternal age effect. Statistical power was improved by models accounting for the family-to-family variability. Our power analyses suggest that sufficient statistical power can be attained with 4-28 four-sibling families per treatment group, when the increase in mutations ranges from 40 to 10% respectively. Modeling family variability using mixed effect models provided a reduction in sample size compared to a multiple regression approach. Much larger sample sizes were required to detect an interaction effect between environmental exposures and paternal age. These findings inform study design and statistical modeling approaches to improve power and reduce sequencing costs for future studies in this area. Crown Copyright © 2018. Published by Elsevier B.V. All rights reserved.
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Directory of Open Access Journals (Sweden)
Omnia Gamal El-Dien
2016-03-01
Full Text Available The open-pollinated (OP family testing combines the simplest known progeny evaluation and quantitative genetics analyses as candidates’ offspring are assumed to represent independent half-sib families. The accuracy of genetic parameter estimates is often questioned as the assumption of “half-sibling” in OP families may often be violated. We compared the pedigree- vs. marker-based genetic models by analysing 22-yr height and 30-yr wood density for 214 white spruce [Picea glauca (Moench Voss] OP families represented by 1694 individuals growing on one site in Quebec, Canada. Assuming half-sibling, the pedigree-based model was limited to estimating the additive genetic variances which, in turn, were grossly overestimated as they were confounded by very minor dominance and major additive-by-additive epistatic genetic variances. In contrast, the implemented genomic pairwise realized relationship models allowed the disentanglement of additive from all nonadditive factors through genetic variance decomposition. The marker-based models produced more realistic narrow-sense heritability estimates and, for the first time, allowed estimating the dominance and epistatic genetic variances from OP testing. In addition, the genomic models showed better prediction accuracies compared to pedigree models and were able to predict individual breeding values for new individuals from untested families, which was not possible using the pedigree-based model. Clearly, the use of marker-based relationship approach is effective in estimating the quantitative genetic parameters of complex traits even under simple and shallow pedigree structure.
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Genetics Home Reference: Meesmann corneal dystrophy
... was first described in a large, multi-generational German family with more than 100 affected members. Since ... be inherited? More about Inheriting Genetic Conditions Diagnosis & Management Resources Genetic Testing (1 link) Genetic Testing Registry: ...
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Statistical fingerprinting for malware detection and classification
Prowell, Stacy J.; Rathgeb, Christopher T.
2015-09-15
A system detects malware in a computing architecture with an unknown pedigree. The system includes a first computing device having a known pedigree and operating free of malware. The first computing device executes a series of instrumented functions that, when executed, provide a statistical baseline that is representative of the time it takes the software application to run on a computing device having a known pedigree. A second computing device executes a second series of instrumented functions that, when executed, provides an actual time that is representative of the time the known software application runs on the second computing device. The system detects malware when there is a difference in execution times between the first and the second computing devices.
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Jia, Ying; Li, Xiaoge; Yang, Dong; Xu, Yi; Guo, Ying; Li, Xin
2018-01-01
The current study aims to identify the pathogenic sites in a core pedigree of Usher syndrome (USH). A core pedigree of USH was analyzed by whole exome sequencing (WES). Mutations were verified by polymerase chain reaction (PCR) amplification and Sanger sequencing. Two pathogenic variations (c.849+2T>C and c.5994G>A) in MYO7A were successfully identified and individually separated from parents. One variant (c.849+2T>C) was nonsense mutation, causing the protein terminated in advance, and the other one (c.5994G>A) located near the boundary of exon could cause aberrant splicing. This study provides a meaningful exploration for identification of clinical core genetic pedigrees. Copyright © 2017 Elsevier B.V. All rights reserved.
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Madhavan, Sangeetha; Collinson, Mark; Gómez-Olivé, F. Xavier; Ralston, Margaret
2015-01-01
South Africa’s population is aging. Most of the older Black South Africans continue to live in extended household structures with children, grandchildren, and other kin. They also constitute a source of income through a means-tested noncontributory state-funded pension available at age 60. Using census data from the Agincourt Health and Demographic Surveillance System in 2000, 2005, and 2010, we develop a typology of living arrangements that is reflective of the social positioning of elderly persons as dependent or productive household members and analyze changes in the distribution over time. Older persons, in general, live in large, complex, and multigenerational households. Multigenerational households with “productive” older persons are increasing in proportion over the period, although there are few differences by gender or pension eligibility at any time point. PMID:25651584
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Tribble, Leta Meole
Nowhere is the influence of genetics more extensively seen than in medicine. More precise diagnostic testing, prevention methods, and risk counseling have resulted from recent decades of genetics research, including the Human Genome Project (HGP). The expansion in genetics knowledge and related technologies will drive a major paradigm shift from diagnosis and treatment to preventive medicine. Resulting from this predicted shift are educational challenges for healthcare professionals including both physicians and nurses. The largest group of healthcare providers is registered professional nurses whose work allows a unique and holistic view of patients and families, often caring for patients throughout the life span. Nurses need to understand basic genetic concepts including the role of genes in common diseases, to identify individuals at risk through the collection of informed family histories, to provide information about genetic testing and informed consent, and to know when and how to make appropriate referrals to genetic specialists. The purpose of this study was to expand the clinical application and use of genetic principles in patient management and care. To do this, a survey of South Carolina nursing educators from twenty two nursing programs was conducted to determine the extent of genetic content in the curriculum. The second part of the study was teaching a semester course in human genetics to undergraduate nursing students, a need identified in the literature review and supported by results of the nursing programs survey. Through the use of clinical case studies, PBL activities, and "shrink wrapped" lectures, all congruent with the constructivist viewpoint of learning, student's objective post-intervention measurements indicated significant improvement in content knowledge with an effect size of 1.6 and significant improvement in their ability to analyze and draw the family history in a pedigree format. An attitudinal tool used to assess student
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Middelton, L A; Peters, K F
2001-10-01
The information gained from the Human Genome Project and related genetic research will undoubtedly create significant changes in healthcare practice. It is becoming increasingly clear that nurses in all areas of clinical practice will require a fundamental understanding of basic genetics. This article provides the oncology nurse with an overview of basic genetic concepts, including inheritance patterns of single gene conditions, pedigree construction, chromosome aberrations, and the multifactorial basis underlying the common diseases of adulthood. Normal gene structure and function are introduced and the biochemistry of genetic errors is described.
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Clinical and genetic investigation of families with type II Waardenburg syndrome.
Chen, Yong; Yang, Fuwei; Zheng, Hexin; Zhou, Jianda; Zhu, Ganghua; Hu, Peng; Wu, Weijing
2016-03-01
The present study aimed to investigate the molecular pathology of Waardenburg syndrome type II in three families, in order to provide genetic diagnosis and hereditary counseling for family members. Relevant clinical examinations were conducted on the probands of the three pedigrees. Peripheral blood samples of the probands and related family members were collected and genomic DNA was extracted. The coding sequences of paired box 3 (PAX3), microphthalmia‑associated transcription factor (MITF), sex‑determining region Y‑box 10 (SOX10) and snail family zinc finger 2 (SNAI2) were analyzed by polymerase chain reaction and DNA sequencing. The heterozygous mutation, c.649_651delAGA in exon 7 of the MITF gene was detected in the proband and all patients of pedigree 1; however, no pathological mutation of the relevant genes (MITF, SNAI2, SOX10 or PAX3) was detected in pedigrees 2 and 3. The heterozygous mutation c.649_651delAGA in exon 7 of the MITF gene is therefore considered the disease‑causing mutation in pedigree 1. However, there are novel disease‑causing genes in Waardenburg syndrome type II, which require further research.
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A novel OPA1 mutation in a Chinese family with autosomal dominant optic atrophy
International Nuclear Information System (INIS)
Zhang, Juanjuan; Yuan, Yimin; Lin, Bing; Feng, Hao; Li, Yan; Dai, Xianning; Zhou, Huihui; Dong, Xujie; Liu, Xiao-Ling; Guan, Min-Xin
2012-01-01
Highlights: ► We report the characterization of a four-generation large Chinese family with ADOA. ► We find a new heterozygous mutation c.C1198G in OPA1 gene which may be a novel pathogenic mutation in this pedigree. ► We do not find any mitochondrial DNA mutations associated with optic atrophy. ► Other factors may also contribute to the phenotypic variability of ADOA in this pedigree. -- Abstract: A large four-generation Chinese family with autosomal dominant optic atrophy (ADOA) was investigated in the present study. Eight of the family members were affected in this pedigree. The affected family members exhibited early-onset and progressive visual impairment, resulting in mild to profound loss of visual acuity. The average age-at-onset was 15.9 years. A new heterozygous mutation c.C1198G was identified by sequence analysis of the 12th exon of the OPA1 gene. This mutation resulted in a proline to alanine substitution at codon 400, which was located in an evolutionarily conserved region. This missense mutation in the GTPase domain was supposed to result in a loss of function for the encoded protein and act through a dominant negative effect. No other mutations associated with optic atrophy were found in our present study. The c.C1198G heterozygous mutation in the OPA1 gene may be a novel key pathogenic mutation in this pedigree with ADOA. Furthermore, additional nuclear modifier genes, environmental factors, and psychological factors may also contribute to the phenotypic variability of ADOA in this pedigree.
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A Mission Concept to Study Multigenerational Mammalian Reproduction in Partial Gravity
Rodgers, Erica M.; Simon, Matthew A.; Chai, Patrick R.; Neilan, James H.; Stillwagen, Fred H.; Williams, Phillip A.; Lewis, Weston
2016-01-01
A team at NASA Langley Research Center conducted a study during which a conceptual space mission was designed. In this study, rodents are used as human analogs to gather biological and systems data in a relevant environment applicable to future settlements on Mars. The mission concept uniquely addresses the combined effects of long-durations (one-year or greater), autonomous and robotic operations, and biological responses to partial gravity with an emphasis on reproduction. The objectives of this study were to 1) understand challenges associated with designing an artificial gravity habitat that supports the reproduction and maturation of a large animal colony, 2) identify mission architectures and operational concepts to transport and maintain such a facility, and 3) identify fundamental science considerations for mammalian reproduction studies to inform vehicle design. A model demonstration unit was developed to visualize and test certain design concepts that resulted from these considerations. Three versions of this demonstration unit were built over the course of the study, each taking into account lessons learned from the previous version. This paper presents the updated baseline mission and spacecraft design concepts to achieve these objectives, with a specific emphasis on updates since publication in previous works. Analyses of the integrated system trades among the elements which make up the conceptual vehicle are described to address overall feasibility and identify potential integrated design opportunities. The latest iteration of the habitat robotics design and a conceptual design example for autonomous care of crew and systems are also presented. Finally, the conclusion of this conceptual design study, necessary future analyses to enable such a facility, and comments upon other applications of a similar exploration-focused research facilities are addressed.
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Determination of gene action for some biometrical traits in Lens ...
Indian Academy of Sciences (India)
Medik. under mid-hill conditions of northwestern Himalayas. Naresh Kumar, B. C. Sood, T. R. Sharma, R. K. Chahota and Salej Sood. J. Genet. 90, 493–497. Table 1. Pedigree/source of genotypes used. Genotype. Pedigree/source. Yield (q/ha). Days to maturity. L-652. L-4145 × PL-639. 8–10. 160–165. L-651. L-4145 × PL- ...
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Population Structure and Genomic Breed Composition in an Angus-Brahman Crossbred Cattle Population.
Gobena, Mesfin; Elzo, Mauricio A; Mateescu, Raluca G
2018-01-01
Crossbreeding is a common strategy used in tropical and subtropical regions to enhance beef production, and having accurate knowledge of breed composition is essential for the success of a crossbreeding program. Although pedigree records have been traditionally used to obtain the breed composition of crossbred cattle, the accuracy of pedigree-based breed composition can be reduced by inaccurate and/or incomplete records and Mendelian sampling. Breed composition estimation from genomic data has multiple advantages including higher accuracy without being affected by missing, incomplete, or inaccurate records and the ability to be used as independent authentication of breed in breed-labeled beef products. The present study was conducted with 676 Angus-Brahman crossbred cattle with genotype and pedigree information to evaluate the feasibility and accuracy of using genomic data to determine breed composition. We used genomic data in parametric and non-parametric methods to detect population structure due to differences in breed composition while accounting for the confounding effect of close familial relationships. By applying principal component analysis (PCA) and the maximum likelihood method of ADMIXTURE to genomic data, it was possible to successfully characterize population structure resulting from heterogeneous breed ancestry, while accounting for close familial relationships. PCA results offered additional insight into the different hierarchies of genetic variation structuring. The first principal component was strongly correlated with Angus-Brahman proportions, and the second represented variation within animals that have a relatively more extended Brangus lineage-indicating the presence of a distinct pattern of genetic variation in these cattle. Although there was strong agreement between breed proportions estimated from pedigree and genetic information, there were significant discrepancies between these two methods for certain animals. This was most likely due
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Population Structure and Genomic Breed Composition in an Angus–Brahman Crossbred Cattle Population
Directory of Open Access Journals (Sweden)
Mesfin Gobena
2018-03-01
Full Text Available Crossbreeding is a common strategy used in tropical and subtropical regions to enhance beef production, and having accurate knowledge of breed composition is essential for the success of a crossbreeding program. Although pedigree records have been traditionally used to obtain the breed composition of crossbred cattle, the accuracy of pedigree-based breed composition can be reduced by inaccurate and/or incomplete records and Mendelian sampling. Breed composition estimation from genomic data has multiple advantages including higher accuracy without being affected by missing, incomplete, or inaccurate records and the ability to be used as independent authentication of breed in breed-labeled beef products. The present study was conducted with 676 Angus–Brahman crossbred cattle with genotype and pedigree information to evaluate the feasibility and accuracy of using genomic data to determine breed composition. We used genomic data in parametric and non-parametric methods to detect population structure due to differences in breed composition while accounting for the confounding effect of close familial relationships. By applying principal component analysis (PCA and the maximum likelihood method of ADMIXTURE to genomic data, it was possible to successfully characterize population structure resulting from heterogeneous breed ancestry, while accounting for close familial relationships. PCA results offered additional insight into the different hierarchies of genetic variation structuring. The first principal component was strongly correlated with Angus–Brahman proportions, and the second represented variation within animals that have a relatively more extended Brangus lineage—indicating the presence of a distinct pattern of genetic variation in these cattle. Although there was strong agreement between breed proportions estimated from pedigree and genetic information, there were significant discrepancies between these two methods for certain animals
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LGI2 truncation causes a remitting focal epilepsy in dogs.
Directory of Open Access Journals (Sweden)
Eija H Seppälä
2011-07-01
Full Text Available One quadrillion synapses are laid in the first two years of postnatal construction of the human brain, which are then pruned until age 10 to 500 trillion synapses composing the final network. Genetic epilepsies are the most common neurological diseases with onset during pruning, affecting 0.5% of 2-10-year-old children, and these epilepsies are often characterized by spontaneous remission. We previously described a remitting epilepsy in the Lagotto romagnolo canine breed. Here, we identify the gene defect and affected neurochemical pathway. We reconstructed a large Lagotto pedigree of around 34 affected animals. Using genome-wide association in 11 discordant sib-pairs from this pedigree, we mapped the disease locus to a 1.7 Mb region of homozygosity in chromosome 3 where we identified a protein-truncating mutation in the Lgi2 gene, a homologue of the human epilepsy gene LGI1. We show that LGI2, like LGI1, is neuronally secreted and acts on metalloproteinase-lacking members of the ADAM family of neuronal receptors, which function in synapse remodeling, and that LGI2 truncation, like LGI1 truncations, prevents secretion and ADAM interaction. The resulting epilepsy onsets at around seven weeks (equivalent to human two years, and remits by four months (human eight years, versus onset after age eight in the majority of human patients with LGI1 mutations. Finally, we show that Lgi2 is expressed highly in the immediate post-natal period until halfway through pruning, unlike Lgi1, which is expressed in the latter part of pruning and beyond. LGI2 acts at least in part through the same ADAM receptors as LGI1, but earlier, ensuring electrical stability (absence of epilepsy during pruning years, preceding this same function performed by LGI1 in later years. LGI2 should be considered a candidate gene for common remitting childhood epilepsies, and LGI2-to-LGI1 transition for mechanisms of childhood epilepsy remission.
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Pantsulaia, Ia; Pantsulaia, I; Trofimov, Svetlana; Kobyliansky, Eugene; Livshits, Gregory
2005-07-01
Recent literature has shown that circulating levels of insulin-like growth factor I (IGF-I) and/or IGF binding proteins (IGF-BPs) may be of importance in the risk assessment of several chronic diseases including cancer, cardiovascular disease, diabetes mellitus and so on. The present study examined the extent of genetic and environmental influences on the populational variation of circulating IGF-I and IGF-BP-1 in apparently healthy and ethnically homogeneous white families. The plasma levels of each of the studied biochemical indices were determined by enzyme-linked immunoassay in 563 individuals aged 18 to 80 years. Quantitative genetic analysis showed that the IGF-I variation was appreciably attributable to genetic effects (47.1% +/- 9.0%), whereas for IGF-BP-1, only 23.3% +/- 7.8% of the interindividual variation was explained by genetic determinants. Common familial environment factors contributed significantly only to IGF-BP-1 variation (23.3% +/- 7.8%). In addition, we examined the covariations between these molecules and between them and IGF-BP-3 and leptin that were previously studied in the same sample. The analysis revealed that the pleiotropic genetic effects were significant for 2 pairs of traits, namely for IGF-I and IGF-BP-3, and for IGF-BP-1 and leptin. The bivariate heritability estimates were 0.21 +/- 0.04 and 0.15 +/- 0.05. The common environmental factors were consistently a significant source of correlation between all pairs (barring IGF-I and leptin) of the studied molecules; they were the sole predictors of correlation between IGF-I and IGF-BP-1, and between IGF-BP-1 and IGF-BP-3. Our results affirm the existence of specific and common genetic pathways that in combination determine a substantial proportion of the circulating variation of these molecules.
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Accurate measurement of gene copy number for human alpha-defensin DEFA1A3.
Khan, Fayeza F; Carpenter, Danielle; Mitchell, Laura; Mansouri, Omniah; Black, Holly A; Tyson, Jess; Armour, John A L
2013-10-20
Multi-allelic copy number variants include examples of extensive variation between individuals in the copy number of important genes, most notably genes involved in immune function. The definition of this variation, and analysis of its impact on function, has been hampered by the technical difficulty of large-scale but accurate typing of genomic copy number. The copy-variable alpha-defensin locus DEFA1A3 on human chromosome 8 commonly varies between 4 and 10 copies per diploid genome, and presents considerable challenges for accurate high-throughput typing. In this study, we developed two paralogue ratio tests and three allelic ratio measurements that, in combination, provide an accurate and scalable method for measurement of DEFA1A3 gene number. We combined information from different measurements in a maximum-likelihood framework which suggests that most samples can be assigned to an integer copy number with high confidence, and applied it to typing 589 unrelated European DNA samples. Typing the members of three-generation pedigrees provided further reassurance that correct integer copy numbers had been assigned. Our results have allowed us to discover that the SNP rs4300027 is strongly associated with DEFA1A3 gene copy number in European samples. We have developed an accurate and robust method for measurement of DEFA1A3 copy number. Interrogation of rs4300027 and associated SNPs in Genome-Wide Association Study SNP data provides no evidence that alpha-defensin copy number is a strong risk factor for phenotypes such as Crohn's disease, type I diabetes, HIV progression and multiple sclerosis.
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[Familial febrile convulsions is supposed to link to human chromosome 19p13.3].
Qi, Y; Lü, J; Wu, X
2001-01-10
To localize the familial febrile convulsion (FC) genes on human chromosomes. For 63 FC pedigrees, tetranucleotide repeat markers D19S253 D19S395 and D19S591 on the short arm of chromosome 19, as well as dinucleotide repeat markers D8S84 and D8S85 on the long arm of chromosome 8 were genotyped. Transmission disequilibrium test (TDT) and Lod score calculation were carried out. The data were processed by PPAP software package. All the alleles in every locus of FC probands and normal controls were in Hardy-Weinburg balance. Transmission disequilibrium was found on D8S84, D19S395 and D19S591 in FC families. chi(2) values were 4.0, 5.124 and 7.364 separately. Each P value was < 0.05, and significantly meaningful. The two-point Lod scores between D8S84 and FC, D8S85 and FC, D19S253 and FC, D19S395 and FC, D19S591 and FC are 0.00002, 0.000017, 0.58, 1.53 and 1.42 respectively. The multi-point Lod score among markers on chromosome 8q and FC was 0.88, while Lod score among markers on chromosome 19p and FC reached 2.78. The results by both the non-parameter (TDT) and parameter (Lod score) methods were consistant on a whole. FC is linked with chromosome region 19p13.3, but not with chromosome 8q.
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Livshits, G; Yakovenko, K; Ginsburg, E; Kobyliansky, E
1998-01-01
The present study utilized pedigree data from three ethnically different populations of Kirghizstan, Turkmenia and Chuvasha. Principal component analysis was performed on a matrix of genetic correlations between 22 measures of adiposity, including skinfolds, circumferences and indices. Findings are summarized as follows: (1) All three genetic matrices were not positive definite and the first four factors retained even after exclusion RG > or = 1.0, explained from 88% to 97% of the total additive genetic variation in the 22 trials studied. This clearly emphasizes the massive involvement of pleiotropic gene effects in the variability of adiposity traits. (2) Despite the quite natural differences in pairwise correlations between the adiposity traits in the three ethnically different samples under study, factor analysis revealed a common basic pattern of covariability for the adiposity traits. In each of the three samples, four genetic factors were retained, namely, the amount of subcutaneous fat, the total body obesity, the pattern of distribution of subcutaneous fat and the central adiposity distribution. (3) Genetic correlations between the retained four factors were virtually non-existent, suggesting that several independent genetic sources may be governing the variation of adiposity traits. (4) Variance decomposition analysis on the obtained genetic factors leaves no doubt regarding the substantial familial and (most probably genetic) effects on variation of each factor in each studied population. The similarity of results in the three different samples indicates that the findings may be deemed valid and reliable descriptions of the genetic variation and covariation pattern of adiposity traits in the human species.
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Directory of Open Access Journals (Sweden)
Michaela Wiedmer
2016-02-01
Full Text Available We observed a hereditary phenotype in Alaskan Huskies that was characterized by polyneuropathy with ocular abnormalities and neuronal vacuolation (POANV. The affected dogs developed a progressive severe ataxia, which led to euthanasia between 8 and 16 months of age. The pedigrees were consistent with a monogenic autosomal recessive inheritance. We localized the causative genetic defect to a 4 Mb interval on chromosome 19 by a combined linkage and homozygosity mapping approach. Whole genome sequencing of one affected dog, an obligate carrier, and an unrelated control revealed a 218-bp SINE insertion into exon 7 of the RAB3GAP1 gene. The SINE insertion was perfectly associated with the disease phenotype in a cohort of 43 Alaskan Huskies, and it was absent from 541 control dogs of diverse other breeds. The SINE insertion induced aberrant splicing and led to a transcript with a greatly altered exon 7. RAB3GAP1 loss-of-function variants in humans cause Warburg Micro Syndrome 1 (WARBM1, which is characterized by additional developmental defects compared to canine POANV, whereas Rab3gap1-deficient mice have a much milder phenotype than either humans or dogs. Thus, the RAB3GAP1 mutant Alaskan Huskies provide an interesting intermediate phenotype that may help to better understand the function of RAB3GAP1 in development. Furthermore, the identification of the presumed causative genetic variant will enable genetic testing to avoid the nonintentional breeding of affected dogs.
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Single-Step BLUP with Varying Genotyping Effort in Open-Pollinated Picea glauca
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Blaise Ratcliffe
2017-03-01
Full Text Available Maximization of genetic gain in forest tree breeding programs is contingent on the accuracy of the predicted breeding values and precision of the estimated genetic parameters. We investigated the effect of the combined use of contemporary pedigree information and genomic relatedness estimates on the accuracy of predicted breeding values and precision of estimated genetic parameters, as well as rankings of selection candidates, using single-step genomic evaluation (HBLUP. In this study, two traits with diverse heritabilities [tree height (HT and wood density (WD] were assessed at various levels of family genotyping efforts (0, 25, 50, 75, and 100% from a population of white spruce (Picea glauca consisting of 1694 trees from 214 open-pollinated families, representing 43 provenances in Québec, Canada. The results revealed that HBLUP bivariate analysis is effective in reducing the known bias in heritability estimates of open-pollinated populations, as it exposes hidden relatedness, potential pedigree errors, and inbreeding. The addition of genomic information in the analysis considerably improved the accuracy in breeding value estimates by accounting for both Mendelian sampling and historical coancestry that were not captured by the contemporary pedigree alone. Increasing family genotyping efforts were associated with continuous improvement in model fit, precision of genetic parameters, and breeding value accuracy. Yet, improvements were observed even at minimal genotyping effort, indicating that even modest genotyping effort is effective in improving genetic evaluation. The combined utilization of both pedigree and genomic information may be a cost-effective approach to increase the accuracy of breeding values in forest tree breeding programs where shallow pedigrees and large testing populations are the norm.
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Single-Step BLUP with Varying Genotyping Effort in Open-Pollinated Picea glauca.
Ratcliffe, Blaise; El-Dien, Omnia Gamal; Cappa, Eduardo P; Porth, Ilga; Klápště, Jaroslav; Chen, Charles; El-Kassaby, Yousry A
2017-03-10
Maximization of genetic gain in forest tree breeding programs is contingent on the accuracy of the predicted breeding values and precision of the estimated genetic parameters. We investigated the effect of the combined use of contemporary pedigree information and genomic relatedness estimates on the accuracy of predicted breeding values and precision of estimated genetic parameters, as well as rankings of selection candidates, using single-step genomic evaluation (HBLUP). In this study, two traits with diverse heritabilities [tree height (HT) and wood density (WD)] were assessed at various levels of family genotyping efforts (0, 25, 50, 75, and 100%) from a population of white spruce ( Picea glauca ) consisting of 1694 trees from 214 open-pollinated families, representing 43 provenances in Québec, Canada. The results revealed that HBLUP bivariate analysis is effective in reducing the known bias in heritability estimates of open-pollinated populations, as it exposes hidden relatedness, potential pedigree errors, and inbreeding. The addition of genomic information in the analysis considerably improved the accuracy in breeding value estimates by accounting for both Mendelian sampling and historical coancestry that were not captured by the contemporary pedigree alone. Increasing family genotyping efforts were associated with continuous improvement in model fit, precision of genetic parameters, and breeding value accuracy. Yet, improvements were observed even at minimal genotyping effort, indicating that even modest genotyping effort is effective in improving genetic evaluation. The combined utilization of both pedigree and genomic information may be a cost-effective approach to increase the accuracy of breeding values in forest tree breeding programs where shallow pedigrees and large testing populations are the norm. Copyright © 2017 Ratcliffe et al.
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A novel OPA1 mutation in a Chinese family with autosomal dominant optic atrophy
Energy Technology Data Exchange (ETDEWEB)
Zhang, Juanjuan; Yuan, Yimin; Lin, Bing; Feng, Hao; Li, Yan [School of Ophthalmology and Optometry, Wenzhou Medical College, Wenzhou 325027, Zhejiang (China); Dai, Xianning; Zhou, Huihui [Attardi Institute of Mitochondrial Biomedicine and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Life Sciences, Wenzhou Medical College, Wenzhou 325035, Zhejiang (China); Dong, Xujie [School of Ophthalmology and Optometry, Wenzhou Medical College, Wenzhou 325027, Zhejiang (China); Liu, Xiao-Ling, E-mail: lxl@mail.eye.ac.cn [School of Ophthalmology and Optometry, Wenzhou Medical College, Wenzhou 325027, Zhejiang (China); Guan, Min-Xin, E-mail: min-xin.guan@cchmc.org [Attardi Institute of Mitochondrial Biomedicine and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Life Sciences, Wenzhou Medical College, Wenzhou 325035, Zhejiang (China); Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang 310012 (China); Division of Human Genetics, Cincinnati Children' s Hospital Medical Center, OH 45229 (United States)
2012-03-23
Highlights: Black-Right-Pointing-Pointer We report the characterization of a four-generation large Chinese family with ADOA. Black-Right-Pointing-Pointer We find a new heterozygous mutation c.C1198G in OPA1 gene which may be a novel pathogenic mutation in this pedigree. Black-Right-Pointing-Pointer We do not find any mitochondrial DNA mutations associated with optic atrophy. Black-Right-Pointing-Pointer Other factors may also contribute to the phenotypic variability of ADOA in this pedigree. -- Abstract: A large four-generation Chinese family with autosomal dominant optic atrophy (ADOA) was investigated in the present study. Eight of the family members were affected in this pedigree. The affected family members exhibited early-onset and progressive visual impairment, resulting in mild to profound loss of visual acuity. The average age-at-onset was 15.9 years. A new heterozygous mutation c.C1198G was identified by sequence analysis of the 12th exon of the OPA1 gene. This mutation resulted in a proline to alanine substitution at codon 400, which was located in an evolutionarily conserved region. This missense mutation in the GTPase domain was supposed to result in a loss of function for the encoded protein and act through a dominant negative effect. No other mutations associated with optic atrophy were found in our present study. The c.C1198G heterozygous mutation in the OPA1 gene may be a novel key pathogenic mutation in this pedigree with ADOA. Furthermore, additional nuclear modifier genes, environmental factors, and psychological factors may also contribute to the phenotypic variability of ADOA in this pedigree.
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PedGenie: meta genetic association testing in mixed family and case-control designs
Directory of Open Access Journals (Sweden)
Allen-Brady Kristina
2007-11-01
Full Text Available Abstract Background- PedGenie software, introduced in 2006, includes genetic association testing of cases and controls that may be independent or related (nuclear families or extended pedigrees or mixtures thereof using Monte Carlo significance testing. Our aim is to demonstrate that PedGenie, a unique and flexible analysis tool freely available in Genie 2.4 software, is significantly enhanced by incorporating meta statistics for detecting genetic association with disease using data across multiple study groups. Methods- Meta statistics (chi-squared tests, odds ratios, and confidence intervals were calculated using formal Cochran-Mantel-Haenszel techniques. Simulated data from unrelated individuals and individuals in families were used to illustrate meta tests and their empirically-derived p-values and confidence intervals are accurate, precise, and for independent designs match those provided by standard statistical software. Results- PedGenie yields accurate Monte Carlo p-values for meta analysis of data across multiple studies, based on validation testing using pedigree, nuclear family, and case-control data simulated under both the null and alternative hypotheses of a genotype-phenotype association. Conclusion- PedGenie allows valid combined analysis of data from mixtures of pedigree-based and case-control resources. Added meta capabilities provide new avenues for association analysis, including pedigree resources from large consortia and multi-center studies.
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Sprinkle, Therese A.; Urick, Michael J.
2018-01-01
Purpose: Methods for facilitating learning and knowledge transfer in multigenerational workplaces are of importance to organizations. Yet, intergenerational learning is vastly understudied in academic organizational literature. This conceptual paper aims to recommend future directions for studying intergenerational learning by examining three…
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Parent-Child Agreement on Parent-to-Child Maltreatment
Compier-de Block, Laura H.C.G.; Alink, Lenneke R.A.; Linting, Mariëlle; van den Berg, Lisa J.M.; Elzinga, Bernet M.; Voorthuis, Alexandra; Tollenaar, Marieke S.; Bakermans-Kranenburg, Marian J.
2017-01-01
Parent-child agreement on child maltreatment was examined in a multigenerational study. Questionnaires on perpetrated and experienced child maltreatment were completed by 138 parent-child pairs. Multi-level analyses were conducted to explore whether parents and children agreed about levels of
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Energy Technology Data Exchange (ETDEWEB)
Sunden, S.L.F.; Nichols, B.E.; Alward, W.L.M. [Univ. of Iowa, Iowa City, IA (United States)] [and others
1994-09-01
Juvenile onset primary open angle glaucoma has been mapped by linkage to 1q21-q31. Several candidate genes were evaluated in the same family used to identify the primary linkage. Atrionatriuretic peptide receptor A (NPR1) and laminin C1 (LAMC1) have been previously mapped to this region and could putatively play a role in the pathogenesis of glaucoma. A third gene, the peripheral cannabis receptor (CNR2) was not initially mapped in humans but was a candidate because of the relief that cannabis affords some patients with primary open angle glaucoma. Microsatellites associated with NPR1 and LAMC1 revealed multiple recombinations in affected members of this pedigree. CNR2 was shown to be on chromosome 1 by PCR amplification of a 150 bp fragment of the 3{prime} untranslated region in monochromosomal somatic cell hybrids (NIGMS panel No. 2). These primers also revealed a two allele single strand conformation polymorphism which showed multiple recombinants with juvenile onset primary open angle glaucoma in large pedigrees, segregating this disorder. The marker was then mapped to 1p34-p36 by linkage, with the most likely location between liver alkaline phosphatase (ALPL) and alpha-L-1 fucosidase (FUCA1).
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Development and Analysis of New Integrated Energy Systems for Sustainable Buildings
Khalid, Farrukh
Excessive consumption of fossil fuels in the residential sector and their associated negative environmental impacts bring a significant challenge to engineers within research and industrial communities throughout the world to develop more environmentally benign methods of meeting energy needs of residential sector in particular. This thesis addresses potential solutions for the issue of fossils fuel consumption in residential buildings. Three novel renewable energy based multigeneration systems are proposed for different types of residential buildings, and a comprehensive assessment of energetic and exergetic performances is given on the basis of total occupancy, energy load, and climate conditions. System 1 is a multigeneration system based on two renewable energy sources. It uses biomass and solar resources. The outputs of System 1 are electricity, space heating, cooling, and hot water. The energy and exergy efficiencies of System 1 are 91.0% and 34.9%, respectively. The results of the optimisation analysis show that the net present cost of System 1 is 2,700,496 and that the levelised cost of electricity is 0.117/kWh. System 2 is a multigeneration system, integrating three renewable energy based subsystems; wind turbine, concentrated solar collector, and Organic Rankine Cycle supplied by a ground source heat exchanger. The outputs of the System 2 are electricity, hot water, heating and cooling. The optimisation analysis shows that net present cost is 35,502 and levelised cost of electricity is 0.186/kWh. The energy and exergy efficiencies of System 2 are found to be 34.6% and 16.2%, respectively. System 3 is a multigeneration system, comprising two renewable energy subsystems-- geothermal and solar to supply power, cooling, heating, and hot water. The optimisation analysis shows that the net present cost of System 3 is 598,474, and levelised cost of electricity of 0.111/kWh. The energy and exergy efficiencies of System 3 are 20.2% and 19.2%, respectively, with
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Epilepsy Genetics—Past, Present, and Future
Poduri, Annapurna; Lowenstein, Daniel
2014-01-01
Human epilepsy is a common and heterogeneous condition in which genetics play an important etiological role. We begin by reviewing the past history of epilepsy genetics, a field that has traditionally included studies of pedigrees with epilepsy caused by defects in ion channels and neurotransmitters. We highlight important recent discoveries that have expanded the field beyond the realm of channels and neurotransmitters and that have challenged the notion that single genes produce single disorders. Finally, we project toward an exciting future for epilepsy genetics as large-scale collaborative phenotyping studies come face to face with new technologies in genomic medicine. PMID:21277190
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A visual interface to computer programs for linkage analysis.
Chapman, C J
1990-06-01
This paper describes a visual approach to the input of information about human families into computer data bases, making use of the GEM graphic interface on the Atari ST. Similar approaches could be used on the Apple Macintosh or on the IBM PC AT (to which it has been transferred). For occasional users of pedigree analysis programs, this approach has considerable advantages in ease of use and accessibility. An example of such use might be the analysis of risk in families with Huntington disease using linked RFLPs. However, graphic interfaces do make much greater demands on the programmers of these systems.
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Ran, J; Cheng, H; Li, F
2000-01-01
To investigate the characteristics of insulin secretion rate (ISR), metabolic clearance rate (MCR-I) and sensitivity and to explore their relationship with obesity in non-insulin-dependent diabetic subjects from multiplex diabetic pedigrees (MDP). Fifteen subjects with normal glucose tolerance and 11 non-insulin-dependent diabetic patients from MDP were included in the study. Frequently sampled intravenous glucose tolerance test (FSIVGTT) was performed. Glucose, insulin (INS) and connecting-peptide (C-P) concentrations were measured. A computer procedure devised by our laboratory was used to calculate the value of ISR at each time point, then MCR-I was acquired. Insulin sensitivity index (SI) was calculated according to minimal model technique about glucose in FSIVGTT. The ISR curve in control group was biphasic, while in non-insulin. In non-insulin-dependent diabetic group, areas under the curves of C-P (AUCC) and ISR level (AUCS) measured during 0 approximately 16 min were 7.9 nmol.min(-1).L(-1) +/- 2.8 nmol.min(-1).L(-1), and 6.1 nmol +/- 2.2 nmol, respectively, which were significantly lower than those in control group 17.7 nmol.min(-1).L(-1) +/- 4.92 nmol.min(-1).L(-1) and 12.3 nmol +/- 3.9 nmol (P < 0.01). The two parameters were slightly higher than those in control group 155 nmol.min(-1).L(-1) +/- 44 nmol.min(-1).L(-1) vs 101 nmol.min(-1).L(-1) +/- 30 nmol.min(-1).L(-1) and 76 nmol +/- 26 nmol vs 54 nmol +/- 20.0 nmol (P < 0.05)measured during 16 approximately 180 min. There was no significant difference, between the two groups about the amount of insulin secretion during 3 hours (82 nmol +/- 28nmol vs 68 nmol +/- 21 nmol, P = 0.2). In control group, there were significant positive correlation, between AUCS, waist-hip ratio (WHR), and body surface area, (BSA) and significant negative correlation between MCR-I, SI and WHR, BSA (P < 0.01), and also between MCR-I and SI. In non-insulin-dependent diabetic group, AUCS were significantly correlated with body mass
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Directory of Open Access Journals (Sweden)
Svenja eCaspers
2014-07-01
Full Text Available The ongoing 1000 brains study (1000BRAINS is an epidemiological and neuroscientific investigation of structural and functional variability in the human brain during aging. The two recruitment sources are the 10-year follow-up cohort of the German Heinz Nixdorf Recall (HNR Study, and the HNR MultiGeneration Study cohort, which comprises spouses and offspring of HNR subjects. The HNR is a longitudinal epidemiological investigation of cardiovascular risk factors, with a comprehensive collection of clinical, laboratory, socioeconomic, and environmental data from population-based subjects aged 45-75 years on inclusion. HNR subjects underwent detailed assessments in 2000, 2006, and 2011, and completed annual postal questionnaires on health status. 1000BRAINS accesses these HNR data and applies a separate protocol comprising: neuropsychological tests of attention, memory, executive functions & language; examination of motor skills; ratings of personality, life quality, mood & daily activities; analysis of laboratory and genetic data; and state-of-the-art magnetic resonance imaging (MRI, 3 Tesla of the brain. The latter includes (i 3D-T1- and 3D-T2-weighted scans for structural analyses and myelin mapping; (ii three diffusion imaging sequences optimized for diffusion tensor imaging, high-angular resolution diffusion imaging for detailed fibre tracking and for diffusion kurtosis imaging; (iii resting-state and task-based functional MRI; and (iv fluid-attenuated inversion recovery and MR angiography for the detection of vascular lesions and the mapping of white matter lesions. The unique design of 1000BRAINS allows: (i comprehensive investigation of various influences including genetics, environment and health status on variability in brain structure and function during aging; and (ii identification of the impact of selected influencing factors on specific cognitive subsystems and their anatomical correlates.
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Nonspecific X-linked mental retardation with macrocephaly and obesity: A further family
Energy Technology Data Exchange (ETDEWEB)
Baraitser, M.; Reardon, W. [Hospital for Sick Children, London (United Kingdom); Vijeratnam, S. [Highlands Hospital, London (United Kingdom)
1995-07-03
The phenotypic nonspecificity of many forms of X-linked mental retardation has hampered attempts to classify them into clinically homogeneous groups. One such condition, described by Clark and Baraitser, has been the subject of a single pedigree report to date. We now describe a further pedigree whose affected members share many manifestations with those reported by Clark and Baraitser, and we consider the possible distinction between this condition and Atkin-Flaitz syndrome. 9 refs., 4 figs., 1 tab.
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Epilogue: Systems Approaches and Systems Practice
Reynolds, Martin; Holwell, Sue
Each of the five systems approaches discussed in this volume: system dynamics (SD), the viable systems model (VSM), strategic options development and analysis (SODA), soft systems methodology (SSM) and critical systems heuristics (CSH) has a pedigree. Not in the sense of the sometimes absurd spectacle of animals paraded at dog shows. Rather, their pedigree derives from their systems foundations, their capacity to evolve and their flexibility in use. None of the five approaches has developed out of use in restricted and controlled contexts of either low or high levels of complicatedness. Neither has any one of them evolved as a consequence of being applied only to situations with either presumed stakeholder agreement on purpose, or courteous disagreement amongst stakeholders, or stakeholder coercion. The compilation is not a celebration of abstract ‘methodologies', but of theoretically robust approaches that have a genuine pedigree in practice.
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Lessons learned from family history in ocular genetics.
Marino, Meghan J
2015-07-01
Given the vast genetic and phenotypic heterogeneity seen in ocular genetic disorders, considering a patient's clinical phenotype in the context of the family history is essential. Clinicians can improve patient care by appropriately incorporating a patient's family history into their evaluation. Obtaining, reviewing, and accurately interpreting the pedigree are skills geneticists and genetic counselors possess. However, with the field of ophthalmic genetics vastly growing, it is becoming essential for ophthalmologists to understand the utility of the pedigree and develop their abilities in eliciting this information. By not considering a patient's clinical history in the context of the family history, diagnoses can be missed or inaccurate. The purpose of this review is to inform ophthalmologists on the importance of the family history and highlight how the pedigree can aid in establishing an accurate genetic diagnosis. This review also provides to ophthalmologists helpful tips on eliciting and interpreting a patient's family history.
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Acclimatization and Adaptive Capacity of Marine Species in a Changing Ocean.
Foo, S A; Byrne, M
To persist in an ocean changing in temperature, pH and other stressors related to climate change, many marine species will likely need to acclimatize or adapt to avoid extinction. If marine populations possess adequate genetic variation in tolerance to climate change stressors, species might be able to adapt to environmental change. Marine climate change research is moving away from single life stage studies where individuals are directly placed into projected scenarios ('future shock' approach), to focus on the adaptive potential of populations in an ocean that will gradually change over coming decades. This review summarizes studies that consider the adaptive potential of marine invertebrates to climate change stressors and the methods that have been applied to this research, including quantitative genetics, laboratory selection studies and trans- and multigenerational experiments. Phenotypic plasticity is likely to contribute to population persistence providing time for genetic adaptation to occur. Transgenerational and epigenetic effects indicate that the environmental and physiological history of the parents can affect offspring performance. There is a need for long-term, multigenerational experiments to determine the influence of phenotypic plasticity, genetic variation and transgenerational effects on species' capacity to persist in a changing ocean. However, multigenerational studies are only practicable for short generation species. Consideration of multiple morphological and physiological traits, including changes in molecular processes (eg, DNA methylation) and long-term studies that facilitate acclimatization will be essential in making informed predictions of how the seascape and marine communities will be altered by climate change. © 2016 Elsevier Ltd. All rights reserved.
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Directory of Open Access Journals (Sweden)
Dominik Müller
2017-03-01
Full Text Available Recurrent selection (RS has been used in plant breeding to successively improve synthetic and other multiparental populations. Synthetics are generated from a limited number of parents ( Np , but little is known about how Np affects genomic selection (GS in RS, especially the persistency of prediction accuracy (rg , g ^ and genetic gain. Synthetics were simulated by intermating Np= 2–32 parent lines from an ancestral population with short- or long-range linkage disequilibrium (LDA and subjected to multiple cycles of GS. We determined rg , g ^ and genetic gain across 30 cycles for different training set (TS sizes, marker densities, and generations of recombination before model training. Contributions to rg , g ^ and genetic gain from pedigree relationships, as well as from cosegregation and LDA between QTL and markers, were analyzed via four scenarios differing in (i the relatedness between TS and selection candidates and (ii whether selection was based on markers or pedigree records. Persistency of rg , g ^ was high for small Np , where predominantly cosegregation contributed to rg , g ^ , but also for large Np , where LDA replaced cosegregation as the dominant information source. Together with increasing genetic variance, this compensation resulted in relatively constant long- and short-term genetic gain for increasing Np > 4, given long-range LDA in the ancestral population. Although our scenarios suggest that information from pedigree relationships contributed to rg , g ^ for only very few generations in GS, we expect a longer contribution than in pedigree BLUP, because capturing Mendelian sampling by markers reduces selective pressure on pedigree relationships. Larger TS size (NTS and higher marker density improved persistency of rg , g ^ and hence genetic gain, but additional recombinations could not increase genetic gain.
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Directory of Open Access Journals (Sweden)
John S K Kauwe
Full Text Available Alzheimer's disease (AD is an international health concern that has a devastating effect on patients and families. While several genetic risk factors for AD have been identified much of the genetic variance in AD remains unexplained. There are limited published assessments of the familiality of Alzheimer's disease. Here we present the largest genealogy-based analysis of AD to date.We assessed the familiality of AD in The Utah Population Database (UPDB, a population-based resource linking electronic health data repositories for the state with the computerized genealogy of the Utah settlers and their descendants. We searched UPDB for significant familial clustering of AD to evaluate the genetic contribution to disease. We compared the Genealogical Index of Familiality (GIF between AD individuals and randomly selected controls and estimated the Relative Risk (RR for a range of family relationships. Finally, we identified pedigrees with a significant excess of AD deaths.The GIF analysis showed that pairs of individuals dying from AD were significantly more related than expected. This excess of relatedness was observed for both close and distant relationships. RRs for death from AD among relatives of individuals dying from AD were significantly increased for both close and more distant relatives. Multiple pedigrees had a significant excess of AD deaths.These data strongly support a genetic contribution to the observed clustering of individuals dying from AD. This report is the first large population-based assessment of the familiality of AD mortality and provides the only reported estimates of relative risk of AD mortality in extended relatives to date. The high-risk pedigrees identified show a true excess of AD mortality (not just multiple cases and are greater in depth and width than published AD pedigrees. The presence of these high-risk pedigrees strongly supports the possibility of rare predisposition variants not yet identified.
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The Molecular Basis for Altered Cation Permeability in Hereditary Stomatocytic Human Red Blood Cells
Directory of Open Access Journals (Sweden)
Joanna F. Flatt
2018-04-01
Full Text Available Normal human RBCs have a very low basal permeability (leak to cations, which is continuously corrected by the Na,K-ATPase. The leak is temperature-dependent, and this temperature dependence has been evaluated in the presence of inhibitors to exclude the activity of the Na,K-ATPase and NaK2Cl transporter. The severity of the RBC cation leak is altered in various conditions, most notably the hereditary stomatocytosis group of conditions. Pedigrees within this group have been classified into distinct phenotypes according to various factors, including the severity and temperature-dependence of the cation leak. As recent breakthroughs have provided more information regarding the molecular basis of hereditary stomatocytosis, it has become clear that these phenotypes elegantly segregate with distinct genetic backgrounds. The cryohydrocytosis phenotype, including South-east Asian Ovalocytosis, results from mutations in SLC4A1, and the very rare condition, stomatin-deficient cryohydrocytosis, is caused by mutations in SLC2A1. Mutations in RHAG cause the very leaky condition over-hydrated stomatocytosis, and mutations in ABCB6 result in familial pseudohyperkalemia. All of the above are large multi-spanning membrane proteins and the mutations may either modify the structure of these proteins, resulting in formation of a cation pore, or otherwise disrupt the membrane to allow unregulated cation movement across the membrane. More recently mutations have been found in two RBC cation channels, PIEZO1 and KCNN4, which result in dehydrated stomatocytosis. These mutations alter the activation and deactivation kinetics of these channels, leading to increased opening and allowing greater cation fluxes than in wild type.
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Leung, W.H.M.
2011-01-01
This paper examines the impact of transnational geographical mobility among Chinese and German scholars using the concepts of 'development corridors' and 'development chains'. A temporal-spatial analysis of two case studies – (1) a multi-generation actor-based network of social scientists and (2)
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Archetypal and new families with Alexander disease and novel mutations in GFAP
Messing, Albee; Li, Rong; Naidu, Sakkubai; Taylor, J. Paul; Silverman, Lital; Flint, Daniel; van der Knaap, Marjo S.; Brenner, Michael
2012-01-01
To describe genetic analyses of the 2 most thoroughly studied, historically seminal multigenerational families with Alexander disease described prior to the identification of GFAP as the related gene, as well as 1 newly discovered family. Clinical histories were obtained and DNA was analyzed from
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Wolsink, M.; Frantál, B.; Martinát, S.
2014-01-01
According to the major trend in the literature on distributed generation adoption of composite multi-generation systems may yield significant benefits in terms of energy efficiency and reduced carbon emissions. The microgrid is a cluster of loads of electricity users and micro-sources that operate
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Non-syndromic posterior lenticonus a cause of childhood cataract: evidence for X-linked inheritance.
Russell-Eggitt, I M
2000-12-01
When an X-linked pedigree of posterior lenticonus with cataract was identified further evidence for X-linked inheritance of this condition was sought. Forty-three cases of posterior lenticonus were identified from a database of 354 children with cataract. Two children with the X-linked syndromes of Lowe and Nance-Horan and 3 children with Fanconi syndrome have been excluded from further analysis. None of the children was deaf. None of the non-syndromic cases had microcornea. There were 38 cases of non-syndromic posterior lenticonus (approximately 11%). There were 15 children from 13 pedigrees and 23 apparently sporadic cases. Of the 106 cases on the database with unilateral cataract 15 had posterior lenticonus (approximately 14%). Eleven of 13 pedigrees were compatible with X-linked inheritance or autosomal dominant inheritance with variable expression. However, in 2 pedigrees there was father to son transmission. Posterior lenticonus is a common cause of unilateral infantile cataract, but is thought to be a rare cause of bilateral cataracts. This study suggests that posterior lenticonus is responsible for a significant proportion of childhood cataracts (approximately 14% of unilateral and approximately 9% of bilateral cases). Posterior lenticonus is generally thought to occur as a sporadic condition. This study demonstrates that there is a family history of early-onset cataract in a significant number of bilateral cases (approximately 58%).
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Nazarian, Alireza; Gezan, Salvador A
2016-03-01
The study of genetic architecture of complex traits has been dramatically influenced by implementing genome-wide analytical approaches during recent years. Of particular interest are genomic prediction strategies which make use of genomic information for predicting phenotypic responses instead of detecting trait-associated loci. In this work, we present the results of a simulation study to improve our understanding of the statistical properties of estimation of genetic variance components of complex traits, and of additive, dominance, and genetic effects through best linear unbiased prediction methodology. Simulated dense marker information was used to construct genomic additive and dominance matrices, and multiple alternative pedigree- and marker-based models were compared to determine if including a dominance term into the analysis may improve the genetic analysis of complex traits. Our results showed that a model containing a pedigree- or marker-based additive relationship matrix along with a pedigree-based dominance matrix provided the best partitioning of genetic variance into its components, especially when some degree of true dominance effects was expected to exist. Also, we noted that the use of a marker-based additive relationship matrix along with a pedigree-based dominance matrix had the best performance in terms of accuracy of correlations between true and estimated additive, dominance, and genetic effects. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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International Nuclear Information System (INIS)
Zhu Yi; Qian Yaping; Tang Xiaowen; Wang Jindan; Yang Li; Liao Zhisu; Li Ronghua; Ji Jinzhang; Li Zhiyuan; Chen Jianfu; Choo, Daniel I.; Lu Jianxin; Guan Minxin
2006-01-01
We report here the clinical, genetic, and molecular characterization of two Chinese families with aminoglycoside induced and non-syndromic hearing impairment. Clinical and genetic evaluations revealed the variable severity and age-of-onset in hearing impairment in these families. Strikingly, there were extremely low penetrances of hearing impairment in these Chinese families. Sequence analysis of the complete mitochondrial genomes in these pedigrees showed the distinct sets of mtDNA polymorphism, in addition to the identical G7444A mutation associated with hearing loss. Indeed, the G7444A mutation in the CO1 gene and the precursor of tRNA Ser(UCN) gene is present in homoplasmy only in the maternal lineage of those pedigrees but not other members of these families and 164 Chinese controls. Their mitochondrial genomes belong to the Eastern Asian haplogroups C5a and D4a, respectively. In fact, the occurrence of the G7444A mutation in these several genetically unrelated subjects affected by hearing impairment strongly indicates that this mutation is involved in the pathogenesis of hearing impairment. However, there was the absence of other functionally significant mtDNA mutations in two Chinese pedigrees carrying the G7444A mutation. Therefore, nuclear modifier gene(s) or aminoglycoside(s) may play a role in the phenotypic expression of the deafness-associated G7444A mutation in these Chinese pedigrees
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Identification and utilization of cleistogamy gene cl7(t) in rice (Oryza sativa L.).
Ni, Da-Hu; Li, Juan; Duan, Yong-Bo; Yang, Ya-Chun; Wei, Peng-Cheng; Xu, Rong-Fang; Li, Chun-Rong; Liang, Dan-Dan; Li, Hao; Song, Feng-Shun; Ni, Jin-Long; Li, Li; Yang, Jian-Bo
2014-05-01
Gene transformation is an important method for improvement of plants into elite varieties. However, the possibility of gene flow between genetically modified (GM) crops and similar species is a serious public issue that may potentially endanger ecological stability. Cleistogamy is expected to be an ideal genetic tool for preventing transgene propagation from GM crops. A rice mutant, cl7(t), was created by ethyl methanesulfonate mutagenesis. The mutant exhibited cleistogamy, and had closed spikelets, reduced plant height, and altered morphology of the leaves, panicle, and seeds. Anatomical investigations revealed that the cl7(t) mutant contained more vascular bundles and thicker stems than the wild type, which increased the mechanical strength of its internodes, and anti-lodging ability. Further studies demonstrated that the force required to open the lemma and palea was higher in the cl7(t) mutant, and there was weak swelling ability in the lodicules, which leads to cleistogamy. Allelic analyses and complementation tests indicated that cl7(t) was a novel allele of dep2, a mutant that was previously reported to have similar panicle morphology. Sequence analysis showed that cl7(t) had a single nucleotide substitution (C to A) in the third exon that leads to a Ser substitution with a stop codon, giving a truncated DEP2 protein. Quantitative RT-PCR and in situ hybridization tests demonstrated that there was lower CL7(t) expression level in the spikelets and weaker CL7(t) signals in the lodicules of the cl7(t) mutant compared with wild type, which implies that CL7(t) might participate in the development of lodicules. To improve the agronomic traits of cl7(t) to fit the needs of field production, the cl7(t) mutant was crossed with an intermediate-type rice variety named Guanghui102, which bears some important agronomic traits, including increased grain numbers and high rate of seed setting. Through multi-generational pedigree selection, cleistogamy lines with improved
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Energy Technology Data Exchange (ETDEWEB)
Weber, B.H.F.; Vogt, G. [Institut fuer Humangenetik, Wuerzburg (Germany); Walker, D. [UBC, Vancouver (Canada)] [and others
1994-09-01
Vitelliform macular dystrophy, also known as Best`s disease, is a juvenile-onset macular degeneration with autosomal dominant inheritance. It is characterized by well-demarcated accumulation of lipofuscin-like material within and beneath the retinal pigment epithelium (RPE) and classically results in an egg yolk-like appearance of the macula. Typically, carriers of the disease gene show a specific electrophysiological sign which can be detected by electrooculography (EOG). The EOG measures a standing potential between the cornea and the retina which is primarily generated by the RPE. The histopathological findings as well as the EOG abnormalities suggest that Best`s disease is a generalized disorder of the RPE. The basic biochemical defect is still unknown. As a first step in the positional cloning of the defective gene, the Best`s disease locus was mapped to chromosome 11 between markers at D11S871 and INT2. Subsequently, his region was refined to a 3.7 cM interval flanked by loci D11S903 and PYGM. To further narrow the D11S903-PYGM interval and to obtain an estimate of the physical size of the minimal candidate region, we used a combination of high-resolution PCR hybrid mapping and analysis of recombinant Best`s disease chromosomes. We identified six markers from within the D11S903-PYGM interval that show no recombination with the defective gene in three multigeneration Best`s disease pedigrees. Our hybrid panel localizes these markers on either side of the centromere on chromosome 11. The closest markers flanking the disease gene are at D11S986 in band p12-11.22 and at D11S480 in band q13.2-13.3. Our study demonstrates that the physical size of the Best`s disease region is exceedingly larger than was previously estimated from the genetic data due to the proximity of the defective gene to the centromere of chromosome 11.
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Directory of Open Access Journals (Sweden)
Thomas Frisell
Full Text Available BACKGROUND: Research has consistently found lower cognitive ability to be related to increased risk for violent and other antisocial behaviour. Since this association has remained when adjusting for childhood socioeconomic position, ethnicity, and parental characteristics, it is often assumed to be causal, potentially mediated through school adjustment problems and conduct disorder. Socioeconomic differences are notoriously difficult to quantify, however, and it is possible that the association between intelligence and delinquency suffer substantial residual confounding. METHODS: We linked longitudinal Swedish total population registers to study the association of general cognitive ability (intelligence at age 18 (the Conscript Register, 1980-1993 with the incidence proportion of violent criminal convictions (the Crime Register, 1973-2009, among all men born in Sweden 1961-1975 (N = 700,514. Using probit regression, we controlled for measured childhood socioeconomic variables, and further employed sibling comparisons (family pedigree data from the Multi-Generation Register to adjust for shared familial characteristics. RESULTS: Cognitive ability in early adulthood was inversely associated to having been convicted of a violent crime (β = -0.19, 95% CI: -0.19; -0.18, the association remained when adjusting for childhood socioeconomic factors (β = -0.18, 95% CI: -0.18; -0.17. The association was somewhat lower within half-brothers raised apart (β = -0.16, 95% CI: -0.18; -0.14, within half-brothers raised together (β = -0.13, 95% CI: (-0.15; -0.11, and lower still in full-brother pairs (β = -0.10, 95% CI: -0.11; -0.09. The attenuation among half-brothers raised together and full brothers was too strong to be attributed solely to attenuation from measurement error. DISCUSSION: Our results suggest that the association between general cognitive ability and violent criminality is confounded partly by factors shared by
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The Protos mandate a scientific novel
Kanas, Nick
2014-01-01
In the 25th Century, the effects of overpopulation and global warming on Earth have led to the formation of human colonies on the Moon, Mars and elsewhere in the Solar System, yet the limited number of viable places forces humanity to look to the stars. A crash program has been developed to send Protos 1, a giant multigenerational starship, to a newly discovered Earth-like planet orbiting a nearby star. The plan is for awake crewmembers to run the ship, and for people in suspended animation to be roused before planetfall to use their skills in exploration and colony formation. To fulfill the goals of the mission and ensure that the in-flight population does not deplete the limited resources, the Protos Mandate is set up to govern a tightly controlled social system for the duration of the journey, which will take several generations. But problems threaten to sabotage the mission during its launch and transit, and what finally awaits the crewmembers shocks them in an unpredictable way. This novel chronicl...
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Numerical unit spread assessment pedigree (NUSAP)
International Nuclear Information System (INIS)
Schaffhauser, A. Jr.
1994-01-01
Data estimates and information require a system for signaling the uncertainty and quality of the entries for users. Few of the entries will be known with certainty, or even generally agreed upon as the prevalent quantity or relation. For example, the ecological or health responses of resources exposed to energy-related pollutants cannot be known with certainty given current knowledge of the relationships. The monetary valuations associated with the imperfectly known impacts are also uncertain and sometimes controversial. To leave entries standing alone without signaling their uncertainty and quality would overstate the precision with which the entries are known. In addition, signaling the uncertainty and quality for entries will indicate areas where further study is needed most. Uncertainty and quality are signaled through a notational system named NUSAP as an acronym for its categories. NUSAP was developed by Funtowicz and Ravetz to provide a 'quality control' of quantitative information.' We have adapted the NUSAP system for signaling the uncertainty and quality of quantitative information to be used in estimating the emissions, impacts, NUSAP and external costs of fuel cycles. Uncertainty refers to the spread of plausible values for a cell entry and the level of confidence placed in a quantitative statement. Quality refers to both an entry's worth as a piece of information and the credibility of the theory, data, and methods used to generate the entry
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The teratology testing of food additives.
Barrow, Paul C; Spézia, François
2013-01-01
The developmental and reproductive toxicity testing (including teratogenicity) of new foods and food additives is performed worldwide according to the guidelines given in the FDA Redbook. These studies are not required for substances that are generally recognized as safe, according to the FDA inventory. The anticipated cumulated human exposure level above which developmental or reproduction studies are required depends on the structure-alert category. For food additives of concern, both developmental (prenatal) and reproduction (multigeneration) studies are required. The developmental studies are performed in two species, usually the rat and the rabbit. The reproduction study is generally performed in the rat. The two rat studies are preferably combined into a single experimental design, if possible. The test methods described in the FDA Redbook are similar to those specified by the OECD for the reproductive toxicity testing of chemicals.
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The Extended Family in U.S. Black Societies: Findings and Problems.
Shimkin, Demitri B.; Shimkin, Edith M.
Investigations of the structure, rule systems, and histories of black families in rural Mississippi, Chicago, New Orleans, East Texas, and Southern California have shown the presence of well-integrated, multigeneration, multihousehold, bilateral extended families in varying U.S. social environments. These families, while varying in detail, share…
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Vamos a Jugar Counters! Learning Mathematics through Funds of Knowledge, Play, and the Third Space
Razfar, Aria
2012-01-01
Drawing on Cultural Historical Activity Theory (CHAT), funds of knowledge, and third space, this article presents a model for practitioners and researchers to think about how Latina/o, bilingual children develop explicit mathematics strategies through multilingual and multigenerational interactions. Using data collected through fieldwork in an…
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DEFF Research Database (Denmark)
Kristensen, Mette; Østergaard, Lars F.; Halekoh, Ulrich
2008-01-01
major and trace element contents of dried foodstuffs (carrots, kale, peas, potatoes and apples) grown in two consecutive years, as well as mineral retention determined in 36 rats (second generation in a multi-generation study) fed diets based on these foodstuffs from one year. RESULTS: Overall...
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A novel susceptibility locus for Hirschsprung's disease maps to 4q31.3-q32.3
Brooks, AS; Leegwater, PA; Burzynski, GM; Willems, PJ; de Graaf, B; van Langen, [No Value; Heutink, P; Oostra, BA; Hofstra, RMW; Bertoli-Avella, AM
2006-01-01
We report on a multigenerational family with isolated Hirschsprung's disease (HSCR). Five patients were affected by either short segment or long segment HSCR. The family consists of two main branches: one with four patients ( three siblings and one maternal uncle) and one with one patient. Analysis
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McInnes, L. Alison; Service, Susan K.; Reus, Victor I.; Barnes, Glenn; Charlat, Olga; Jawahar, Satya; Lewitzky, Steve; Yang, Qing; Duong, Quyen; Spesny, Mitzi; Araya, Carmen; Araya, Xinia; Gallegos, Alvaro; Meza, Luis; Molina, Julio; Ramirez, Rolando; Mendez, Roxana; Silva, Sandra; Fournier, Eduardo; Batki, Steven L.; Mathews, Carol A.; Neylan, Thomas; Glatt, Charles E.; Escamilla, Michael A.; Luo, David; Gajiwala, Paresh; Song, Terry; Crook, Stephen; Nguyen, Jasmine B.; Roche, Erin; Meyer, Joanne M.; Leon, Pedro; Sandkuijl, Lodewijk A.; Freimer, Nelson B.; Chen, Hong
2001-01-01
We have searched for genes predisposing to bipolar disorder (BP) by studying individuals with the most extreme form of the affected phenotype, BP-I, ascertained from the genetically isolated population of the Central Valley of Costa Rica (CVCR). The results of a previous linkage analysis on two extended CVCR BP-I pedigrees, CR001 and CR004, and of linkage disequilibrium (LD) analyses of a CVCR population sample of BP-I patients implicated a candidate region on 18p11.3. We further investigated this region by creating a physical map and developing 4 new microsatellite and 26 single-nucleotide polymorphism markers for typing in the pedigree and population samples. We report the results of fine-scale association analyses in the population sample, as well as evaluation of haplotypes in pedigree CR001. Our results suggest a candidate region containing six genes but also highlight the complexities of LD mapping of common disorders. PMID:11572994
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Energy Technology Data Exchange (ETDEWEB)
Fridovich-Keil, J.L.; Langley, S.D.; Mazur, L.A.; Lennon, J.C.; Dembure, P.O.; Elsas, L.J. II [Emory Univ. School of Medicine, Atlanta, GA (United States)
1995-03-01
We have identified three mutations associated with transferase-deficiency galactosemia in a three-generation family including affected members in two generations and have modeled all three mutations in a yeast-expression system. A sequence of pedigree, biochemical, and molecular analyses of the galactose-1-phosphate uridyltransferase (GALT) enzyme and genetic locus in both affected and carrier individuals revealed three distinct base substitutions in this family, two (Q188R and S135L) that had been reported previously and one (V151A) that was novel. Biochemical analyses of red-blood-cell lysates from the relevant family members suggested that each of these mutations was associated with dramatic impairment of GALT activity in these cells. While this observation was consistent with our previous findings concerning the Q188R mutation expressed both in humans and in a yeast-model system, it was at odds with a report by Reichardt and colleagues, indicating that in their COS cell-expression system the S135L substitution behaved as a neutral polymorphism. To address this apparent paradox, as well as to investigate the functional significance of the newly identified V151A substitution, all three mutations were recreated by site-directed mutagenesis of the otherwise wild-type human GALT sequence and were expressed both individually and in the appropriate allelic combinations in a GALT-deficient strain of the yeast Saccharomyces cerevisiae. The results of these yeast-modeling studies were fully consistent with the patient data, leading us to conclude that, at least within the context of the cell types studied, in the homozygous state Q188R is a mutation that eliminates GALT activity, and S135L and V151A are both mutations that impair GALT activity to <6% of wild-type values. 22 refs., 5 figs.
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Ma, Prettiny K.; Zhao, Yunliang; Robinson, Allen L.; Worton, David R.; Goldstein, Allen H.; Ortega, Amber M.; Jimenez, Jose L.; Zotter, Peter; Prévôt, André S. H.; Szidat, Sönke; Hayes, Patrick L.
2017-08-01
Secondary organic aerosol (SOA) is an important contributor to fine particulate matter (PM) mass in polluted regions, and its modeling remains poorly constrained. A box model is developed that uses recently published literature parameterizations and data sets to better constrain and evaluate the formation pathways and precursors of urban SOA during the CalNex 2010 campaign in Los Angeles. When using the measurements of intermediate-volatility organic compounds (IVOCs) reported in Zhao et al. (2014) and of semi-volatile organic compounds (SVOCs) reported in Worton et al. (2014) the model is biased high at longer photochemical ages, whereas at shorter photochemical ages it is biased low, if the yields for VOC oxidation are not updated. The parameterizations using an updated version of the yields, which takes into account the effect of gas-phase wall losses in environmental chambers, show model-measurement agreement at longer photochemical ages, even though some low bias at short photochemical ages still remains. Furthermore, the fossil and non-fossil carbon split of urban SOA simulated by the model is consistent with measurements at the Pasadena ground site. Multi-generation oxidation mechanisms are often employed in SOA models to increase the SOA yields derived from environmental chamber experiments in order to obtain better model-measurement agreement. However, there are many uncertainties associated with these aging mechanisms. Thus, SOA formation in the model is compared to data from an oxidation flow reactor (OFR) in order to constrain SOA formation at longer photochemical ages than observed in urban air. The model predicts similar SOA mass at short to moderate photochemical ages when the aging mechanisms or the updated version of the yields for VOC oxidation are implemented. The latter case has SOA formation rates that are more consistent with observations from the OFR though. Aging mechanisms may still play an important role in SOA chemistry, but the
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Genomic evaluation of both purebred and crossbred performances
DEFF Research Database (Denmark)
Christensen, Ole Fredslund; Madsen, Per; Nielsen, Bjarne
2014-01-01
relationship matrices for the two breeds; (2) marker-based partial relationship matrices are constructed; (3) marker-based partial relationship matrices are adjusted to be compatible to pedigree-based partial relationship matrices and (4) combined partial relationship matrices are constructed using information...... from both pedigree and marker genotypes. The extension of the Wei van der Werf model can be implemented using software that allows inverse covariance matrices in sparse format as input. A method for genomic evaluation of both purebred and crossbred performances was developed for a two...
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Young families become mindful of their possibilities through the ...
African Journals Online (AJOL)
Young families, as viewed through a multi-generational lens, provide the environment in which children can be nurtured and socialised. The purpose of the research is to explore and describe how the parents and grandparents of young families appreciate their family life. A qualitative, exploratory, descriptive and contextual ...
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Edge, Karen
2014-01-01
Most schools currently employ three generations of teachers and leaders: Baby Boomers (1946-65), Generation X (1966-80) and Generation Y (1981-2003). However, the implications for school leaders of multi-generational schools remain relatively unexplored. This paper examines the empirical multi-disciplinary generations at work evidence to identify…
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Directory of Open Access Journals (Sweden)
Maria Augustyniak
Full Text Available In the case of the pests inhabiting metal polluted or fields where the use of pesticides is common, a natural selection of resistant individuals can occur. This may pose serious problems for humans, agriculture, as well as the economies of many countries. In this study, the hypothesis that multigenerational (120 generations exposure to cadmium of a beet armyworm population could be a selecting factor toward a more efficient DNA protection was verified. The hemocytes of individuals from two culture strains (control and Cd-exposed were treated with H2O2 (a DNA-damaging agent or PBS (reference. The level of DNA damage was assessed using the Comet assay immediately and 5, 15 and 30 min. after the treatment. The immediate result of the contact with H2O2 was that the level of DNA damage in the hemocytes of the insects from both strains increased significantly. However, in the cells of the Cd-exposed individuals, the level of DNA damage decreased over time, while in the cells from the control insects it remained at the same level with no evidence of repair. These results suggest that efficient defense mechanisms may exist in the cells of insects that have prolonged contact with cadmium. Some evolutionary and trade-off aspects of the phenomenon are discussed. In a wider context, comparing the results obtained in the laboratory with field studies may be beneficial for understanding basic mechanisms of the resistance of an organism. To summarize, the high potential for the repair of DNA damage that was observed in the insects from the cadmium strain may confirm the hypothesis that multigenerational exposure to that metal may possibly contribute to the selection of insects that have a wider tolerance to oxidative stress. However, our investigations of polymorphism using AFLP did not reveal differences between the two main insect strains.
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Li, Dong; Opas, Evan E; Tuluc, Florin; Metzger, Daniel L; Hou, Cuiping; Hakonarson, Hakon; Levine, Michael A
2014-09-01
Most cases of autosomal dominant hypoparathyroidism (ADH) are caused by gain-of-function mutations in CASR or dominant inhibitor mutations in GCM2 or PTH. Our objectives were to identify the genetic basis for ADH in a multigenerational family and define the underlying disease mechanism. Here we evaluated a multigenerational family with ADH in which affected subjects had normal sequences in these genes and were shorter than unaffected family members. We collected clinical and biochemical data from 6 of 11 affected subjects and performed whole-exome sequence analysis on DNA from two affected sisters and their affected father. Functional studies were performed after expression of wild-type and mutant Gα11 proteins in human embryonic kidney-293-CaR cells that stably express calcium-sensing receptors. Whole-exome-sequencing followed by Sanger sequencing revealed a heterozygous mutation, c.179G>T; p.R60L, in GNA11, which encodes the α-subunit of G11, the principal heterotrimeric G protein that couples calcium-sensing receptors to signal activation in parathyroid cells. Functional studies of Gα11 R60L showed increased accumulation of intracellular concentration of free calcium in response to extracellular concentration of free calcium with a significantly decreased EC50 compared with wild-type Gα11. By contrast, R60L was significantly less effective than the oncogenic Q209L form of Gα11 as an activator of the MAPK pathway. Compared to subjects with CASR mutations, patients with GNA11 mutations lacked hypercalciuria and had normal serum magnesium levels. Our findings indicate that the germline gain-of-function mutation of GNA11 is a cause of ADH and implicate a novel role for GNA11 in skeletal growth.
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Unal Gulsuner, Hilal; Gulsuner, Suleyman; Mercan, Fatma Nazli; Onat, Onur Emre; Walsh, Tom; Shahin, Hashem; Lee, Ming K; Dogu, Okan; Kansu, Tulay; Topaloglu, Haluk; Elibol, Bulent; Akbostanci, Cenk; King, Mary-Claire; Ozcelik, Tayfun; Tekinay, Ayse B
2014-12-23
Essential tremor is one of the most frequent movement disorders of humans and can be associated with substantial disability. Some but not all persons with essential tremor develop signs of Parkinson disease, and the relationship between the conditions has not been clear. In a six-generation consanguineous Turkish kindred with both essential tremor and Parkinson disease, we carried out whole exome sequencing and pedigree analysis, identifying HTRA2 p.G399S as the allele likely responsible for both conditions. Essential tremor was present in persons either heterozygous or homozygous for this allele. Homozygosity was associated with earlier age at onset of tremor (P relationship to Parkinson disease.
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Directory of Open Access Journals (Sweden)
Wilmien Smit
2015-08-01
Full Text Available Orientation: Currently there is much debate whether modifying traditional reward packages to focus on the preferences of multi-generations would be essential in attracting, motivating and retaining talent. Total reward factors, perceived organisational support and perceived supervisor support are distinct but related concepts, all of which appear to influence an employee’s decision to stay at an organisation. Research purpose: The objective of this study was to identify the different total reward components that multi-generations prefer as most important for retention. In essence, the study aims to establish possible relationships between multi-generations’ total reward components, perceived organisational support, and perceived supervisor support. Motivation for the study: This study is useful as it conducts a contemporary retention exploration that considers both the emerging demographic workforce shift and the new paradigm shift towards talent management. Research methodology: A quantitative, cross-sectional research design was applied to gather data from employees (N = 303 from different industry sectors in South African organisations. Main findings: The results showed that performance management and remuneration are considered to be the most important retention factors amongst multi-generation groups. Differences between total reward preferences and demographical variables, which include age, gender, race, industry and job level, were found. Practical/managerial implications: Organisations should design their reward packages by taking employees preferences into account. More specifically, organisations should focus on remuneration, performance management and development opportunities in order to retain scarce skills. Contribution/value additions: The results of the study can assist managers to design effective retention strategies, whilst also providing crucial information for the retention and motivation of employees.
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A high-density Diversity Arrays Technology (DArT microarray for genome-wide genotyping in Eucalyptus
Directory of Open Access Journals (Sweden)
Myburg Alexander A
2010-06-01
Full Text Available Abstract Background A number of molecular marker technologies have allowed important advances in the understanding of the genetics and evolution of Eucalyptus, a genus that includes over 700 species, some of which are used worldwide in plantation forestry. Nevertheless, the average marker density achieved with current technologies remains at the level of a few hundred markers per population. Furthermore, the transferability of markers produced with most existing technology across species and pedigrees is usually very limited. High throughput, combined with wide genome coverage and high transferability are necessary to increase the resolution, speed and utility of molecular marker technology in eucalypts. We report the development of a high-density DArT genome profiling resource and demonstrate its potential for genome-wide diversity analysis and linkage mapping in several species of Eucalyptus. Findings After testing several genome complexity reduction methods we identified the PstI/TaqI method as the most effective for Eucalyptus and developed 18 genomic libraries from PstI/TaqI representations of 64 different Eucalyptus species. A total of 23,808 cloned DNA fragments were screened and 13,300 (56% were found to be polymorphic among 284 individuals. After a redundancy analysis, 6,528 markers were selected for the operational array and these were supplemented with 1,152 additional clones taken from a library made from the E. grandis tree whose genome has been sequenced. Performance validation for diversity studies revealed 4,752 polymorphic markers among 174 individuals. Additionally, 5,013 markers showed segregation when screened using six inter-specific mapping pedigrees, with an average of 2,211 polymorphic markers per pedigree and a minimum of 859 polymorphic markers that were shared between any two pedigrees. Conclusions This operational DArT array will deliver 1,000-2,000 polymorphic markers for linkage mapping in most eucalypt pedigrees
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Phenotypic heterogeneity associated with a novel mutation (Gly112Glu) in the Norrie disease protein.
Allen, R C; Russell, S R; Streb, L M; Alsheikheh, A; Stone, E M
2006-02-01
To determine the molecular pathology and clinical severity of two pedigrees with a history of early retinal detachment and peripheral retinal vascular abnormalities. Longitudinal cohort study. A longitudinal clinical study and DNA analysis was performed on 49 family members of two pedigrees. Nine individuals were found to be hemizygous for a mutation at codon 112 (Gly112Glu) of the Norrie disease protein (NDP) in one pedigree. Significant phenotypic heterogeneity was found. The proband presented with a unilateral subtotal retinal detachment at the age of 3 years, and subsequently developed a slowly progressive tractional retinal detachment involving the macula in the contralateral eye at the age of 4 years. One individual had only mild peripheral retinal pigmentary changes with normal vision at the age of 79 years. The remaining seven individuals had varying degrees of peripheral retinal vascular abnormalities and anterior segment findings. Seven affected members of a second pedigree affected by a previously reported mutation, Arg74Cys, also demonstrated wide ocular phenotypic variation. A novel mutation (Gly112Glu), which represents the most carboxy located, NDP mutation reported, results in significant phenotypic heterogeneity. These data support the contention that the spectrum of ocular disease severity associated with these NDP mutations is broad. Use of terms that characterize this entity by phenotypic appearance, such as familial exudative vitreoretinopathy, do not adequately communicate the potential spectrum of severity of this disorder to affected or carrier family members.
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Comparing estimates of genetic variance across different relationship models.
Legarra, Andres
2016-02-01
Use of relationships between individuals to estimate genetic variances and heritabilities via mixed models is standard practice in human, plant and livestock genetics. Different models or information for relationships may give different estimates of genetic variances. However, comparing these estimates across different relationship models is not straightforward as the implied base populations differ between relationship models. In this work, I present a method to compare estimates of variance components across different relationship models. I suggest referring genetic variances obtained using different relationship models to the same reference population, usually a set of individuals in the population. Expected genetic variance of this population is the estimated variance component from the mixed model times a statistic, Dk, which is the average self-relationship minus the average (self- and across-) relationship. For most typical models of relationships, Dk is close to 1. However, this is not true for very deep pedigrees, for identity-by-state relationships, or for non-parametric kernels, which tend to overestimate the genetic variance and the heritability. Using mice data, I show that heritabilities from identity-by-state and kernel-based relationships are overestimated. Weighting these estimates by Dk scales them to a base comparable to genomic or pedigree relationships, avoiding wrong comparisons, for instance, "missing heritabilities". Copyright © 2015 Elsevier Inc. All rights reserved.
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Meiotic recombination is a major driving force in promoting genetic and phenotypic variations in sexually reproducing organisms. Although PRDM9 is known to modulate the binding-specificity and location of recombination hotspots in humans and mice, its role, especially in domesticated animals like ca...
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Human Rights, Human Needs, Human Development, Human Security
Gasper, Des
2009-01-01
Human rights, human development and human security form increasingly important, partly interconnected, partly competitive and misunderstood ethical and policy discourses. Each tries to humanize a pre-existing and unavoidable major discourse of everyday life, policy and politics; each has emerged within the United Nations world; each relies implicitly on a conceptualisation of human need; each has specific strengths. Yet mutual communication, understanding and co-operation are deficient, espec...
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Association analysis of whole genome sequencing data accounting for longitudinal and family designs.
Hu, Yijuan; Hui, Qin; Sun, Yan V
2014-01-01
Using the whole genome sequencing data and the simulated longitudinal phenotypes for 849 pedigree-based individuals from Genetic Analysis Workshop 18, we investigated various approaches to detecting the association of rare and common variants with blood pressure traits. We compared three strategies for longitudinal data: (a) using the baseline measurement only, (b) using the average from multiple visits, and (c) using all individual measurements. We also compared the power of using all of the pedigree-based data and the unrelated subset. The analyses were performed without knowledge of the underlying simulating model.
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The Spiritual Genogram in Training and Supervision.
Frame, Marsha Wiggins
2001-01-01
Describes the spiritual genogram, a blueprint of family members' multigenerational religious and spiritual affiliations, events, and conflicts. Used as a tool in both training and supervision, the spiritual genogram enables students and supervisees to make sense of their own religious and spiritual heritage and to explore the ways in which their…
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Smith, Sara D.; Galbraith, Quinn
2012-01-01
Working with younger staff and student employees can be a challenge for library supervisors in a multigenerational workplace. Because members of the Millennial Generation have different work expectations, managers need to adjust to best meet their needs. By surveying its five hundred student employees, Brigham Young University's Harold B. Lee…
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A case study of culturally appropriate conservation education
David N. Bengston; Michele Schermann
2016-01-01
Create culturally appropriate conservation education materials for Hmong Americans, including new refugees and elders with little proficiency in English, as well as the broader, multigenerational Hmong community. This case study discusses an organizational response from the USDA Forest Service, in partnership with others, to better serve the Hmong American community....
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Lester, Melinda
2011-01-01
As the economy has become increasingly global, organizations whose employees are more creative and innovative compete at a higher level than those who do not. And, organizations that incorporate multi-generations into their workforce will realize more creativity and innovation within their organizations. Now, and in the future, leaders will…
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Novel Sonic Hedgehog Mutation in a Couple with Variable Expression of Holoprosencephaly
Directory of Open Access Journals (Sweden)
M. Aguinaga
2011-01-01
Full Text Available Holoprosencephaly (HPE is the most common developmental defect of the forebrain and midface in humans. sporadic and inherited mutations in the human sonic hedgehog (SHH gene cause 37% of familial HPE. A couple was referred to our unit with a family history of two spontaneous first trimester miscarriages and a daughter with HPE who presented early neonatal death. The father had a repaired median cleft lip, absence of central incisors, facial medial hypoplasia, and cleft palate. Intelligence and a brain CT scan were normal. Direct paternal sequencing analysis showed a novel nonsense mutation (W127X. Facial characteristics are considered as HPE microforms, and the pedigree suggested autosomal dominant inheritance with a variable expression of the phenotype. This study reinforces the importance of an exhaustive evaluation of couples with a history of miscarriages and neonatal deaths with structural defects.
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Job satisfaction among a multigenerational nursing workforce.
Wilson, Barbara; Squires, Mae; Widger, Kimberley; Cranley, Lisa; Tourangeau, Ann
2008-09-01
To explore generational differences in job satisfaction. Effective retention strategies are required to mitigate the international nursing shortage. Job satisfaction, a strong and consistent predictor of retention, may differ across generations. Understanding job satisfaction generational differences may lead to increasing clarity about generation-specific retention approaches. The Ontario Nurse Survey collected data from 6541 Registered Nurses. Participants were categorized as Baby Boomer, Generation X or Generation Y based on birth year. Multivariate analysis of variance explored generational differences for overall and specific satisfaction components. In overall job satisfaction and five specific satisfaction components, Baby Boomers were significantly more satisfied than Generations X and Y. It is imperative to improve job satisfaction for younger generations of nurses. Strategies to improve job satisfaction for younger generations of nurses may include creating a shared governance framework where nurses are empowered to make decisions. Implementing shared governance, through nurse-led unit-based councils, may lead to greater job satisfaction, particularly for younger nurses. Opportunities to self schedule or job share may be other potential approaches to increase job satisfaction, especially for younger generations of nurses. Another potential strategy would be to aggressively provide and support education and career-development opportunities.
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Aging Families and Breast Cancer: Multigenerational Issues
National Research Council Canada - National Science Library
Raveis, Victoria
2001-01-01
With the continuing shift of cancer care to community-based care the necessity to develop programs that will enable the family to meet patients' needs for support and assistance is of paramount importance...
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Aging Families and Breast Cancer: Multigenerational Issues
National Research Council Canada - National Science Library
Raveis, Victoria
2003-01-01
With the continuing shift of cancer care to community-based care the necessity to develop programs that will enable the family to meet patients' needs for support and assistance is of paramount importance...
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Directory of Open Access Journals (Sweden)
Emily J Telfer
Full Text Available Pedigree reconstruction using molecular markers enables efficient management of inbreeding in open-pollinated breeding strategies, replacing expensive and time-consuming controlled pollination. This is particularly useful in preferentially outcrossed, insect pollinated Eucalypts known to suffer considerable inbreeding depression from related matings. A single nucleotide polymorphism (SNP marker panel consisting of 106 markers was selected for pedigree reconstruction from the recently developed high-density Eucalyptus Infinium SNP chip (EuCHIP60K. The performance of this SNP panel for pedigree reconstruction in open-pollinated progenies of two Eucalyptus nitens seed orchards was compared with that of two microsatellite panels with 13 and 16 markers respectively. The SNP marker panel out-performed one of the microsatellite panels in the resolution power to reconstruct pedigrees and out-performed both panels with respect to data quality. Parentage of all but one offspring in each clonal seed orchard was correctly matched to the expected seed parent using the SNP marker panel, whereas parentage assignment to less than a third of the expected seed parents were supported using the 13-microsatellite panel. The 16-microsatellite panel supported all but one of the recorded seed parents, one better than the SNP panel, although there was still a considerable level of missing and inconsistent data. SNP marker data was considerably superior to microsatellite data in accuracy, reproducibility and robustness. Although microsatellites and SNPs data provide equivalent resolution for pedigree reconstruction, microsatellite analysis requires more time and experience to deal with the uncertainties of allele calling and faces challenges for data transferability across labs and over time. While microsatellite analysis will continue to be useful for some breeding tasks due to the high information content, existing infrastructure and low operating costs, the multi
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Telfer, Emily J; Stovold, Grahame T; Li, Yongjun; Silva-Junior, Orzenil B; Grattapaglia, Dario G; Dungey, Heidi S
2015-01-01
Pedigree reconstruction using molecular markers enables efficient management of inbreeding in open-pollinated breeding strategies, replacing expensive and time-consuming controlled pollination. This is particularly useful in preferentially outcrossed, insect pollinated Eucalypts known to suffer considerable inbreeding depression from related matings. A single nucleotide polymorphism (SNP) marker panel consisting of 106 markers was selected for pedigree reconstruction from the recently developed high-density Eucalyptus Infinium SNP chip (EuCHIP60K). The performance of this SNP panel for pedigree reconstruction in open-pollinated progenies of two Eucalyptus nitens seed orchards was compared with that of two microsatellite panels with 13 and 16 markers respectively. The SNP marker panel out-performed one of the microsatellite panels in the resolution power to reconstruct pedigrees and out-performed both panels with respect to data quality. Parentage of all but one offspring in each clonal seed orchard was correctly matched to the expected seed parent using the SNP marker panel, whereas parentage assignment to less than a third of the expected seed parents were supported using the 13-microsatellite panel. The 16-microsatellite panel supported all but one of the recorded seed parents, one better than the SNP panel, although there was still a considerable level of missing and inconsistent data. SNP marker data was considerably superior to microsatellite data in accuracy, reproducibility and robustness. Although microsatellites and SNPs data provide equivalent resolution for pedigree reconstruction, microsatellite analysis requires more time and experience to deal with the uncertainties of allele calling and faces challenges for data transferability across labs and over time. While microsatellite analysis will continue to be useful for some breeding tasks due to the high information content, existing infrastructure and low operating costs, the multi-species SNP resource
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Müller, Dominik; Schopp, Pascal; Melchinger, Albrecht E
2017-03-10
Recurrent selection (RS) has been used in plant breeding to successively improve synthetic and other multiparental populations. Synthetics are generated from a limited number of parents [Formula: see text] but little is known about how [Formula: see text] affects genomic selection (GS) in RS, especially the persistency of prediction accuracy ([Formula: see text]) and genetic gain. Synthetics were simulated by intermating [Formula: see text]= 2-32 parent lines from an ancestral population with short- or long-range linkage disequilibrium ([Formula: see text]) and subjected to multiple cycles of GS. We determined [Formula: see text] and genetic gain across 30 cycles for different training set ( TS ) sizes, marker densities, and generations of recombination before model training. Contributions to [Formula: see text] and genetic gain from pedigree relationships, as well as from cosegregation and [Formula: see text] between QTL and markers, were analyzed via four scenarios differing in (i) the relatedness between TS and selection candidates and (ii) whether selection was based on markers or pedigree records. Persistency of [Formula: see text] was high for small [Formula: see text] where predominantly cosegregation contributed to [Formula: see text], but also for large [Formula: see text] where [Formula: see text] replaced cosegregation as the dominant information source. Together with increasing genetic variance, this compensation resulted in relatively constant long- and short-term genetic gain for increasing [Formula: see text] > 4, given long-range LD A in the ancestral population. Although our scenarios suggest that information from pedigree relationships contributed to [Formula: see text] for only very few generations in GS, we expect a longer contribution than in pedigree BLUP, because capturing Mendelian sampling by markers reduces selective pressure on pedigree relationships. Larger TS size ([Formula: see text]) and higher marker density improved persistency of
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Parenting stress of caregivers of young children who are HIV Positive
African Journals Online (AJOL)
Objective: Paediatric HIV remains a major challenge in Sub-Saharan Africa. Paediatric HIV is a multi-generational disorder with far-reaching implications for the whole family. Parenting stress in caregivers of HIV infected children has been studied in developed countries but never in South Africa. The aim of this study was to ...
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Button, Le; Peter, Beate; Stoel-Gammon, Carol; Raskind, Wendy H.
2013-01-01
The purpose of this study was to address the hypothesis that childhood apraxia of speech (CAS) is influenced by an underlying deficit in sequential processing that is also expressed in other modalities. In a sample of 21 adults from five multigenerational families, 11 with histories of various familial speech sound disorders, 3 biologically…
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76 FR 59909 - Amisulbrom; Pesticide Tolerances
2011-09-28
... apply to certain entities. If you have any questions regarding the applicability of this action to a.../ day from the multigenerational study (parental systemic NOAEL). The LOAEL of 96 mg/kg/day is from the... amended as follows: PART 180--[AMENDED] 0 1. The authority citation for part 180 continues to read as...
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Biotic resistance: Exclusion of native rodent consumers releases populations of a weak invader
Dean E. Pearson; Teal Potter; John L. Maron
2012-01-01
Biotic resistance is a commonly invoked hypothesis to explain why most exotic plant species naturalize at low abundance. Although numerous studies have documented negative impacts of native consumers on exotic plant performance, longer-term multi-generation studies are needed to understand how native consumer damage to exotics translates to their population-level...
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Population structure of Nellore cattle in northeastern Brazil
Directory of Open Access Journals (Sweden)
Ana Carla Borges Barbosa
2013-09-01
Full Text Available The objective of this study was to evaluate the population genetic structure of Nellore cattle in northeastern Brazil. Pedigree information was collected from 175,231 animals born from 1967 to 2007. Probability of gene origin, inbreeding, average relatedness coefficient (AR, completeness pedigree, effective population size and generation interval were calculated. Generation interval was high due to the long period of time animals were used as reproducers. The bottleneck effect was evidenced as a result of intensive use of limited breeders over the last years. Low values were observed in the effective number of founder animals (434 and ancestors (427 comparing with the number on the base (175,231 and reference populations (130,038. Generally, the variability explained by the founders and ancestors is considered low. The average coefficient of inbreeding (0.11% and AR (0.14% estimated for this population is considered low and can be partly explained by the increased population effective number in recent periods; however, it may be underestimated by shallow pedigree.
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Y-chromosome-specific microsatellite mutation rates re-examined using a minisatellite, MSY1.
Jobling, M A; Heyer, E; Dieltjes, P; de Knijff, P
1999-10-01
Polymorphic Y-chromosome-specific microsatellites are becoming increasingly used in evolutionary and forensic studies and, in particular, in dating the origins of Y-chromosomal lineages. Previously, haplotyping of Y chromosomes from males belonging to a set of deep-rooting pedigrees was used to estimate a conservative average Y-chromosomal microsatellite mutation rate of 2.1 x 10(-3)per locus per generation. A number of males showed multiple differences in haplotypes compared with other males within their pedigrees, and these were excluded from the calculation of this estimate, on the grounds that non-paternity was a more probable explanation than multiple mutation within a lineage. Here we reanalyse the pedigrees using an independent highly polymorphic system, the Y-specific minisatellite, MSY1. This supports the hypothesis of non-paternity where more than one microsatellite difference was observed, provides further support for the previously deduced microsatellite mutation rate and throws light on the mutation dynamics of MSY1 itself, suggesting that single-step changes are not the only mode of mutation.
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Dorais, Gregory A.
2015-01-01
This document defines the design concept for a ground-based, extended-stay hypergravity facility as a precursor for space-based artificial-gravity facilities that extend the permanent presence of both human and non-human life beyond Earth in artificial-gravity settlements. Since the Earth's current human population is stressing the environment and the resources off-Earth are relatively unlimited, by as soon as 2040 more than one thousand people could be living in Earthorbiting artificial-gravity habitats. Eventually, the majority of humanity may live in artificialgravity habitats throughout this solar system as well as others, but little is known about the longterm (multi-generational) effects of artificial-gravity habitats on people, animals, and plants. In order to extend life permanently beyond Earth, it would be useful to create an orbiting space facility that generates 1g as well as other gravity levels to rigorously address the numerous challenges of such an endeavor. Before doing so, developing a ground-based artificial-gravity facility is a reasonable next step. Just as the International Space Station is a microgravity research facility, at a small fraction of the cost and risk a ground-based artificial-gravity facility can begin to address a wide-variety of the artificial-gravity life-science questions and engineering challenges requiring long-term research to enable people, animals, and plants to live off-Earth indefinitely.
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Ma, Jianzhong; Amos, Christopher I; Warwick Daw, E
2007-09-01
Although extended pedigrees are often sampled through probands with extreme levels of a quantitative trait, Markov chain Monte Carlo (MCMC) methods for segregation and linkage analysis have not been able to perform ascertainment corrections. Further, the extent to which ascertainment of pedigrees leads to biases in the estimation of segregation and linkage parameters has not been previously studied for MCMC procedures. In this paper, we studied these issues with a Bayesian MCMC approach for joint segregation and linkage analysis, as implemented in the package Loki. We first simulated pedigrees ascertained through individuals with extreme values of a quantitative trait in spirit of the sequential sampling theory of Cannings and Thompson [Cannings and Thompson [1977] Clin. Genet. 12:208-212]. Using our simulated data, we detected no bias in estimates of the trait locus location. However, in addition to allele frequencies, when the ascertainment threshold was higher than or close to the true value of the highest genotypic mean, bias was also found in the estimation of this parameter. When there were multiple trait loci, this bias destroyed the additivity of the effects of the trait loci, and caused biases in the estimation all genotypic means when a purely additive model was used for analyzing the data. To account for pedigree ascertainment with sequential sampling, we developed a Bayesian ascertainment approach and implemented Metropolis-Hastings updates in the MCMC samplers used in Loki. Ascertainment correction greatly reduced biases in parameter estimates. Our method is designed for multiple, but a fixed number of trait loci. Copyright (c) 2007 Wiley-Liss, Inc.
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Sun, Jin; Rutkoski, Jessica E; Poland, Jesse A; Crossa, José; Jannink, Jean-Luc; Sorrells, Mark E
2017-07-01
High-throughput phenotyping (HTP) platforms can be used to measure traits that are genetically correlated with wheat ( L.) grain yield across time. Incorporating such secondary traits in the multivariate pedigree and genomic prediction models would be desirable to improve indirect selection for grain yield. In this study, we evaluated three statistical models, simple repeatability (SR), multitrait (MT), and random regression (RR), for the longitudinal data of secondary traits and compared the impact of the proposed models for secondary traits on their predictive abilities for grain yield. Grain yield and secondary traits, canopy temperature (CT) and normalized difference vegetation index (NDVI), were collected in five diverse environments for 557 wheat lines with available pedigree and genomic information. A two-stage analysis was applied for pedigree and genomic selection (GS). First, secondary traits were fitted by SR, MT, or RR models, separately, within each environment. Then, best linear unbiased predictions (BLUPs) of secondary traits from the above models were used in the multivariate prediction models to compare predictive abilities for grain yield. Predictive ability was substantially improved by 70%, on average, from multivariate pedigree and genomic models when including secondary traits in both training and test populations. Additionally, (i) predictive abilities slightly varied for MT, RR, or SR models in this data set, (ii) results indicated that including BLUPs of secondary traits from the MT model was the best in severe drought, and (iii) the RR model was slightly better than SR and MT models under drought environment. Copyright © 2017 Crop Science Society of America.
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International Nuclear Information System (INIS)
Dai Pu; Liu Xin; Han Dongyi; Qian Yaping; Huang Deliang; Yuan Huijun; Li Weiming; Yu Fei; Zhang Ruining; Lin Hongyan; He Yong; Yu Youjun; Sun Quanzhu; Qin Huaiyi; Li Ronghua; Zhang Xin; Kang Dongyang; Cao Juyang; Young Wieyen; Guan Minxin
2006-01-01
Mutations in mitochondrial DNA (mtDNA) have been found to be associated with sensorineural hearing loss. We report here the clinical, genetic, and molecular characterization of 16 Chinese pedigrees (a total of 246 matrilineal relatives) with aminoglycoside-induced impairment. Clinical evaluation revealed the variable phenotype of hearing impairment including audiometric configuration in these subjects, although these subjects share some common features: being bilateral and sensorineural hearing impairment. Strikingly, these Chinese pedigrees exhibited extremely low penetrance of hearing loss, ranging from 4% to 18%, with an average of 8%. In particular, nineteen of 246 matrilineal relatives in these pedigrees had aminoglycoside-induced hearing loss. Mutational analysis of the mtDNA in these pedigrees showed the presence of homoplasmic 12S rRNA A1555G mutation, which has been associated with hearing impairment in many families worldwide. The extremely low penetrance of hearing loss in these Chinese families carrying the A1555G mutation strongly supports the notion that the A1555G mutation itself is not sufficient to produce the clinical phenotype. Children carrying the A1555G mutation are susceptible to the exposure of aminoglycosides, thereby inducing or worsening hearing impairment, as in the case of these Chinese families. Using those genetic and molecular approaches, we are able to diagnose whether children carry the ototoxic mtDNA mutation. Therefore, these data have been providing valuable information and technology to predict which individuals are at risk for ototoxicity, to improve the safety of aminoglycoside therapy, and eventually to decrease the incidence of deafness
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The myosin chaperone UNC45B is involved in lens development and autosomal dominant juvenile cataract
DEFF Research Database (Denmark)
Hansen, Lars; Comyn, Sophie; Mang, Yuan
2014-01-01
Genome-wide linkage analysis, followed by targeted deep sequencing, in a Danish multigeneration family with juvenile cataract revealed a region of chromosome 17 co-segregating with the disease trait. Affected individuals were heterozygous for two potentially protein-disrupting alleles in this reg...... advance online publication, 19 February 2014; doi:10.1038/ejhg.2014.21....
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D.R. Gasper (Des)
2007-01-01
markdownabstractAbstract: Human rights, human development and human security form increasingly important, partly interconnected, partly competitive and misunderstood ethical and policy discourses. Each tries to humanize a pre-existing and unavoidable major discourse of everyday life, policy and