Witchcraft, genealogy, Foucault.

Science.gov (United States)

Russell, S

2001-03-01

This paper is a genealogical reflection on both the historiography of European witchcraft and the dynamics of witchcraft trials. I argue that traditional scholarly assumptions about the 'unsophisticated' nature of early modern European mentalities result in inadequate representations of accused witches and of the social contexts and processes of the trials. Genealogy, by contrast, problematizes fundamental notions such as reason, order, power and progress in ways that not only provide a different range of effective tools for the analysis of belief in witchcraft, but also underline its crucial significance for social theory. In the final section, an analysis of a typical trial is undertaken employing key genealogical insights into confession, torture, truth, governmentality, power, pleasure and pain.

Using maps in genealogy

Science.gov (United States)

,

2002-01-01

In genealogical research, maps can provide clues to where our ancestors may have lived and where to look for written records about them. Beginners should master basic genealogical research techniques before starting to use topographic maps.

Inter-genomic displacement via lateral gene transfer of bacterial trp operons in an overall context of vertical genealogy

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Keyhani Nemat O

2004-06-01

Full Text Available Abstract Background The growing conviction that lateral gene transfer plays a significant role in prokaryote genealogy opens up a need for comprehensive evaluations of gene-enzyme systems on a case-by-case basis. Genes of tryptophan biosynthesis are frequently organized as whole-pathway operons, an attribute that is expected to facilitate multi-gene transfer in a single step. We have asked whether events of lateral gene transfer are sufficient to have obscured our ability to track the vertical genealogy that underpins tryptophan biosynthesis. Results In 47 complete-genome Bacteria, the genes encoding the seven catalytic domains that participate in primary tryptophan biosynthesis were distinguished from any paralogs or xenologs engaged in other specialized functions. A reliable list of orthologs with carefully ascertained functional roles has thus been assembled and should be valuable as an annotation resource. The protein domains associated with primary tryptophan biosynthesis were then concatenated, yielding single amino-acid sequence strings that represent the entire tryptophan pathway. Lateral gene transfer of several whole-pathway trp operons was demonstrated by use of phylogenetic analysis. Lateral gene transfer of partial-pathway trp operons was also shown, with newly recruited genes functioning either in primary biosynthesis (rarely or specialized metabolism (more frequently. Conclusions (i Concatenated tryptophan protein trees are congruent with 16S rRNA subtrees provided that the genomes represented are of sufficiently close phylogenetic spacing. There are currently seven tryptophan congruency groups in the Bacteria. Recognition of a succession of others can be expected in the near future, but ultimately these should coalesce to a single grouping that parallels the 16S rRNA tree (except for cases of lateral gene transfer. (ii The vertical trace of evolution for tryptophan biosynthesis can be deduced. The daunting complexities engendered

Genealogy Remediated

DEFF Research Database (Denmark)

Marselis, Randi

2007-01-01

Genealogical websites are becoming an increasingly popular genre on the Web. This chapter will examine how remediation is used creatively in the construction of family history. While remediation of different kinds of old memory materials is essential in genealogy, digital technology opens new...... possibilities. Genealogists use their private websites to negotiate family identity and hereby create a sense of belonging in an increasingly complex society. Digital technologies enhance the possibilities of coorporation between genealogists. Therefore, the websites are also used to present archival...

8 CFR 103.40 - Genealogical Research Requests.

Science.gov (United States)

2010-01-01

.... Genealogy requests are requests for searches and/or copies of historical records relating to a deceased person, usually for genealogy and family history research purposes. (b) Manner of requesting genealogical searches and records. Requests must be submitted on Form G-1041, Genealogy Index Search Request, or Form G...

8 CFR 103.38 - Genealogy Program.

Science.gov (United States)

2010-01-01

... 8 Aliens and Nationality 1 2010-01-01 2010-01-01 false Genealogy Program. 103.38 Section 103.38...; AVAILABILITY OF RECORDS § 103.38 Genealogy Program. (a) Purpose. The Department of Homeland Security, U.S. Citizenship and Immigration Services Genealogy Program is a fee-for-service program designed to provide...

8 CFR 103.41 - Genealogy request fees.

Science.gov (United States)

2010-01-01

... 8 Aliens and Nationality 1 2010-01-01 2010-01-01 false Genealogy request fees. 103.41 Section 103...; AVAILABILITY OF RECORDS § 103.41 Genealogy request fees. (a) Genealogy search fee. See 8 CFR 103.7(b)(1). (b) Genealogy records fees. See 8 CFR 103.7(b)(1). (c) Manner of submission. When a request is submitted online...

Invented genealogies as political mythologies: definitionand examples

Directory of Open Access Journals (Sweden)

Filip-Lucian Iorga

2012-10-01

Full Text Available The genealogical imaginary is a subcategory of the imaginary referring to the origin and it comprises a wide range of genealogical myths: fictitious ancestors, whether divine or human, fabulous kinships, invented genealogies, descendancies which are impossible to certify with documents, erroneous interpretations of certain degrees of kinship, real genealogies that have received unexpected interpretations and historiographic clichés grown on more or less attestable genealogies. The case of the Balş family is one of the most interesting: trying to integrate in the political structures of the Austrian and Russian Empire, some members of this old Moldavian family invent a fictitious genealogy that links the French counts of Baux, the Balsa family, a Serbian medieval dynasty and the Balş family, Moldavian boyars.

Gaussian process-based Bayesian nonparametric inference of population size trajectories from gene genealogies.

Science.gov (United States)

Palacios, Julia A; Minin, Vladimir N

2013-03-01

Changes in population size influence genetic diversity of the population and, as a result, leave a signature of these changes in individual genomes in the population. We are interested in the inverse problem of reconstructing past population dynamics from genomic data. We start with a standard framework based on the coalescent, a stochastic process that generates genealogies connecting randomly sampled individuals from the population of interest. These genealogies serve as a glue between the population demographic history and genomic sequences. It turns out that only the times of genealogical lineage coalescences contain information about population size dynamics. Viewing these coalescent times as a point process, estimating population size trajectories is equivalent to estimating a conditional intensity of this point process. Therefore, our inverse problem is similar to estimating an inhomogeneous Poisson process intensity function. We demonstrate how recent advances in Gaussian process-based nonparametric inference for Poisson processes can be extended to Bayesian nonparametric estimation of population size dynamics under the coalescent. We compare our Gaussian process (GP) approach to one of the state-of-the-art Gaussian Markov random field (GMRF) methods for estimating population trajectories. Using simulated data, we demonstrate that our method has better accuracy and precision. Next, we analyze two genealogies reconstructed from real sequences of hepatitis C and human Influenza A viruses. In both cases, we recover more believed aspects of the viral demographic histories than the GMRF approach. We also find that our GP method produces more reasonable uncertainty estimates than the GMRF method. Copyright © 2013, The International Biometric Society.

Sorted gene genealogies and species-specific nonsynonymous substitutions point to putative postmating prezygotic isolation genes in Allonemobius crickets

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Suegene Noh

2016-02-01

Full Text Available In the Allonemobius socius complex of crickets, reproductive isolation is primarily accomplished via postmating prezygotic barriers. We tested seven protein-coding genes expressed in the male ejaculate for patterns of evolution consistent with a putative role as postmating prezygotic isolation genes. Our recently diverged species generally lacked sequence variation. As a result, ω-based tests were only mildly successful. Some of our genes showed evidence of elevated ω values on the internal branches of gene trees. In a couple of genes, these internal branches coincided with both species branching events of the species tree, between A. fasciatus and the other two species, and between A. socius and A. sp. nov. Tex. In comparison, more successful approaches were those that took advantage of the varying degrees of lineage sorting and allele sharing among our young species. These approaches were particularly powerful within the contact zone. Among the genes we tested we found genes with genealogies that indicated relatively advanced degrees of lineage sorting across both allopatric and contact zone alleles. Within a contact zone between two members of the species complex, only a subset of genes maintained allelic segregation despite evidence of ongoing gene flow in other genes. The overlap in these analyses was arginine kinase (AK and apolipoprotein A-1 binding protein (APBP. These genes represent two of the first examples of sperm maturation, capacitation, and motility proteins with fixed non-synonymous substitutions between species-specific alleles that may lead to postmating prezygotic isolation. Both genes express ejaculate proteins transferred to females during copulation and were previously identified through comparative proteomics. We discuss the potential function of these genes in the context of the specific postmating prezygotic isolation phenotype among our species, namely conspecific sperm precedence and the superior ability of

Genetic structure and gene flows within horses: a genealogical study at the french population scale.

Science.gov (United States)

Pirault, Pauline; Danvy, Sophy; Verrier, Etienne; Leroy, Grégoire

2013-01-01

Since horse breeds constitute populations submitted to variable and multiple outcrossing events, we analyzed the genetic structure and gene flows considering horses raised in France. We used genealogical data, with a reference population of 547,620 horses born in France between 2002 and 2011, grouped according to 55 breed origins. On average, individuals had 6.3 equivalent generations known. Considering different population levels, fixation index decreased from an overall species FIT of 1.37%, to an average [Formula: see text] of -0.07% when considering the 55 origins, showing that most horse breeds constitute populations without genetic structure. We illustrate the complexity of gene flows existing among horse breeds, a few populations being closed to foreign influence, most, however, being submitted to various levels of introgression. In particular, Thoroughbred and Arab breeds are largely used as introgression sources, since those two populations explain together 26% of founder origins within the overall horse population. When compared with molecular data, breeds with a small level of coancestry also showed low genetic distance; the gene pool of the breeds was probably impacted by their reproducer exchanges.

[Clinical genealogical and molecular genetic study of patients with mental retardation].

Science.gov (United States)

Hryshchenko, N V; B'ichkova, A M; Lyvshyts, A B; Kravchenko, S A; Pampukha, V N; Solov'ev, A A; Kucherenko, A M; Tatarskiĭ, P F; Afanas'eva, N A; Dubrovskaia, E V; Patskun, Ie Y; Zymak-Zakutnaia, N O; Nykytchina, T V; Lohysh, S Iu; Lyvshyts, L A

2012-01-01

The results of clinical, genealogical, cytogenetic and molecular genetic studies of 113 patients from 96 families with different forms of mental retardation from Ukraine are presented. This study was held as part of the CHERISH project of the 7-th Framework Program. The aim of the project is to improve diagnostics of mental retardation in children in Eastern Europe and Central Asia through detailed analysis of known chromosomal and gene's aberrations and to find the new gene-candidates that cause mental retardation. All patients have normal chromosome number (46XY or 46XX). The cases with fragile-X syndrome were eliminated using molecular genetic methods. Genome rearrangements were found among 28 patients using cytogenetic analysis, multiplex ligation-dependent probe amplification (MLPA analysis) ofsubtelomeric regions and array-based comparative genomic hybridisation (array CGH screening). In 10 cases known pathogenic CNV's were identified, 11 cases are unknown aberrations; their pathogenicity is being determined. The rest cases are known nonpathogenic gene rearrangements. Obtained results show the strong genetic heterogeneity of hereditary forms of mental retardation. The further studies will allow to identificate genes candidates and certain mutations in these genes that may be associated with this pathology.

38 CFR 1.505 - Genealogy.

Science.gov (United States)

2010-07-01

... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Genealogy. 1.505 Section 1.505 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS GENERAL PROVISIONS Release of Information from Department of Veterans Affairs Claimant Records § 1.505 Genealogy. Information...

Foucault, Maoism, Genealogy

DEFF Research Database (Denmark)

Karlsen, Mads Peter; Villadsen, Kaspar

2015-01-01

and his critique of “totalizing institutions,” “uniform discourse” and “juridical universality.” The second part of the article offers a close reading of Foucault’s reflections on genealogy in his 1976 lecture series which demonstrates how the Maoist activist principles noticeably resonate...... often portrayed as unambiguously negative. And third, the goal is to demonstrate how principles developed in Maoist political activism are not only realized in Foucault’s activities within the GIP, but also in his lecture-hall formulations of genealogy, power, and critique....

[Fragments of a health work genealogy: genealogy as a research technique].

Science.gov (United States)

Nardi, Henrique Caetano; Tittoni, Jaqueline; Giannechini, Letícia; Ramminger, Tatiana

2005-01-01

The article aims to explore the influence of health work in subjectification processes. The notion of history commonly used in health-related scientific output is based on an evolutionist and developmental logic. As a counterpoint, the genealogical approach used in this article and based on Michel Foucault highlights the notions of discontinuity, event, and the production of truth as tools to rethink the ethical and political implications involved in the production of knowledge, practices, and subjects. To illustrate these aspects we sketch a health work genealogy, specifically in the field of mental health and HIV/AIDS work.

Genetic structure and gene flows within horses: a genealogical study at the french population scale.

Directory of Open Access Journals (Sweden)

Pauline Pirault

Full Text Available Since horse breeds constitute populations submitted to variable and multiple outcrossing events, we analyzed the genetic structure and gene flows considering horses raised in France. We used genealogical data, with a reference population of 547,620 horses born in France between 2002 and 2011, grouped according to 55 breed origins. On average, individuals had 6.3 equivalent generations known. Considering different population levels, fixation index decreased from an overall species FIT of 1.37%, to an average [Formula: see text] of -0.07% when considering the 55 origins, showing that most horse breeds constitute populations without genetic structure. We illustrate the complexity of gene flows existing among horse breeds, a few populations being closed to foreign influence, most, however, being submitted to various levels of introgression. In particular, Thoroughbred and Arab breeds are largely used as introgression sources, since those two populations explain together 26% of founder origins within the overall horse population. When compared with molecular data, breeds with a small level of coancestry also showed low genetic distance; the gene pool of the breeds was probably impacted by their reproducer exchanges.

Genealogical series method. Hyperpolar points screen effect

International Nuclear Information System (INIS)

Gorbatov, A.M.

1991-01-01

The fundamental values of the genealogical series method -the genealogical integrals (sandwiches) have been investigated. The hyperpolar points screen effect has been found. It allows one to calculate the sandwiches for the Fermion systems with large number of particles and to ascertain the validity of the iterated-potential method as well. For the first time the genealogical-series method has been realized numerically for the central spin-independent potential

Genealogical information and the structure of rural Latin-American populations: reality and fantasy.

Science.gov (United States)

Castilla, E E; Adams, J

1996-01-01

Genetic data organized in the form of genealogies can provide much information regarding the history and genetic structure of human populations. A large proportion of the population of Latin America is organized in small rural semi-isolated communities, with little immigration, and until the last 50-100 years, little emigration. These communities have a strong sense of their genealogical history, and this "genealogical conscience' is a frequent leitmotif in modern Latin-American literature. In this communication, we compare the characteristics of fictitious genealogies described in two masterpieces of Latin-American literature, García Márquez' Cien Años de Soledad (A Hundred Years of Solitude), and Verissimo's O Tempo e o Vento (Time and the Wind), with one existing well-studied population in Argentina, Aicuña. All three populations exhibit a number of common characteristics, such as histories of long periods of civil war, and large pedigrees with complex paths of inheritance resulting in complex patterns of inbreeding. Genetic themes common to all three are: (1) the use of genealogical records to substantiate the property of the land or the political power of a kinship; (2) the genealogical registry of biological descendants, independent of their legal or marital status in the clan; (3) the existence of pedigrees of the aristocratic branches in the same kindreds, which illustrate the legal principle of primogeniture; (4) the value of last names as indicators of kinships and the extent of genetic isolation, and (5) the awareness of the deleterious consequences of consanguinity.

The Astronomy Genealogy Project

Science.gov (United States)

Tenn, Joseph S.

2014-01-01

The Astronomy Genealogy Project, to be known as AstroGen, will list as many as possible of the world's astronomers with their academic parents (aka thesis advisors) and enable the reader to trace both academic ancestors and descendants. It will be very similar to the highly successful Mathematics Genealogy Project (MGP), available at http://genealogy.math.ndsu.nodak.edu. The MGP, which has been in operation since 1996, now contains the names of about 170,000 "mathematicians." These include many physicists and astronomers, as well as practitioners of related sciences. Mitchel Keller, the director of the MGP, has generously shared the software used in that project, and the American Astronomical Society (AAS) will host AstroGen, a project of the Historical Astronomy Division, on its website. We expect to start seeking entries soon, depending on the availability of computational assistance from the AAS IT department. We are seeking volunteers to help run the project. If you are interested, please contact me at joe.tenn@sonoma.edu.

Genealogical analyses in open populations: the case of three Arab-derived Spanish horse breeds.

Science.gov (United States)

Cervantes, I; Gutiérrez, J P; Molina, A; Goyache, F; Valera, M

2009-10-01

This research assesses the genetic composition of three Arab-derived Spanish horse breeds as an example to highlight the major shortcomings related to genealogical analyses in open populations and to propose approaches useful to deal with this task. The studbooks of three Spanish Arab (SA)-derived horse breeds, Spanish Anglo-Arab (dAA), Hispano-Arab (dHA) and Spanish Sport Horse (dSSH) and those of their parental breeds SA, Spanish Purebred (SPB) and Thoroughbred (TB), totalling 211 754 individuals, were available. The genealogies of the dAA, dHA and dSSH were analysed not only using the corresponding studbook (breed exclusive dataset) but also including the genealogies of the founders from parental breeds (completed dataset). Coancestry analyses revealed that the present SA-derived populations share more genes with the Arab than with the other parental breeds. Effective population size was computed by accounting for migration rates to obtain an equivalent closed-population effective size ((eq)N(e)) of 39.2 for the dAA, 56.3 for dHA and 114.1 for dSSH. The essayed methodologies were useful for characterising populations involving migration. The consequences of the management of the analysed breeds are discussed. The results emphasize the need to include the complete genealogies of the individuals to attain reliable genealogical parameters.

To Alleviate or Elevate the Euroamerican Genealogy Fever

Directory of Open Access Journals (Sweden)

Iain Riddell

2018-03-01

Full Text Available There has been a quiet cultural drift towards professionalism in genealogy over the last two decades. Developments in the UK on this subject have resulted in educational offerings that support professionalism through accountability to service consumers while a US debate has pushed for a recognised and regarded scholarship to underpin the professional genealogist. This article places the educational and learning needs of three broad groups of genealogists into the framework of the professional debate in its generality and genealogical specifics. With a concentration on the British context, the article considers the cultural–commercial signals and support offered to ‘armchair enthusiasts’; the emerging models of professional education and formation aimed at lineage makers and the ongoing fractured models of scholastic genealogy. Looking ahead at educational needs, genealogy like other professions is now under threat from advances in artificial intelligence and algorithms, which could slice through the underpinnings of genealogical professionalism. The article concludes with a discussion of an alternative approach to genealogical education derived from the proposition that professionalism is to be found in the outputs and outcomes rather than the organisation of the practitioners of economic activity. From this stance, the needs of a full range of people pursuing genealogy can be addressed and their work informed by the developing understanding of Euroamerican kinship.

[Genetic aspects of genealogy].

Science.gov (United States)

Tetushkin, E Iu

2011-11-01

The supplementary historical discipline genealogy is also a supplementary genetic discipline. In its formation, genetics borrowed from genealogy some methods of pedigree analysis. In the 21th century, it started receiving contribution from computer-aided genealogy and genetic (molecular) genealogy. The former provides novel tools for genetics, while the latter, which employing genetic methods, enriches genetics with new evidence. Genealogists formulated three main laws ofgenealogy: the law of three generations, the law of doubling the ancestry number, and the law of declining ancestry. The significance and meaning of these laws can be fully understood only in light of genetics. For instance, a controversy between the exponential growth of the number of ancestors of an individual, i.e., the law of doubling the ancestry number, and the limited number of the humankind is explained by the presence of weak inbreeding because of sibs' interference; the latter causes the pedigrees' collapse, i.e., explains also the law of diminishing ancestry number. Mathematic modeling of pedigrees' collapse presented in a number of studies showed that the number of ancestors of each individual attains maximum in a particular generation termed ancestry saturated generation. All representatives of this and preceding generation that left progeny are common ancestors of all current members of the population. In subdivided populations, these generations are more ancient than in panmictic ones, whereas in small isolates and social strata with limited numbers of partners, they are younger. The genealogical law of three generations, according to which each hundred years contain on average three generation intervals, holds for generation lengths for Y-chromosomal DNA, typically equal to 31-32 years; for autosomal and mtDNA, this time is somewhat shorter. Moving along ascending lineas, the number of genetically effective ancestors transmitting their DNA fragment to descendants increases far

Legendary genealogies of Byzantine Emperors and their families

Directory of Open Access Journals (Sweden)

Krsmanović Bojana T.

2004-01-01

a rule, the genealogies postulate a kinship with him, often confirming it with the alleged physical resemblance. Depending on the purpose of the genealogy, certain purported features of Constantine's character were emphasized, so that he is alternately mentioned as a protector of the Christian faith, a triumphant military leader, or as a wise administrator of the Empire. Apart from that, the motifs of founding the new Capital and the migration of the Roman patrician families to Constantinople represent important topoi in this literary genre. The two most fascinating specimens of legendary genealogies in the Byzantine literature — those of Basil I the Macedonian and Nikephoros III Botaneiates — show that the choice of the elements of which the genealogy is composed (personality, family, dynasty is at the same time a strong indication of the reason why it was composed in the first place. The genealogy of Basil the Macedonian was doubtlessly conceived by more than one person. It is quite certain that the idea to compose it originally came from Photios and was taken over by Basil's descendents — his son Leo VI and his grandson Constantine VII Porphyrogennetos. The core of Basil's legendary genealogy is the story of his origin from the Parthian-Armenian dynasty of Arsacids (an indication of the Armenian origin of the founder of the Macedonian dynasty?. Constantine Porphyrogennetos elaborated this story further, describing in some detail the fate of Arsac's descendents, to whom Basil was allegedly related on his father's side, in the Byzantine Empire. This, of course, does not mean that he forgot to create connections between his grandfather and the standard legendary ancestors, like Constantine the Great (on Basil's mother's side and Alexander the Great (the common ancestors of both Basil's parents. This apocryphal family tree certainly has its roots in the fact that the founder of the Macedonian dynasty was a parvenu of low origin, whose ascent to the throne was

Comparing models on the genealogical relationships among Neandertal, Cro-Magnoid and modern Europeans by serial coalescent simulations.

Science.gov (United States)

Belle, E M S; Benazzo, A; Ghirotto, S; Colonna, V; Barbujani, G

2009-03-01

Populations of anatomically archaic (Neandertal) and early modern (Cro-Magnoid) humans are jointly documented in the European fossil record, in the period between 40 000 and 25 000 years BP, but the large differences between their cultures, morphologies and DNAs suggest that the two groups were not close relatives. However, it is still unclear whether any genealogical continuity between them can be ruled out. Here, we simulated a broad range of demographic scenarios by means of a serial coalescence algorithm in which Neandertals, Cro-Magnoids and modern Europeans were either part of the same mitochondrial genealogy or of two separate genealogies. Mutation rates, population sizes, population structure and demographic growth rates varied across simulations. All models in which anatomically modern (that is, Cro-Magnoid and current) Europeans belong to a distinct genealogy performed better than any model in which the three groups were assigned to the same mitochondrial genealogy. The maximum admissible level of gene flow between Neandertals and the ancestors of current Europeans is 0.001% per generation, one order of magnitude lower than estimated in previous studies not considering genetic data on Cro-Magnoid people.

Gene genealogies indicates abundant gene conversions and independent evolutionary histories of the mating-type chromosomes in the evolutionary history of Neurospora tetrasperma

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Whittle Carrie A

2010-07-01

Full Text Available Abstract Background The self-fertile filamentous ascomycete Neurospora tetrasperma contains a large (~7 Mbp and young (mat chromosomes. The objective of the present study is to reveal the evolutionary history, including key genomic events, associated with the various regions of the mat chromosomes among ten strains representing all the nine known species (lineages contained within the N. tetrasperma species complex. Results Comparative analysis of sequence divergence among alleles of 24 mat-linked genes (mat A and mat a indicates that a large region of suppressed recombination exists within the mat chromosome for each of nine lineages of N. tetrasperma sensu latu. The recombinationally suppressed region varies in size and gene composition among lineages, and is flanked on both ends by normally recombining regions. Genealogical analyses among lineages reveals that eight gene conversion events have occurred between homologous mat A and mat a-linked alleles of genes located within the region of restricted recombination during the evolutionary history of N. tetrasperma. Conclusions We conclude that the region of suppressed recombination in the mat chromosomes has likely been subjected to independent contraction and/or expansion during the evolutionary history of the N. tetrasperma species complex. Furthermore, we infer that gene conversion events are likely a common phenomenon within this recombinationally suppressed genomic region. We argue that gene conversions might provide an efficient mechanism of adaptive editing of functional genes, including the removal of deleterious mutations, within the young recombinationally suppressed region of the mat chromosomes.

A Multigene Approach for Comparing Genealogy of Betacoronavirus from Cattle and Horses

Directory of Open Access Journals (Sweden)

Iracema N. Barros

2013-01-01

Full Text Available Gastroenteritis is one of the leading causes of morbidity and mortality among young and newborn animals and is often caused by multiple intestinal infections, with rotavirus and bovine coronavirus (BCoV being the main viral causes in cattle. Given that BCoV is better studied than equine coronaviruses and given the possibility of interspecies transmission of these viruses, this research was designed to compare the partial sequences of the spike glycoprotein (S, hemagglutinin-esterase protein (HE, and nucleoprotein (N genes from coronaviruses from adult cattle with winter dysentery, calves with neonatal diarrhea, and horses. To achieve this, eleven fecal samples from dairy cows with winter dysentery, three from calves, and two from horses, all from Brazil, were analysed. It could be concluded that the enteric BCoV genealogy from newborn and adult cattle is directly associated with geographic distribution patterns, when S and HE genes are taken into account. A less-resolved genealogy exists for the HE and N genes in cattle, with a trend for an age-related segregation pattern. The coronavirus strains from horses revealed Betacoronavirus sequences indistinguishable from those found in cattle, a fact previously unknown.

Til kulturhistoriens genealogi

Directory of Open Access Journals (Sweden)

Tine Damsholt

2010-11-01

Full Text Available Hvad er kulturhistorie? Dette retoriske spørgsmål stillede en af dansk kulturhistories faddere Troels Troels-Lund allerede på tærsklen til det 20. århundrede og gav sit eget veloplagte og polemiske svar, hvor han hyldede dagliglivets historie frem for staternes og krigenes historie. Men er dette svar - såvel som spørgsmålet - stadig relevant i det 21. århundrede? I det følgende skal vi se lidt nærmere på, hvad det særligt er kulturhistorie kan, og hvorvidt og hvordan den adskiller sigfra den almindelige historie.Abstract: The Genealogy of Cultural HistoryWhat is cultural history? The paper discusses whether cultural history still should be defined by having a specific empirical object such as the history of everyday life. Taking the point of departure in the current mainstreaming of cultural history and topics outside political history within the discipline of history after the cultural turn, it is argued that cultural history should rather be a specific analytical strategy. The paper investigates the Foucauldian notion of genealogy or "history of the present" and proposes an understanding of cultural history asan analytical strategy that seeks to destabilize a present that has forgotten its contingency and the time-bound questions that gave rise to its beliefs and practices. Genealogy is therefore about tracing the heterogeneous pathways that led to the apparent solidity of the present. A first sketch to a genealogy of cultural history in Denmark is given through a discussion of the canonized text by T. Troels-Lund, On Cultural History from 1894. The idea of everyday life as the analytical and defining object of cultural history is constituted in this text as well as in the disciplinary battles that formed the situational background for Troels-Lunds argument. Instead of taking this situated definition for a given fact cultural history is - in the tradition from Foucault - understood as a critical, destabilizing and thus self

On finding algebraic expressions for genealogical coefficients

International Nuclear Information System (INIS)

Kanyauskas, J.M.; Shimonis, V.Ch.; Rudzikas, Z.B.

1979-01-01

It has been attempted to obtain analytical expressions for genealogical coefficients with one detached electron in the case of L-S coupling. A method of second quantization and tensorial properties of the quasi-spin operator are applied. It is restricted to the states for the classification of which the seigniority quantum number v is sufficient. Three ways of the acquirement of these expressions are discussed: 1. In the recurrent way wave functions of N and N-1 electrons are built, consequently expressing these functions in terms of the creation-annihilation operators. 2. Recurrent summation with the use of evident, simple genealogical coefficients. 3. Using the ratios, connecting the genealogical coefficients with the normalized multiplier. The data are presented in formulae and discussions. The generalization of the Redmond's formula is obtained and relatively simple algebraic expressions of the genealogical coefficients of the equivalent electron configurations, for the distinction of the recurrent terms of which introduction of the seigniority quantum number v is sufficient, are given

Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees.

Science.gov (United States)

Zhu, Sha; Degnan, James H; Goldstien, Sharyn J; Eldon, Bjarki

2015-09-15

There has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously. Hybrid-Lambda is a software package that simulates gene genealogies under multiple merger and Kingman's coalescent processes within species networks or species trees. Hybrid-Lambda allows different coalescent processes to be specified for different populations, and allows for time to be converted between generations and coalescent units, by specifying a population size for each population. In addition, Hybrid-Lambda can generate simulated datasets, assuming the infinitely many sites mutation model, and compute the F ST statistic. As an illustration, we apply Hybrid-Lambda to infer the time of subdivision of certain marine invertebrates under different coalescent processes. Hybrid-Lambda makes it possible to investigate biogeographic concordance among high fecundity species exhibiting skewed offspring distribution.

Narrative Reflection in the Philosophy of Teaching: Genealogies and Portraits

Science.gov (United States)

McEwan, Hunter

2011-01-01

How has philosophical reflection contributed to the ways that we think about teaching? In this paper I explore two forms of narrative reflection on teaching--genealogies and portraits. Genealogies tell a story about the origins of teaching; portraits find expression in myths and other narrative forms. I explore two genealogies of teaching--one…

The effect of genealogy-based haplotypes on genomic prediction

DEFF Research Database (Denmark)

Edriss, Vahid; Fernando, Rohan L.; Su, Guosheng

2013-01-01

on haplotypes instead of regression on individual markers. The aim of this study was to investigate the accuracy of genomic prediction using haplotypes based on local genealogy information. Methods A total of 4429 Danish Holstein bulls were genotyped with the 50K SNP chip. Haplotypes were constructed using...... local genealogical trees. Effects of haplotype covariates were estimated with two types of prediction models: (1) assuming that effects had the same distribution for all haplotype covariates, i.e. the GBLUP method and (2) assuming that a large proportion (pi) of the haplotype covariates had zero effect......, i.e. a Bayesian mixture method. Results About 7.5 times more covariate effects were estimated when fitting haplotypes based on local genealogical trees compared to fitting individuals markers. Genealogy-based haplotype clustering slightly increased the accuracy of genomic prediction and, in some...

Modeling the genealogy of a cultural trait.

Science.gov (United States)

Aguilar, Elliot; Ghirlanda, Stefano

2015-05-01

The mathematical study of genealogies has yielded important insights in population biology, such as the ability to estimate the time to the most recent common ancestor (MRCA) of a sample of genetic sequences or of a group of individuals. Here we introduce a model of cultural genealogies that is a step toward answering similar questions for cultural traits. In our model individuals can inherit from a variable, potentially large number of ancestors, rather than from a fixed, small number of ancestors (one or two) as is typical of genetic evolution. We first show that, given a sample of individuals, a cultural common ancestor does not necessarily exist. We then introduce a related concept: the most recent unique ancestor (MRUA), i.e., the most recent single individual who is the earliest cultural ancestor of the sample. We show that, under neutral evolution, the time to the MRUA can be staggeringly larger than the time to MRCA in a single ancestor model, except when the average number of learning opportunities per individuals is small. Our results point out that the properties of cultural genealogies may be very different from those of genetic genealogies, with potential implications for reconstructing the histories of cultural traits. Copyright © 2014 Elsevier Inc. All rights reserved.

An interactive, web-based tool for genealogical entity resolution

NARCIS (Netherlands)

Efremova, I.; Ranjbar-Sahraei, B.; Oliehoek, F.A.; Calders, T.G.K.; Tuyls, K.P.

2013-01-01

We demonstrate an interactive, web-based tool which helps historians to do Genealogical Entitiy Resolution. This work has two main goals. First, it uses Machine Learning (ML) algorithms to assist humanites researchers to perform Genealogical Entity Resolution. Second, it facilitates the generation

The effect of using genealogy-based haplotypes for genomic prediction.

Science.gov (United States)

Edriss, Vahid; Fernando, Rohan L; Su, Guosheng; Lund, Mogens S; Guldbrandtsen, Bernt

2013-03-06

Genomic prediction uses two sources of information: linkage disequilibrium between markers and quantitative trait loci, and additive genetic relationships between individuals. One way to increase the accuracy of genomic prediction is to capture more linkage disequilibrium by regression on haplotypes instead of regression on individual markers. The aim of this study was to investigate the accuracy of genomic prediction using haplotypes based on local genealogy information. A total of 4429 Danish Holstein bulls were genotyped with the 50K SNP chip. Haplotypes were constructed using local genealogical trees. Effects of haplotype covariates were estimated with two types of prediction models: (1) assuming that effects had the same distribution for all haplotype covariates, i.e. the GBLUP method and (2) assuming that a large proportion (π) of the haplotype covariates had zero effect, i.e. a Bayesian mixture method. About 7.5 times more covariate effects were estimated when fitting haplotypes based on local genealogical trees compared to fitting individuals markers. Genealogy-based haplotype clustering slightly increased the accuracy of genomic prediction and, in some cases, decreased the bias of prediction. With the Bayesian method, accuracy of prediction was less sensitive to parameter π when fitting haplotypes compared to fitting markers. Use of haplotypes based on genealogy can slightly increase the accuracy of genomic prediction. Improved methods to cluster the haplotypes constructed from local genealogy could lead to additional gains in accuracy.

Genetic genealogy: the Woodson family's experience.

Science.gov (United States)

Williams, Sloan R

2005-06-01

In 1998, Foster and colleagues published the results of a genetic study intended to test whether Thomas Jefferson could have fathered any of Sally Hemings' children. They found that the Jefferson Y chromosome haplotype matched that of a descendant of Hemings' youngest child, but not that of the descendants of the eldest son, Thomas Woodson. The Woodson descendants were shocked by the study's finding, which disagreed with their family oral history. They were suspicious of the study conclusions because of the methods used in recruiting participants for the study and the manner in which they learned of the results. The Woodsons' experience as participants in one of the first examples of genetic genealogy illustrates several issues that both geneticists and amateur genetic genealogists will face in studies of this kind. Misperceptions about the relationship between biology and race, and group genetics in general, can make the interpretation of genetic data difficult. Continuing collaborations between the media and the scientific community will help the public to better understand the risks as well as the benefits of genetic genealogy. Researchers must decide prior to beginning their research what role the human subjects will play in the study and when they will be notified of the study's conclusions. Amateur genetic genealogists should anticipate unexpected outcomes, such as the identification of nonpaternity, to minimize any harmful effects to study participants. Although modern genetic methods provide a powerful new tool for genealogical study, they cannot resolve all genealogical issues, as this study shows, and can involve unanticipated risks to the participants.

Genealogical and evolutionary inference with the human Y chromosome.

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Stumpf, M P; Goldstein, D B

2001-03-02

Population genetics has emerged as a powerful tool for unraveling human history. In addition to the study of mitochondrial and autosomal DNA, attention has recently focused on Y-chromosome variation. Ambiguities and inaccuracies in data analysis, however, pose an important obstacle to further development of the field. Here we review the methods available for genealogical inference using Y-chromosome data. Approaches can be divided into those that do and those that do not use an explicit population model in genealogical inference. We describe the strengths and weaknesses of these model-based and model-free approaches, as well as difficulties associated with the mutation process that affect both methods. In the case of genealogical inference using microsatellite loci, we use coalescent simulations to show that relatively simple generalizations of the mutation process can greatly increase the accuracy of genealogical inference. Because model-free and model-based approaches have different biases and limitations, we conclude that there is considerable benefit in the continued use of both types of approaches.

Polyphyly and gene flow between non-sibling Heliconius species

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Jiggins Chris D

2006-04-01

Full Text Available Abstract Background The view that gene flow between related animal species is rare and evolutionarily unimportant largely antedates sensitive molecular techniques. Here we use DNA sequencing to investigate a pair of morphologically and ecologically divergent, non-sibling butterfly species, Heliconius cydno and H. melpomene (Lepidoptera: Nymphalidae, whose distributions overlap in Central and Northwestern South America. Results In these taxa, we sequenced 30–45 haplotypes per locus of a mitochondrial region containing the genes for cytochrome oxidase subunits I and II (CoI/CoII, and intron-spanning fragments of three unlinked nuclear loci: triose-phosphate isomerase (Tpi, mannose-6-phosphate isomerase (Mpi and cubitus interruptus (Ci genes. A fifth gene, dopa decarboxylase (Ddc produced sequence data likely to be from different duplicate loci in some of the taxa, and so was excluded. Mitochondrial and Tpi genealogies are consistent with reciprocal monophyly, whereas sympatric populations of the species in Panama share identical or similar Mpi and Ci haplotypes, giving rise to genealogical polyphyly at the species level despite evidence for rapid sequence divergence at these genes between geographic races of H. melpomene. Conclusion Recent transfer of Mpi haplotypes between species is strongly supported, but there is no evidence for introgression at the other three loci. Our results demonstrate that the boundaries between animal species can remain selectively porous to gene flow long after speciation, and that introgression, even between non-sibling species, can be an important factor in animal evolution. Interspecific gene flow is demonstrated here for the first time in Heliconius and may provide a route for the transfer of switch-gene adaptations for Müllerian mimicry. The results also forcefully demonstrate how reliance on a single locus may give an erroneous picture of the overall genealogical history of speciation and gene flow.

The Genealogical Consequences of Fecundity Variance Polymorphism

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Taylor, Jesse E.

2009-01-01

The genealogical consequences of within-generation fecundity variance polymorphism are studied using coalescent processes structured by genetic backgrounds. I show that these processes have three distinctive features. The first is that the coalescent rates within backgrounds are not jointly proportional to the infinitesimal variance, but instead depend only on the frequencies and traits of genotypes containing each allele. Second, the coalescent processes at unlinked loci are correlated with the genealogy at the selected locus; i.e., fecundity variance polymorphism has a genomewide impact on genealogies. Third, in diploid models, there are infinitely many combinations of fecundity distributions that have the same diffusion approximation but distinct coalescent processes; i.e., in this class of models, ancestral processes and allele frequency dynamics are not in one-to-one correspondence. Similar properties are expected to hold in models that allow for heritable variation in other traits that affect the coalescent effective population size, such as sex ratio or fecundity and survival schedules. PMID:19433628

Philological Remarks on Two Genealogies of the Crimean-Tatar Clan Shirin

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Göncöl Cs.

2017-12-01

Full Text Available Objectives: Philological analysis of two genealogies of the Crimean-Tatar clan termed the Shirin, and an identification of a possible common source of these genealogies. Research materials: Two genealogies (family-trees of the most prominent clan of the Crimean Khanate, the Shirin, have survived. The earlier one was preserved in the chronicle of the ʿUmdetü l aḫbār ‘Essence of Histories’ (1748, written by ʿAbdu l Ġaffār Qırımī, a historian of the Crimean Khanate and judge on Shirin estates. The later one was presented by clan-members after 1807 to the Crimean Assembly of Nobility (Таврическое дворянское собрание for the recognition of their noble status and estates. This version was translated into Russian and published by Lashkov. Therefore, the question arises: can the two genealogies have a common source? Results and the novelty of the research: Through a philological comparison of the material, the aim of the author was to demonstrate that the genealogies of the Shirin clan show similarities in content, structure, and text. The author supposes that the texts of ʿAbdu l Ġaffār Qırımī and the genealogy preserved in Russian translation could have been compiled from the same source, perhaps a preliminary Shirin genealogy which, judging from its content, the author dates to the 1660s.

The performance of phylogenetic algorithms in estimating haplotype genealogies with migration.

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Salzburger, Walter; Ewing, Greg B; Von Haeseler, Arndt

2011-05-01

Genealogies estimated from haplotypic genetic data play a prominent role in various biological disciplines in general and in phylogenetics, population genetics and phylogeography in particular. Several software packages have specifically been developed for the purpose of reconstructing genealogies from closely related, and hence, highly similar haplotype sequence data. Here, we use simulated data sets to test the performance of traditional phylogenetic algorithms, neighbour-joining, maximum parsimony and maximum likelihood in estimating genealogies from nonrecombining haplotypic genetic data. We demonstrate that these methods are suitable for constructing genealogies from sets of closely related DNA sequences with or without migration. As genealogies based on phylogenetic reconstructions are fully resolved, but not necessarily bifurcating, and without reticulations, these approaches outperform widespread 'network' constructing methods. In our simulations of coalescent scenarios involving panmictic, symmetric and asymmetric migration, we found that phylogenetic reconstruction methods performed well, while the statistical parsimony approach as implemented in TCS performed poorly. Overall, parsimony as implemented in the PHYLIP package performed slightly better than other methods. We further point out that we are not making the case that widespread 'network' constructing methods are bad, but that traditional phylogenetic tree finding methods are applicable to haplotypic data and exhibit reasonable performance with respect to accuracy and robustness. We also discuss some of the problems of converting a tree to a haplotype genealogy, in particular that it is nonunique. © 2011 Blackwell Publishing Ltd.

Bio science: genetic genealogy testing and the pursuit of African ancestry.

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Nelson, Alondra

2008-10-01

This paper considers the extent to which the geneticization of 'race' and ethnicity is the prevailing outcome of genetic testing for genealogical purposes. The decoding of the human genome precipitated a change of paradigms in genetics research, from an emphasis on genetic similarity to a focus on molecular-level differences among individuals and groups. This shift from lumping to splitting spurred ongoing disagreements among scholars about the significance of 'race' and ethnicity in the genetics era. I characterize these divergent perspectives as 'pragmatism' and 'naturalism'. Drawing upon ethnographic fieldwork and interviews, I argue that neither position fully accounts for how understandings of 'race' and ethnicity are being transformed with genetic genealogy testing. While there is some acquiescence to genetic thinking about ancestry, and by implication, 'race', among African-American and black British consumers of genetic genealogy testing, test-takers also adjudicate between sources of genealogical information and from these construct meaningful biographical narratives. Consumers engage in highly situated 'objective' and 'affiliative' self-fashioning, interpreting genetic test results in the context of their 'genealogical aspirations'. I conclude that issues of site, scale, and subjectification must be attended to if scholars are to understand whether and to what extent social identities are being transformed by recent developments in genetic science.

Single and simultaneous binary mergers in Wright-Fisher genealogies.

Science.gov (United States)

Melfi, Andrew; Viswanath, Divakar

2018-05-01

The Kingman coalescent is a commonly used model in genetics, which is often justified with reference to the Wright-Fisher (WF) model. Current proofs of convergence of WF and other models to the Kingman coalescent assume a constant sample size. However, sample sizes have become quite large in human genetics. Therefore, we develop a convergence theory that allows the sample size to increase with population size. If the haploid population size is N and the sample size is N 1∕3-ϵ , ϵ>0, we prove that Wright-Fisher genealogies involve at most a single binary merger in each generation with probability converging to 1 in the limit of large N. Single binary merger or no merger in each generation of the genealogy implies that the Kingman partition distribution is obtained exactly. If the sample size is N 1∕2-ϵ , Wright-Fisher genealogies may involve simultaneous binary mergers in a single generation but do not involve triple mergers in the large N limit. The asymptotic theory is verified using numerical calculations. Variable population sizes are handled algorithmically. It is found that even distant bottlenecks can increase the probability of triple mergers as well as simultaneous binary mergers in WF genealogies. Copyright © 2018 Elsevier Inc. All rights reserved.

Emancipating Intellectual Property from Proprietarianism: Drahos, Foucault, and a Quasi-Genealogy of IP

Directory of Open Access Journals (Sweden)

Wendyl Luna

2018-01-01

Full Text Available This paper argues that Peter Drahos undertakes a partial Foucauldian genealogy by emancipating intellectual property (IP from proprietarianism. He demonstrates the dominance of proprietarianism in IP by drawing sample practices from trademark, copyright, and patent laws, and then seeks to displace the proprietarian dominance with instrumentalism, which reconstitutes IP as a “liberty-intruding privilege.” Ironically, despite doing a genealogy, Drahos does not eradicate sovereignty altogether as Michel Foucault insists, but instead determines IP as a “sovereignty mechanism” that has a “sovereignty effect.” After explaining what Foucauldian genealogy is, the paper will explain how Drahos undertakes a genealogy of IP, while highlighting the limitations of Drahos’ analysis from a Foucauldian perspective.

Genealogies in simple models of evolution

International Nuclear Information System (INIS)

Brunet, Éric; Derrida, Bernard

2013-01-01

We review the statistical properties of the genealogies of a few models of evolution. In the asexual case, selection leads to coalescence times which grow logarithmically with the size of the population, in contrast with the linear growth of the neutral case. Moreover for a whole class of models, the statistics of the genealogies are those of the Bolthausen–Sznitman coalescent rather than the Kingman coalescent in the neutral case. For sexual reproduction in the neutral case, the time to reach the first common ancestors for the whole population and the time for all individuals to have all their ancestors in common are also logarithmic in the population size, as predicted by Chang in 1999. We discuss how these times are modified by introducing selection in a simple way. (paper)

Genealogy and stability of periodic orbit families around uniformly rotating asteroids

Science.gov (United States)

Hou, Xiyun; Xin, Xiaosheng; Feng, Jinglang

2018-03-01

Resonance orbits around a uniformly rotating asteroid are studied from the approach of periodic orbits in this work. Three periodic families (denoted as I, II, and III in the paper) are fundamental in organizing the resonance families. For the planar case: (1) Genealogy and stability of Families I, II and the prograde resonance families are studied. For extremely irregular asteroids, family genealogy close to the asteroid is greatly distorted from that of the two body-problem (2BP), indicating that it is inappropriate to treat the orbital motions as perturbed Keplerian orbits. (2) Genealogy and stability of Family III are also studied. Stability of this family may be destroyed by the secular resonance between the orbital ascending node's precession and the asteroid's rotation. For the spatial case: (1) Genealogy of the near circular three-dimensional periodic families are studied. The genealogy may be broken apart by families of eccentric frozen orbits whose argument of perigee is ;frozen; in space. (2) The joint effects between the secular resonance and the orbital resonances may cause instability to three-dimensional orbital motion with orbit inclinations close to the critical values. Applying the general methodology to a case study - the asteroid Eros and also considering higher order non-spherical terms, some extraordinary orbits are found, such as the ones with orbital plane co-rotating with the asteroid, and the stable frozen orbits with argument of perigee librating around values different from 0°, 90°, 180°, 270°.

Genealogy as a critical toolbox: deconstructing the professional identity of nurses.

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Miró-Bonet, Margalida; Bover-Bover, Andreu; Moreno-Mulet, Cristina; Miró-Bonet, Rosa; Zaforteza-Lallemand, Concha

2014-04-01

To discuss the Foucauldian concept of genealogy as a framework for understanding and transforming nurses' professional identity. The professional identity of nurses has primarily been defined by personal and interpersonal attributes and by the intradisciplinary dimensions of nursing, leading to its conceptualization as a universal, monolithic phenomenon. The Foucauldian genealogical perspective offers a critical lens to examine what constitutes this professional identity; Spanish nursing offers a historical case study of an active effort to impose an identity that fits the monolithic ideal. Five of the 33 professional conduct manuals for nurses' training published from 1956-1976 during the Franco dictatorship in Spain and six interviews with nursing instructors or students at the time were analysed using a theoretical framework drawn from Foucault's writing. Foucault's genealogical framework considers practices of normalization and resistance as a means of understanding knowledge continuities and discontinuities, clarifying practices that constitute nurses' professional identity in a particular way in specific contexts and analysing the implications of this theoretical frame. The genealogy concept offers valuable tools to determine how professional identities are constituted, questions assumptions about the profession and its professionals and envisions alternative approaches. This theoretical approach helps both scholars and practitioners understand, question and transform their practices as needed. The genealogical approach prioritizes analysis of the phenomenon over its description and challenges many unknown, forgotten, excluded and/or unquestioned aspects of identity from a position of diversity and complexity. © 2013 John Wiley & Sons Ltd.

Impact of strong selection for the PrP major gene on genetic variability of four French sheep breeds (Open Access publication

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Pantano Thais

2008-11-01

Full Text Available Abstract Effective selection on the PrP gene has been implemented since October 2001 in all French sheep breeds. After four years, the ARR "resistant" allele frequency increased by about 35% in young males. The aim of this study was to evaluate the impact of this strong selection on genetic variability. It is focussed on four French sheep breeds and based on the comparison of two groups of 94 animals within each breed: the first group of animals was born before the selection began, and the second, 3–4 years later. Genetic variability was assessed using genealogical and molecular data (29 microsatellite markers. The expected loss of genetic variability on the PrP gene was confirmed. Moreover, among the five markers located in the PrP region, only the three closest ones were affected. The evolution of the number of alleles, heterozygote deficiency within population, expected heterozygosity and the Reynolds distances agreed with the criteria from pedigree and pointed out that neutral genetic variability was not much affected. This trend depended on breed, i.e. on their initial states (population size, PrP frequencies and on the selection strategies for improving scrapie resistance while carrying out selection for production traits.

Generation of genealogical spin eigenfunctions

International Nuclear Information System (INIS)

Grabenstetter, J.E.; Tseng, T.J.; Grein, F.

1976-01-01

A method is given for generating the Yamanouchi-Kotani genealogical spin eigenfunctions which requires neither storage of eigenfunctions for smaller numbers of electrons, nor summations of large order, nor explicit use of results from the theory of representations of the symmetric group. An explicit formula is given for the coefficients of expansion in terms of spin products

[Genealogy of the Meckel anatomy family (from Hem[b]sbach)].

Science.gov (United States)

Viebig, Michael; Schultka, Rüdiger

2002-11-01

The main goal of our investigations is to complete the genealogy of the famous Meckel dynasty. It is important to answer a lot of questions which have remained unanswered until now. During the investigations we were able to find the names of three children who died early and were dissected by their father Philipp Friedrich Theodor Meckel (1755-1803). Besides, it was possible to extend distinctly our knowledge of the various genealogical lines of the Meckel family.

Kinship and Beyond: The Genealogical Model Reconsidered

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Ryan Schram

2010-08-01

Full Text Available Review of Kinship and Beyond: The Genealogical Model Reconsidered. Sandra Bamford and James Leach, eds. 2009. Berghahn Books, New York. 292 pp., 21 illustrations, bibliography, index. $95.00 (hardback. ISBN 9781845454227.

Conditional Genealogies and the Age of a Neutral Mutant

DEFF Research Database (Denmark)

Wiuf, Carsten; Donelly, P

1999-01-01

This paper is concerned with the structure of the genealogy of a sample in which it is observed that some subset of chromosomes carries a particular mutation, assumed to have arisen uniquely in the history of the population. A rigorous theoretical study of this conditional genealogy is given using...... coalescent methods. Particular results include the mean, variance, and density of the age of the mutation conditional on its frequency in the sample. Most of the development relates to populations of constant size, but we discuss the extension to populations which have grown exponentially to their present...

"Lolita": Genealogy of a Cover Girl

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Savage, Shari L.

2015-01-01

At the publication of Vladimir Nabokov's controversial novel "Lolita" (1958), the author insisted that a girl never appear on the cover. This discourse analysis of 185 "Lolita" book covers, most of which feature a girl, considers the genealogy of "Lolita" in relation to representation, myth, and tacit knowledge…

The Color of Giftedness: A Policy Genealogy Implicating Educators Past, Present, and Future

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Mansfield, Katherine Cumings

2016-01-01

This article offers a critical rereading of gifted education in the United States using a genealogical framework as defined by postcolonial theory. Using genealogy is appropriate because it sets the education profession within a family research tradition, implies the close connection between past and present, and enables us to systematically trace…

Experimental estimation of mutation rates in a wheat population with a gene genealogy approach.

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Raquin, Anne-Laure; Depaulis, Frantz; Lambert, Amaury; Galic, Nathalie; Brabant, Philippe; Goldringer, Isabelle

2008-08-01

Microsatellite markers are extensively used to evaluate genetic diversity in natural or experimental evolving populations. Their high degree of polymorphism reflects their high mutation rates. Estimates of the mutation rates are therefore necessary when characterizing diversity in populations. As a complement to the classical experimental designs, we propose to use experimental populations, where the initial state is entirely known and some intermediate states have been thoroughly surveyed, thus providing a short timescale estimation together with a large number of cumulated meioses. In this article, we derived four original gene genealogy-based methods to assess mutation rates with limited bias due to relevant model assumptions incorporating the initial state, the number of new alleles, and the genetic effective population size. We studied the evolution of genetic diversity at 21 microsatellite markers, after 15 generations in an experimental wheat population. Compared to the parents, 23 new alleles were found in generation 15 at 9 of the 21 loci studied. We provide evidence that they arose by mutation. Corresponding estimates of the mutation rates ranged from 0 to 4.97 x 10(-3) per generation (i.e., year). Sequences of several alleles revealed that length polymorphism was only due to variation in the core of the microsatellite. Among different microsatellite characteristics, both the motif repeat number and an independent estimation of the Nei diversity were correlated with the novel diversity. Despite a reduced genetic effective size, global diversity at microsatellite markers increased in this population, suggesting that microsatellite diversity should be used with caution as an indicator in biodiversity conservation issues.

Fitchi: haplotype genealogy graphs based on the Fitch algorithm.

Science.gov (United States)

Matschiner, Michael

2016-04-15

: In population genetics and phylogeography, haplotype genealogy graphs are important tools for the visualization of population structure based on sequence data. In this type of graph, node sizes are often drawn in proportion to haplotype frequencies and edge lengths represent the minimum number of mutations separating adjacent nodes. I here present Fitchi, a new program that produces publication-ready haplotype genealogy graphs based on the Fitch algorithm. http://www.evoinformatics.eu/fitchi.htm : michaelmatschiner@mac.com Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Towards a complete North American Anabaptist Genealogy II: analysis of inbreeding.

Science.gov (United States)

Agarwala, R; Schäffer, A A; Tomlin, J F

2001-08-01

We describe a large genealogy data base, which can be searched by computer, of 295,095 Amish and Mennonite individuals. The data base was constructed by merging our existing Anabaptist Genealogy Database 2.0 containing approximately 85,000 individuals with a genealogy file containing approximately 242,000 individuals, kindly provided by Mr. James Hostetler. The merging process corrected thousands of inconsistencies and eliminated hundreds of duplicate individuals. Geneticists have long been interested in Anabaptist populations because they are closed and have detailed written genealogies. The creation of an enlarged and unified data base affords the opportunity to examine inbreeding trends and correlates in these populations. We show the following results. The frequency of consanguineous marriages shows steady increase over time and reached approximately 85% for individuals born in 1940-1959. Among consanguineous marriages, the median kinship coefficient stayed stable in the 19th century, but rose from 0.0115 to 0.0151 in the 20th century. There are statistically significant associations (p < 0.0001) between inbreeding and family size and interbirth intervals in the 20th century. There is an association (p < 0.0005) between inbreeding and early death for individuals born in 1920-1959. However, this association reverses dramatically (p < 0.0005 in the opposite direction) for individuals born in 1960-1979. We tested for an association between inbreeding and being the mother of twins, but found none.

A Genealogical Look at Shared Ancestry on the X Chromosome.

Science.gov (United States)

Buffalo, Vince; Mount, Stephen M; Coop, Graham

2016-09-01

Close relatives can share large segments of their genome identical by descent (IBD) that can be identified in genome-wide polymorphism data sets. There are a range of methods to use these IBD segments to identify relatives and estimate their relationship. These methods have focused on sharing on the autosomes, as they provide a rich source of information about genealogical relationships. We hope to learn additional information about recent ancestry through shared IBD segments on the X chromosome, but currently lack the theoretical framework to use this information fully. Here, we fill this gap by developing probability distributions for the number and length of X chromosome segments shared IBD between an individual and an ancestor k generations back, as well as between half- and full-cousin relationships. Due to the inheritance pattern of the X and the fact that X homologous recombination occurs only in females (outside of the pseudoautosomal regions), the number of females along a genealogical lineage is a key quantity for understanding the number and length of the IBD segments shared among relatives. When inferring relationships among individuals, the number of female ancestors along a genealogical lineage will often be unknown. Therefore, our IBD segment length and number distributions marginalize over this unknown number of recombinational meioses through a distribution of recombinational meioses we derive. By using Bayes' theorem to invert these distributions, we can estimate the number of female ancestors between two relatives, giving us details about the genealogical relations between individuals not possible with autosomal data alone. Copyright © 2016 by the Genetics Society of America.

Genetic genealogy comes of age: perspectives on the use of deep-rooted pedigrees in human population genetics.

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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.

The Total Somali Clan Genealogy (second edition)

NARCIS (Netherlands)

Abbink, G.J.

2009-01-01

This paper presents an updated genealogy of all Somali 'clans'. Somali kinship is based on patrilineal descent or 'tol', but there are no equivalents in the Somali language for the words 'clan' and 'lineage'. The Somali terminology for the levels of social segmentation is complex, amongst others

Modelling students' knowledge organisation: Genealogical conceptual networks

Science.gov (United States)

Koponen, Ismo T.; Nousiainen, Maija

2018-04-01

Learning scientific knowledge is largely based on understanding what are its key concepts and how they are related. The relational structure of concepts also affects how concepts are introduced in teaching scientific knowledge. We model here how students organise their knowledge when they represent their understanding of how physics concepts are related. The model is based on assumptions that students use simple basic linking-motifs in introducing new concepts and mostly relate them to concepts that were introduced a few steps earlier, i.e. following a genealogical ordering. The resulting genealogical networks have relatively high local clustering coefficients of nodes but otherwise resemble networks obtained with an identical degree distribution of nodes but with random linking between them (i.e. the configuration-model). However, a few key nodes having a special structural role emerge and these nodes have a higher than average communicability betweenness centralities. These features agree with the empirically found properties of students' concept networks.

Intercoalescence time distribution of incomplete gene genealogies in temporally varying populations, and applications in population genetic inference.

Science.gov (United States)

Chen, Hua

2013-03-01

Tracing back to a specific time T in the past, the genealogy of a sample of haplotypes may not have reached their common ancestor and may leave m lineages extant. For such an incomplete genealogy truncated at a specific time T in the past, the distribution and expectation of the intercoalescence times conditional on T are derived in an exact form in this paper for populations of deterministically time-varying sizes, specifically, for populations growing exponentially. The derived intercoalescence time distribution can be integrated to the coalescent-based joint allele frequency spectrum (JAFS) theory, and is useful for population genetic inference from large-scale genomic data, without relying on computationally intensive approaches, such as importance sampling and Markov Chain Monte Carlo (MCMC) methods. The inference of several important parameters relying on this derived conditional distribution is demonstrated: quantifying population growth rate and onset time, and estimating the number of ancestral lineages at a specific ancient time. Simulation studies confirm validity of the derivation and statistical efficiency of the methods using the derived intercoalescence time distribution. Two examples of real data are given to show the inference of the population growth rate of a European sample from the NIEHS Environmental Genome Project, and the number of ancient lineages of 31 mitochondrial genomes from Tibetan populations. © 2013 Blackwell Publishing Ltd/University College London.

A Baseline Method for Genealogical Entity Resolution

NARCIS (Netherlands)

Efremova, J.; Ranjbar-Sahraei, B.; Oliehoek, F.A.; Calders, T.; Tuyls, K.

2014-01-01

In this paper we study the application of entity resolution (ER) techniques on a real-world multi-source genealogical dataset. Our goal is to identify all persons involved in various notary acts and link them to their birth, marriage and death certificates. In order to evaluate the performance of a

"Safeguarding" Sports Coaching: Foucault, Genealogy and Critique

Science.gov (United States)

Garratt, Dean; Piper, Heather; Taylor, Bill

2013-01-01

This paper offers a genealogical account of safeguarding in sport. Drawing specifically on Foucault's work, it examines the "politics of touch" in relation to the social and historical formation of child protection policy in sports coaching. While the analysis has some resonance with the context of coaching as a whole, for illustrative…

The Astronomy Genealogy Project: A Progress Report

Science.gov (United States)

Tenn, Joseph S.

2016-01-01

Although it is not yet visible, much progress has been made on the Astronomy Genealogy Project (AstroGen) since it was accepted as a project of the Historical Astronomy Division (HAD) three years ago. AstroGen will list the world's astronomers with information about their highest degrees and advisors. (In academic genealogy, your thesis advisor is your parent.) A small group (the AstroGen Team) has compiled a database of approximately 12,000 individuals who have earned doctorates with theses (dissertations) on topics in astronomy, astrophysics, cosmology, or planetary science. These include nearly all those submitted in Australia, Canada, the Netherlands, and New Zealand, and most of those in the United States (all through 2014 for most universities and all through 1990 for all). We are compiling more information than is maintained by the Mathematics Genealogy Project (MGP). In addition to name, degree, university, year of degree, and thesis advisor(s), all provided by MGP as well, we are including years of birth and death when available, mentors in addition to advisors, and links to the thesis when it is online and to the person's web page or obituary, when we can find it. We are still struggling with some questions, such as the boundaries of inclusion and whether or not to include subfields of astronomy. We believe that AstroGen will be a valuable resource for historians of science as well as a source of entertainment for those who like to look up their academic family trees. A dedicated researcher following links from AstroGen will be able to learn quite a lot about the careers of astronomy graduates of a particular university, country, or era. We are still seeking volunteers to enter the graduates of one or more universities.

Impact of medical academic genealogy on publication patterns: An analysis of the literature for surgical resection in brain tumor patients.

Science.gov (United States)

Hirshman, Brian R; Tang, Jessica A; Jones, Laurie A; Proudfoot, James A; Carley, Kathleen M; Marshall, Lawrence; Carter, Bob S; Chen, Clark C

2016-02-01

"Academic genealogy" refers to the linking of scientists and scholars based on their dissertation supervisors. We propose that this concept can be applied to medical training and that this "medical academic genealogy" may influence the landscape of the peer-reviewed literature. We performed a comprehensive PubMed search to identify US authors who have contributed peer-reviewed articles on a neurosurgery topic that remains controversial: the value of maximal resection for high-grade gliomas (HGGs). Training information for each key author (defined as the first or last author of an article) was collected (eg, author's medical school, residency, and fellowship training). Authors were recursively linked to faculty mentors to form genealogies. Correlations between genealogy and publication result were examined. Our search identified 108 articles with 160 unique key authors. Authors who were members of 2 genealogies (14% of key authors) contributed to 38% of all articles. If an article contained an authorship contribution from the first genealogy, its results were more likely to support maximal resection (log odds ratio = 2.74, p < 0.028) relative to articles without such contribution. In contrast, if an article contained an authorship contribution from the second genealogy, it was less likely to support maximal resection (log odds ratio = -1.74, p < 0.026). We conclude that the literature on surgical resection for HGGs is influenced by medical academic genealogies, and that articles contributed by authors of select genealogies share common results. These findings have important implications for the interpretation of scientific literature, design of medical training, and health care policy. © 2016 American Neurological Association.

Genealogical relationships between early medieval and modern inhabitants of Piedmont.

Science.gov (United States)

Vai, Stefania; Ghirotto, Silvia; Pilli, Elena; Tassi, Francesca; Lari, Martina; Rizzi, Ermanno; Matas-Lalueza, Laura; Ramirez, Oscar; Lalueza-Fox, Carles; Achilli, Alessandro; Olivieri, Anna; Torroni, Antonio; Lancioni, Hovirag; Giostra, Caterina; Bedini, Elena; Pejrani Baricco, Luisella; Matullo, Giuseppe; Di Gaetano, Cornelia; Piazza, Alberto; Veeramah, Krishna; Geary, Patrick; Caramelli, David; Barbujani, Guido

2015-01-01

In the period between 400 to 800 AD, also known as the period of the Barbarian invasions, intense migration is documented in the historical record of Europe. However, little is known about the demographic impact of these historical movements, potentially ranging from negligible to substantial. As a pilot study in a broader project on Medieval Europe, we sampled 102 specimens from 5 burial sites in Northwestern Italy, archaeologically classified as belonging to Lombards or Longobards, a Germanic people ruling over a vast section of the Italian peninsula from 568 to 774. We successfully amplified and typed the mitochondrial hypervariable region I (HVR-I) of 28 individuals. Comparisons of genetic diversity with other ancient populations and haplotype networks did not suggest that these samples are heterogeneous, and hence allowed us to jointly compare them with three isolated contemporary populations, and with a modern sample of a large city, representing a control for the effects of recent immigration. We then generated by serial coalescent simulations 16 millions of genealogies, contrasting a model of genealogical continuity with one in which the contemporary samples are genealogically independent from the medieval sample. Analyses by Approximate Bayesian Computation showed that the latter model fits the data in most cases, with one exception, Trino Vercellese, in which the evidence was compatible with persistence up to the present time of genetic features observed among this early medieval population. We conclude that it is possible, in general, to detect evidence of genealogical ties between medieval and specific modern populations. However, only seldom did mitochondrial DNA data allow us to reject with confidence either model tested, which indicates that broader analyses, based on larger assemblages of samples and genetic markers, are needed to understand in detail the effects of medieval migration.

Genealogical relationships between early medieval and modern inhabitants of Piedmont.

Directory of Open Access Journals (Sweden)

Stefania Vai

Full Text Available In the period between 400 to 800 AD, also known as the period of the Barbarian invasions, intense migration is documented in the historical record of Europe. However, little is known about the demographic impact of these historical movements, potentially ranging from negligible to substantial. As a pilot study in a broader project on Medieval Europe, we sampled 102 specimens from 5 burial sites in Northwestern Italy, archaeologically classified as belonging to Lombards or Longobards, a Germanic people ruling over a vast section of the Italian peninsula from 568 to 774. We successfully amplified and typed the mitochondrial hypervariable region I (HVR-I of 28 individuals. Comparisons of genetic diversity with other ancient populations and haplotype networks did not suggest that these samples are heterogeneous, and hence allowed us to jointly compare them with three isolated contemporary populations, and with a modern sample of a large city, representing a control for the effects of recent immigration. We then generated by serial coalescent simulations 16 millions of genealogies, contrasting a model of genealogical continuity with one in which the contemporary samples are genealogically independent from the medieval sample. Analyses by Approximate Bayesian Computation showed that the latter model fits the data in most cases, with one exception, Trino Vercellese, in which the evidence was compatible with persistence up to the present time of genetic features observed among this early medieval population. We conclude that it is possible, in general, to detect evidence of genealogical ties between medieval and specific modern populations. However, only seldom did mitochondrial DNA data allow us to reject with confidence either model tested, which indicates that broader analyses, based on larger assemblages of samples and genetic markers, are needed to understand in detail the effects of medieval migration.

Genealogies and spiritualities in Genesis 4:17-22, 4:25-26, 5:1-32 ...

African Journals Online (AJOL)

The three genealogies in Genesis 4:17-22, 4:25-26 en 5:1-32 show different intentions: the first wants (amongst other purposes) to give an aetiology of the trades; the second wants to stress the importance of a new beginning; the third wants to relate Adam to Noah. Each of these approaches to genealogy has a different ...

Glottochronology as a heuristic for genealogical language relationships

NARCIS (Netherlands)

Wichmann, S.; Holman, E.W.; Müller, A.; Velupillai, V.; List, J.-M.; Belyaev, O.; Urban, M.; Bakker, D.

2010-01-01

This paper applies a computerized method related to that of glottochronology and addresses the question whether such a method is useful as a heuristic for identifying deep genealogical relations among languages. We first measure lexical similarities for pairs of language families that are normally

Lesbian Studies after The Lesbian Postmodern: toward a new genealogy.

Science.gov (United States)

Doan, Laura

2007-01-01

While Lesbian Studies is established as a commodity in the academic marketplace, its disciplinary contours are rather more obscure-and even more problematically, its disciplinary genealogy remains somewhat crude. The dominant genealogy of Lesbian Studies might best be characterized as a 'collision model,' a battle between politics and theory, even though much existing scholarship draws on both Lesbian-Feminist Theory and Queer Theory.1 This article proposes that the tools and methods of a sub-field called 'Lesbian Cultural History' might be useful in generating other historical accounts of the origins and evolution of Lesbian Studies. Such a project is vital because the writing of our disciplinary History clarifies how we envision a disciplinary future.

Bullying, Genealogy of the Concept

DEFF Research Database (Denmark)

Søndergaard, Dorte Marie

2017-01-01

Bullying is a serious problem among children in schools and institutions. However, it is only relatively recently that bullying has emerged as a field of research, although the phenomenon itself has likely existed in various forms among children for as long as mankind has walked the earth. The ge....... The genealogy of bullying as a concept has taken the understanding of bullying in different directions with a varying emphasis on either the roles played by individuals (victims and perpetrators) or on social and relational aspects....

The Y chromosome as the most popular marker in genetic genealogy benefits interdisciplinary research.

Science.gov (United States)

Calafell, Francesc; Larmuseau, Maarten H D

2017-05-01

The Y chromosome is currently by far the most popular marker in genetic genealogy that combines genetic data and family history. This popularity is based on its haploid character and its close association with the patrilineage and paternal inherited surname. Other markers have not been found (yet) to overrule this status due to the low sensitivity and precision of autosomal DNA for genetic genealogical applications, given the vagaries of recombination, and the lower capacities of mitochondrial DNA combined with an in general much lower interest in maternal lineages. The current knowledge about the Y chromosome and the availability of markers with divergent mutation rates make it possible to answer questions on relatedness levels which differ in time depth; from the individual and familial level to the surnames, clan and population level. The use of the Y chromosome in genetic genealogy has led to applications in several well-established research disciplines; namely in, e.g., family history, demography, anthropology, forensic sciences, population genetics and sex chromosome evolution. The information obtained from analysing this chromosome is not only interesting for academic scientists but also for the huge and lively community of amateur genealogists and citizen-scientists, fascinated in analysing their own genealogy or surname. This popularity, however, has also some drawbacks, mainly for privacy reasons related to the DNA donor, his close family and far-related namesakes. In this review paper we argue why Y-chromosomal analysis and its genetic genealogical applications will still perform an important role in future interdisciplinary research.

The total Somali clan genealogy : a preliminary sketch

NARCIS (Netherlands)

Abbink, J.

1999-01-01

This paper presents a preliminary genealogy of all Somali 'clans'. Somali kinship is based on patrilineal descent, but there are no equivalents in the Somali language for the words 'clan' and 'lineage'. The Somali terminology for the levels of social segmentation is complex, amongst others because

Multigenerational information: the example of the Icelandic Genealogy Database.

Science.gov (United States)

Tulinius, Hrafn

2011-01-01

The first part of the chapter describes the Icelandic Genealogical Database, how it was created, what it contains, and how it operates. In the second part, an overview of research accomplished with material from the database is given.

The genealogy of personal names: towards a more productive method in historical onomastics.

Science.gov (United States)

Kotilainen, Sofia

2011-01-01

It is essential to combine genealogical and collective biographical approaches with network analysis if one wants to take full advantage of the evidence provided by (hereditary) personal names in historical and linguistic onomastic research. The naming practices of rural families and clans from the 18th to the 20th century can bring us much fresh information about their enduring attitudes and values, as well as about other mentalities of everyday life. Personal names were cultural symbols that contained socially shared meanings. With the help of genealogical method it is possible to obtain a more nuanced understanding of these past naming practices, for example by comparing the conventions of different communities. A long-term and systematic empirical research also enables us to dispute certain earlier assumptions that have been taken for granted in historical onomastics. Therefore, the genealogical method is crucial in studying the criteria for the choices of personal names in the past.

Genealogical databases as a tool for extending follow-up in clinical reviews.

Science.gov (United States)

Ho, Thuy-Van; Chowdhury, Naweed; Kandl, Christopher; Hoover, Cindy; Robinson, Ann; Hoover, Larry

2016-08-01

Long-term follow-up in clinical reviews often presents significant difficulty with conventional medical records alone. Publicly accessible genealogical databases such as Ancestry.com provide another avenue for obtaining extended follow-up and added outcome information. No previous studies have described the use of genealogical databases in the follow-up of individual patients. Ancestry.com, the largest genealogical database in the United States, houses extensive demographic data on an increasing number of Americans. In a recent retrospective review of esthesioneuroblastoma patients treated at our institution, we used this resource to ascertain the outcomes of patients otherwise lost to follow-up. Additional information such as quality of life and supplemental treatments the patient may have received at home was obtained through direct contact with living relatives. The use of Ancestry.com resulted in a 25% increase (20 months) in follow-up duration as well as incorporation of an additional 7 patients in our study (18%) who would otherwise not have had adequate hospital chart data for inclusion. Many patients within this subset had more advanced disease or were remotely located from our institution. As such, exclusion of these outliers can impact the quality of subsequent outcome analysis. Online genealogical databases provide a unique resource of public information that is acceptable to institutional review boards for patient follow-up in clinical reviews. Utilization of Ancestry.com data led to significant improvement in follow-up duration and increased the number of patients with sufficient data that could be included in our retrospective study. © 2016 ARS-AAOA, LLC.

Heroes and Cowards: Genealogy, Subjectivity and War in the Twenty-First Century

Directory of Open Access Journals (Sweden)

Peter Lee

2018-04-01

Full Text Available From the wars of Ancient Greece to the collapsing Islamic State in the present, the same, apparently timeless protagonists appear and their stories told and re-told: the heroes, cowards and other combatants. This article proposes a framework which combines a Foucauldian genealogical approach with his conception of the subject as both constituted in relation to code-oriented moralities, and creatively self-formed in relation to ethics-oriented moralities (Foucault 1992, pp. 5, 25, to understand how it is possible to speak meaningfully of heroes and cowards in the age of the drone and the jihadist. Section one will explore the applicability of Foucauldian genealogy as the methodological basis for understanding present combatants in the context of war. The second section will assess Foucault’s ‘modes of subjectivation’ and ‘practices of the self’ (Foucault 1992, p. 28, as a means of analyzing the emergence of the subject of war over millennia, with emphasis on the ethical dimension of subjectivity that can be applied to heroes and cowards. Then the third section will use insights from Homer and Augustine to begin to illustrate how Foucault’s genealogical approach and his conception of ethical subjectivity combine to enable heroes and cowards to be meaningfully spoken of and better understood in the domain of war today. The purpose of such a study is to set out the basis on which political genealogy after Foucault can provide a nuanced conceptualization of subjectivity in modern war, as those subjects are formed, claimed, valorized and criticized by competing entities in contemporary political discourse.

Worldwide genealogy of Entamoeba histolytica: an overview to understand haplotype distribution and infection outcome.

Science.gov (United States)

Zermeño, Valeria; Ximénez, Cecilia; Morán, Patricia; Valadez, Alicia; Valenzuela, Olivia; Rascón, Edgar; Diaz, Daniel; Cerritos, René

2013-07-01

Although Entamoeba histolytica is one of the most prevalent intestinal parasites, how the different strains of this species are distributed all over the world and how different genotypes are associated with the infection outcome are yet to be fully understood. Recently, the use of a number of molecular markers has made the characterization of several genotypes in those regions with high incidence of amoebiasis possible. This work proposes the first genealogy of E. histolytica, with an haplotype network based on two tRNA gene-linked array of Short Tandem Repeats (STRs) reported until today, and 47 sequences from 39 new isolates of Mexican Amoebic Liver Abscesses (ALA) samples. One hundred and three sequences were obtained from D-A locus, their information about the geographic region of isolation as well as clinical diagnosis were also collected. One hundred and five sequences from N-K2 locus were also obtained as well as the region of isolation, but the information about clinical diagnosis was not available in all cases. The most abundant and widely distributed haplotype in the world is the one of E. histolytica HM1:IMSS strain. This was found in Mexico, Bangladesh, Japan, China and USA and is associated to symptomatic patients as well as asymptomatic cyst passers. Many other haplotypes were found only in a single country. Both genealogies suggest that there are no lineages within the networks that may be related to a particular geographic region or infection outcome. A concatenated analysis of the two molecular markers revealed 12 different combinations, which suggests the possibility of genetic recombination events. The present study is the first to propose a global genealogy of this species and suggests that there are still many genotypes to be discovered. The genotyping of new isolates will help to understand the great diversity and genetic structure of this parasite. Copyright © 2013 Elsevier B.V. All rights reserved.

Genealogies of Modern Technology

DEFF Research Database (Denmark)

Riis, Søren

2008-01-01

Does modern technology differ from ancient technology and does it have a unique essence? This twofold question opens one of Martin Heidegger's most influential philosophical inquiries, The Question Concerning Technology. The answer Heidegger offers has inspired various critiques and appraisals from...... a vast number of contemporary scholars of technology.1 Heidegger's answer is traditionally thought to suggest a great difference between ancient and modern technology. However, by re-examining Heidegger's text, it is possible to discover previously ignored or misunderstood lines of thoughts that affirm...... a multi-stable interpretation of the origin of modern technology. In what follows, we shall see how The Question Concerning Technology in fact supports three different genealogies of modern technology...

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.

Academic Genealogy and Direct Calorimetry: A Personal Account

Science.gov (United States)

Jackson, Donald C.

2011-01-01

Each of us as a scientist has an academic legacy that consists of our mentors and their mentors continuing back for many generations. Here, I describe two genealogies of my own: one through my PhD advisor, H. T. (Ted) Hammel, and the other through my postdoctoral mentor, Knut Schmidt-Nielsen. Each of these pathways includes distingished scientists…

A parametric interpretation of Bayesian Nonparametric Inference from Gene Genealogies: Linking ecological, population genetics and evolutionary processes.

Science.gov (United States)

Ponciano, José Miguel

2017-11-22

Using a nonparametric Bayesian approach Palacios and Minin (2013) dramatically improved the accuracy, precision of Bayesian inference of population size trajectories from gene genealogies. These authors proposed an extension of a Gaussian Process (GP) nonparametric inferential method for the intensity function of non-homogeneous Poisson processes. They found that not only the statistical properties of the estimators were improved with their method, but also, that key aspects of the demographic histories were recovered. The authors' work represents the first Bayesian nonparametric solution to this inferential problem because they specify a convenient prior belief without a particular functional form on the population trajectory. Their approach works so well and provides such a profound understanding of the biological process, that the question arises as to how truly "biology-free" their approach really is. Using well-known concepts of stochastic population dynamics, here I demonstrate that in fact, Palacios and Minin's GP model can be cast as a parametric population growth model with density dependence and environmental stochasticity. Making this link between population genetics and stochastic population dynamics modeling provides novel insights into eliciting biologically meaningful priors for the trajectory of the effective population size. The results presented here also bring novel understanding of GP as models for the evolution of a trait. Thus, the ecological principles foundation of Palacios and Minin (2013)'s prior adds to the conceptual and scientific value of these authors' inferential approach. I conclude this note by listing a series of insights brought about by this connection with Ecology. Copyright © 2017 The Author. Published by Elsevier Inc. All rights reserved.

Investigation of a baseline method for genealogical entity resolution

NARCIS (Netherlands)

Efremova, I.; Ranjbar-Sahraei, B.; Oliehoek, F.A.; Calders, T.G.K.; Tuyls, K.P.

2014-01-01

In this paper we study the application of entity resolution (ER) techniques on a real-world multi-source genealogical dataset. Our goal is to identify all persons involved in various notary acts and link them to their birth, marriage and death certificates. In order to evaluate the performance of a

Probabilistic models of population evolution scaling limits, genealogies and interactions

CERN Document Server

Pardoux, Étienne

2016-01-01

This expository book presents the mathematical description of evolutionary models of populations subject to interactions (e.g. competition) within the population. The author includes both models of finite populations, and limiting models as the size of the population tends to infinity. The size of the population is described as a random function of time and of the initial population (the ancestors at time 0). The genealogical tree of such a population is given. Most models imply that the population is bound to go extinct in finite time. It is explained when the interaction is strong enough so that the extinction time remains finite, when the ancestral population at time 0 goes to infinity. The material could be used for teaching stochastic processes, together with their applications. Étienne Pardoux is Professor at Aix-Marseille University, working in the field of Stochastic Analysis, stochastic partial differential equations, and probabilistic models in evolutionary biology and population genetics. He obtai...

Temporal differentiation across a West-European Y-chromosomal cline: genealogy as a tool in human population genetics.

Science.gov (United States)

Larmuseau, Maarten H D; Ottoni, Claudio; Raeymaekers, Joost A M; Vanderheyden, Nancy; Larmuseau, Hendrik F M; Decorte, Ronny

2012-04-01

The pattern of population genetic variation and allele frequencies within a species are unstable and are changing over time according to different evolutionary factors. For humans, it is possible to combine detailed patrilineal genealogical records with deep Y-chromosome (Y-chr) genotyping to disentangle signals of historical population genetic structures because of the exponential increase in genetic genealogical data. To test this approach, we studied the temporal pattern of the 'autochthonous' micro-geographical genetic structure in the region of Brabant in Belgium and the Netherlands (Northwest Europe). Genealogical data of 881 individuals from Northwest Europe were collected, from which 634 family trees showed a residence within Brabant for at least one generation. The Y-chr genetic variation of the 634 participants was investigated using 110 Y-SNPs and 38 Y-STRs and linked to particular locations within Brabant on specific time periods based on genealogical records. Significant temporal variation in the Y-chr distribution was detected through a north-south gradient in the frequencies distribution of sub-haplogroup R1b1b2a1 (R-U106), next to an opposite trend for R1b1b2a2g (R-U152). The gradient on R-U106 faded in time and even became totally invisible during the Industrial Revolution in the first half of the nineteenth century. Therefore, genealogical data for at least 200 years are required to study small-scale 'autochthonous' population structure in Western Europe.

A doctoral study of the use of the Internet for genealogy

Directory of Open Access Journals (Sweden)

Kylie J. Veale

2009-11-01

Full Text Available Distintas  investigaciones muestran evidencia de que Internet ha tenido un impacto revolucionario en nuestra sociedad y en nuestra forma de vida cotidiana. Obviamente, ya que Internet influye en los diversos aspectos de la vida cotidiana, los intereses de aficionados en áreas tales como la historia también se han mejorado y han cambiado considerando Internet como una tecnología social. Una afición, la genealogía, se ha elevado por encima de todo para ser uno de los más populares en línea, proporcionando una oportunidad para entender el uso de Internet dentro de un contexto más amplio. Como resultado de ello, el autor ha iniciado un programa de investigación de doctorado con la Universidad Tecnológica de Curtin, Australia, para examinar cómo los genealogistas utilizan Internet, y para investigar las consecuencias del desarrollo de la genealogía como una importante actividad basada en Internet. El propuesto de este artículo, por lo tanto, es presentar las notas de investigación del estudio.____________ABSTRACT:Research evidence shows the Internet has had a revolutionary impact on our society and the way we live everyday. Consequently, as the Internet influences the many aspects of everyday lives, hobbyist interests in areas such as history have also been enhanced and changed by the Internet as a social technology. One hobby, genealogy, has risen above all to be one of the most popular online, providing an opportunity to understand the use of the Internet within a broader context. As a result, the author has commenced a PhD research program with Curtin University of Technology, Australia, to examine how genealogists use the Internet, and to investigate the consequences of the development of genealogy as a significant Internet-based activity. The purposed of this article, therefore, is to present the research notes of the study.

Introducing AstroGen: The Astronomy Genealogy Project

OpenAIRE

Tenn, Joseph S.

2016-01-01

The Astronomy Genealogy Project ("AstroGen"), a project of the Historical Astronomy Division of the American Astronomical Society (AAS), will soon appear on the AAS website. Ultimately, it will list the world's astronomers with their highest degrees, theses for those who wrote them, academic advisors (supervisors), universities, and links to the astronomers or their obituaries, their theses when on-line, and more. At present the AstroGen team is working on those who earned doctorates with ast...

A strong deletion bias in nonallelic gene conversion.

Directory of Open Access Journals (Sweden)

Raquel Assis

Full Text Available Gene conversion is the unidirectional transfer of genetic information between orthologous (allelic or paralogous (nonallelic genomic segments. Though a number of studies have examined nucleotide replacements, little is known about length difference mutations produced by gene conversion. Here, we investigate insertions and deletions produced by nonallelic gene conversion in 338 Drosophila and 10,149 primate paralogs. Using a direct phylogenetic approach, we identify 179 insertions and 614 deletions in Drosophila paralogs, and 132 insertions and 455 deletions in primate paralogs. Thus, nonallelic gene conversion is strongly deletion-biased in both lineages, with almost 3.5 times as many conversion-induced deletions as insertions. In primates, the deletion bias is considerably stronger for long indels and, in both lineages, the per-site rate of gene conversion is orders of magnitudes higher than that of ordinary mutation. Due to this high rate, deletion-biased nonallelic gene conversion plays a key role in genome size evolution, leading to the cooperative shrinkage and eventual disappearance of selectively neutral paralogs.

Getting Started with GeneRecon — An Introduction to the Association Mapping Tool GeneRecon

DEFF Research Database (Denmark)

Mailund, T; Schauser, Leif

2006-01-01

GeneRecon is a software package for linkage disequilibrium mapping using coalescent theory. It is based on Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample...... of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position....

Molecular and genealogical evidence for a founder effect in Fanconi anemia families of the Afrikaner population of South Africa

Science.gov (United States)

Tipping, A. J.; Pearson, T.; Morgan, N. V.; Gibson, R. A.; Kuyt, L. P.; Havenga, C.; Gluckman, E.; Joenje, H.; de Ravel, T.; Jansen, S.; Mathew, C. G.

2001-01-01

Fanconi anemia (FA) is a rare, genetically heterogeneous autosomal recessive disorder associated with progressive aplastic anemia, congenital abnormalities, and cancer. FA has a very high incidence in the Afrikaner population of South Africa, possibly due to a founder effect. Previously we observed allelic association between polymorphic markers flanking the FA group A gene (FANCA) and disease chromosomes in Afrikaners. We genotyped 26 FA families with microsatellite and single nucleotide polymorphic markers and detected five FANCA haplotypes. Mutation scanning of the FANCA gene revealed association of these haplotypes with four different mutations. The most common was an intragenic deletion of exons 12–31, accounting for 60% of FA chromosomes in 46 unrelated Afrikaner FA patients, while two other mutations accounted for an additional 20%. Screening for these mutations in the European populations ancestral to the Afrikaners detected one patient from the Western Ruhr region of Germany who was heterozygous for the major deletion. The mutation was associated with the same unique FANCA haplotype as in Afrikaner patients. Genealogical investigation of 12 Afrikaner families with FA revealed that all were descended from a French Huguenot couple who arrived at the Cape on June 5, 1688, whereas mutation analysis showed that the carriers of the major mutation were descendants of this same couple. The molecular and genealogical evidence is consistent with transmission of the major mutation to Western Germany and the Cape near the end of the 17th century, confirming the existence of a founder effect for FA in South Africa. PMID:11344308

GeneRecon Users' Manual — A coalescent based tool for fine-scale association mapping

DEFF Research Database (Denmark)

Mailund, T

2006-01-01

GeneRecon is a software package for linkage disequilibrium mapping using coalescent theory. It is based on Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample of th...

Preserving local writers, genealogy, photographs, newspapers, and related materials

CERN Document Server

Smallwood, Carol

2012-01-01

Preserving Local Writers, Genealogy, Photographs, Newspapers, and Related Materials draws on the practical knowledge of archivists, preservationists, librarians, and others who share the goal of making local history accessible to future generations. Anyone who plans to start a local history project or preserve important historical materials will find plenty of tips, techniques, sample documents, project ideas, and inspiration in its pages.

Introducing AstroGen: the Astronomy Genealogy Project

Science.gov (United States)

Tenn, Joseph S.

2016-12-01

The Astronomy Genealogy Project (AstroGen), a project of the Historical Astronomy Division of the American Astronomical Society (AAS), will soon appear on the AAS website. Ultimately, it will list the world's astronomers with their highest degrees, theses for those who wrote them, academic advisors (supervisors), universities, and links to the astronomers or their obituaries, their theses when online, and more. At present the AstroGen team is working on those who earned doctorates with astronomy-related theses. We show what can be learned already, with just ten countries essentially completed.

Local Genealogies in a Linear Mixed Model for Genome-wide Association Mapping in Complex Pedigreed Populations

DEFF Research Database (Denmark)

Sahana, Goutam; Mailund, Thomas; Lund, Mogens Sandø

2011-01-01

be extended to incorporate other effects in a straightforward and rigorous fashion. Here, we present a complementary approach, called ‘GENMIX (genealogy based mixed model)’ which combines advantages from two powerful GWAS methods: genealogy-based haplotype grouping and MMA. Subjects and Methods: We validated......Introduction: The state-of-the-art for dealing with multiple levels of relationship among the samples in genome-wide association studies (GWAS) is unified mixed model analysis (MMA). This approach is very flexible, can be applied to both family-based and population-based samples, and can...

A Genealogy of (post-Soviet Dependency: Disabling Productivity

Directory of Open Access Journals (Sweden)

Cassandra Hartblay

2014-02-01

Full Text Available Nancy Fraser and Linda Gordon's 1994 article “A Genealogy of Dependency: Tracing a Keyword of the US Welfare State” explored the historical emergence of "dependency" as a moral category of post-industrial American state. In this article, I engage their framework to explore the genealogy of dependency in America's post-industrial sister, the post-Soviet Russian Federation. I also add disability as a core element of 'dependency' that was largely absent from Fraser and Gordon's original analysis. Considering cross-cultural translation, I ask how Russian deployments of three words that all relate to a concept of interdependence align with and depart from American notions of dependency, and trace historical configurations of the Soviet welfare state vis-a-vis disability. To do so, I draw on historical and cultural texts, linguistic comparisons, secondary sources, and ethnographic research. Given this analysis, I argue that rather than a Cold War interpretation of the Soviet Union and the US as oppositional superpowers in the 20th century, a liberatory disability studies framework suggests that in the postindustrial era the Soviet Union and the United States emerged as dual regimes of productivity. I suggest that reframing postsocialism as a global condition helps us to shift considerations of disability justice from a critique of capitalism to a critique of productivity.    Keywords: dependency, disability, citizenship, russia, productivity

On the Genealogy of Kitsch and the Critique of Ideology: A Reflection on Method

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Andrius Bielskis

2018-02-01

Full Text Available This paper examines similarities and differences between the genealogical approach to social critique and the Marxist critique of ideology. Given the key methodological aspects of Michel Foucault’s genealogy—the fusion of power and discourse and the Nietzschean notion of the aesthetization of life—the paper argues that Hollywood kitsch maybe interpreted as a new dispositif. A key task of the genealogy of kitsch is to analyze the effects of fake Hollywood narratives: how they form and normalize us, what kind of subjectivities they produce, and what type of social relations they create. La La Land, a 2016 American musical, is discussed as a way of illustration. Theorists of the Frankfurt School also advanced their critiques of the popular culture and its forms of kitsch; yet they followed Marx and his conception of ideology. The paper concludes that the differences between genealogy and the critique of ideology are philosophical. Foucault rejected the Marxist conception of history and the notion of ideology as false consciousness. Kitsch, for a genealogist, is formative rather than repressive; it makes people pursue banal dreams. For a Marxist critic, popular culture as a form of ideology dulls our critical capacities and, therefore, leaves the status quo of alienation intact.

[On the philosophical genealogy of Freud].

Science.gov (United States)

Dimitrov, C T

1975-06-01

The origins of psycho-analysis, like those of every other medico-psychological study, have their own particular scientific and specific social, historical and philosophical-theoretical presuppositions. Freud's philosophical genealogy is closely linked to classical german philosophy and subsequent philosophical movements. I. Kant, J.-F. Herbart, A. Schopenhauer, F. Nietzsche, E. v. Hartmann, G. T. Fechner, E. Mach, W. Ostwald, L. Feuerbach and others did not only emphasise the significance of drives and the unconscious in human behaviour, they also described many psychological mechanisms from depth psychology, (for example repression, condensation, substitution, sublimation). Some false theoretical trends in psycho-analysis (biologism, psychologism and simplifying psycho-energetics to simplify) can be explained to some extent by the influences mentioned above.

Frozen Landscapes: A Foucauldian Genealogy of the Ideal Ballet Dancer's Body

Science.gov (United States)

Ritenburg, Heather Margaret

2010-01-01

This paper explores the social construction of the "ideal" body of the female ballet dancer in North America. Specifically, the author constructs a Foucauldian genealogy tracing a body shape that came to dominate the principal female dancers of the New York City Ballet, and how this body shape continues to be normalized through…

Establishing and Maintaining a Local History Collection [and] Local History/Genealogical Resources.

Science.gov (United States)

North Carolina Libraries, 1988

1988-01-01

Theme article on developing local history collections in public libraries begins with a discussion of collection development, and continues with sections on technical services, the library environment, staffing, programing, and marketing. A bibliography and directories of used and rare book dealers, genealogical publishers, professional…

Counselling against HIV in Africa: a genealogy of confessional technologies.

Science.gov (United States)

Nguyen, Vinh-Kim

2013-01-01

This paper contextualises counselling within a broader historical formation that links disclosure to healing and deploys confessional technologies to incite disclosure and awareness of the mysterious substance of the self. Foucault's argument that sexuality was the privileged arena for using confessional technologies to 'produce' the truth of the self is particularly relevant in light of the diffusion of counselling practices in Africa in the wake of the HIV epidemic, particularly with their emphasis on inciting appropriate sexual behaviour. Examination of the historical assemblage of counselling practices shows how they articulate what the self is, the nature of truth and a politics of language. This paper focuses on the genealogy of four key assumptions that express this confessional reason. These are that: (1) people can be 'empowered' to have control on their own lives by working on themselves, (2) secrets untold become pathogens, (3) the ability to heal requires that one first overcome personal illness, (4) the experience of sharing secrets is cathartic and healing. The genealogy intertwines four strands: that of the Unconscious as revealed by Freud and his followers, attempts to treat shell-shocked veterans of World War I, group psychotherapy and participatory research after World War II.

Keeping the Genealogical Structure of Paternal Breed Nuclei in Pigs

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Maria Voiculescu

2012-05-01

Full Text Available For a long period of time pigs as farm animals were considered producing a single ware, pork. Not very long ago the pork market became interested in lean meet. Some breeders tried to have it from the old breeds and lave a lent genetic progress. Other breeders decided to follow the hybridization schemes used in poultry to produce broilers. But in strains with high daily gain and gross muscles the sows fertility declined and by then by disjunction selection they have isolated strains of high fertility. Then the final animal for the market was the cross piglet obtained from these two kinds of strains or lines. The third kind of breeders decided to specializing breeds, selected for as much as possible muscle mass as paternal breeds and breeds specialized for high fertility as maternal breeds. The present paper will present the movement taking place in the genealogy of a breed nucleus of 200sows with closed reproduction. The goal of the families’ movement analysis is to find out how to ensure a convenient genealogy structure preventing consanguinity when some families are extinct by selection for daily gain.

Genealogical Trees of Scientific Papers.

Science.gov (United States)

Waumans, Michaël Charles; Bersini, Hugues

2016-01-01

Many results have been obtained when studying scientific papers citations databases in a network perspective. Articles can be ranked according to their current in-degree and their future popularity or citation counts can even be predicted. The dynamical properties of such networks and the observation of the time evolution of their nodes started more recently. This work adopts an evolutionary perspective and proposes an original algorithm for the construction of genealogical trees of scientific papers on the basis of their citation count evolution in time. The fitness of a paper now amounts to its in-degree growing trend and a "dying" paper will suddenly see this trend declining in time. It will give birth and be taken over by some of its most prevalent citing "offspring". Practically, this might be used to trace the successive published milestones of a research field.

STUDI AWAL TENTANG POLEMIK PERAN WANITA PADA DESAIN RUMAH TINGGAL; DENGAN PENDEKATAN GENEALOGI

Directory of Open Access Journals (Sweden)

J. Lukito Kartono

2000-01-01

Full Text Available Realizing that all of their activities cannot be carried out indoors,people consider that dwelling is a must or tradition for them.The dwelling-house is represented in the forms of space visualizing the dwellers' culture.The indoor spaces reflect the social-structure closely related to the role of the members of the family and to their relation with their relatives.Initially,the space arrangement of traditional society clearly showed the role of man and women but then feminism claimed that women's roles has been discriminating and marginal.We need to prove this point of view in details by always observing the cases of house-designs in genealogical way. Abstract in Bahasa Indonesia : Tradisi berhuni merupakan tradisi yang dilakukan oleh manusia karena sadar bahwa tidak semua kegiatannya dapat dilakukan diudara terbuka.Tempat berhuni yang direpresentasikan dalam wujud ruang mencerminkan kebudayaan yang dianut penghuninya. Ruang-ruang di rumah tinggal menampung struktur sosial yang berkaitan dengan peran suami dan saudaranya,istri dan saudaranya serta anak-anak mereka. Pada awalnya,dalam penataan ruang rumah tinggal masyarakat tradisional terlihat secara jelas adanya ruang-ruang yang mengakomodir kegiatan wanita dan lelaki.Tetapi akhir-akhir ini sejalan dengan lahirnya gerakan feminisme,ada gugatan bahwa telah terjadi diskriminasi dan marjinalisasi terhadap peran wanita dalam rumah tinggal.Kebenaran gugatan memang perlu dibahas lebih mendalam dengan meninjau secara genealogi pada kasus-kasus desain rumah tinggal dari masa ke masa. Kata kunci: lelaki-wanita,rumah tinggal dan genealogi.

Genealogical evidence for epidemics of selfish genes

OpenAIRE

Ingvarsson, Pär K.; Taylor, Douglas R.

2002-01-01

Some genetic elements spread infectiously in populations by increasing their rate of genetic transmission at the expense of other genes in the genome. These so-called selfish genetic elements comprise a substantial portion of eukaryotic genomes and have long been viewed as a potent evolutionary force. Despite this view, little is known about the evolutionary history of selfish genetic elements in natural populations, or their genetic effects on other portions of the genome. Here we use nuclea...

Guidelines for Preservation, Conservation, and Restoration of Local History and Local Genealogical Materials.

Science.gov (United States)

RQ, 1993

1993-01-01

Presents guidelines adopted by the American Library Association (ALA) relating to the preservation, conservation, and restoration of local history and local genealogical materials. Topics addressed include assessing preservation needs; developing a plan; choosing appropriate techniques, including microduplication, photoduplication, electronic…

Office and Agamben's Genealogy of Economy and Government

DEFF Research Database (Denmark)

Dean, Mitchell

2017-01-01

This paper locates Giorgio Agamben’s book Opus Dei in his larger Homo Sacer project and particularly a series of genealogical and archaeological studies within it. It argues for a disenchanted and dispersed reading of Agamben’s approach to office as a resource for concerns that are germane...... for office. More broadly, Agamben’s work on office is shown to bear upon questions of the constitution of sovereignty and government as forms of power, on different forms of rationalisation, and themes of secularisation and modernity found in classical sociology and intellectual history....

Comparative study of reproductive skew and pair-bond stability using genealogies from 80 small-scale human societies.

Science.gov (United States)

Ellsworth, Ryan M; Shenk, Mary K; Bailey, Drew H; Walker, Robert S

2016-05-01

Genealogies contain information on the prevalence of different sibling types that result from past reproductive behavior. Full sibling sets stem from stable monogamy, paternal half siblings primarily indicate male reproductive skew, and maternal half siblings reflect unstable pair bonds. Full and half sibling types are calculated for a total of 61,181 siblings from published genealogies for 80 small-scale societies, including foragers, horticulturalists, agriculturalists, and pastoralists from around the world. Most siblings are full (61%) followed by paternal half siblings (27%) and maternal half siblings (13%). Paternal half siblings are positively correlated with more polygynous marriages, higher at low latitudes, and slightly higher in nonforagers, Maternal half sibling fractions are slightly higher at low latitudes but do not vary with subsistence. Partible paternity societies in Amazonia have more paternal half siblings indicating higher male reproductive skew. Sibling counts from genealogies provide a convenient method to simultaneously investigate the reproductive skew and pair-bond stability dimensions of human mating systems cross-culturally. Am. J. Hum. Biol. 28:335-342, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

The role of genealogy and clinical family histories in documenting possible inheritance patterns for diabetes mellitus in the pre-insulin era: part 2. Genealogic evidence for type 2 diabetes mellitus in Josephine Imperato's paternal and maternal lineages.

Science.gov (United States)

Imperato, Pascal James; Imperato, Gavin H

2009-12-01

Part 2 presents detailed genealogic information on Josephine Imperato's paternal and maternal lineages extending from four to seven generations into the nineteenth and eighteenth centuries. Among these lineages are some where early adult death over successive generations is perhaps indicative of type 2 diabetes mellitus (type 2 DM). These lineages, all in the town of San Prisco in Italy, include both paternal and maternal ones with the following surnames: Casaccia, Casertano, Cipriano, de Angelis, de Paulis, Peccerillo, Foniciello, di Monaco, Vaccarella, Valenziano, Ventriglia, and Zibella. Genealogic studies of eighteenth and nineteenth century vital records in this area of Italy cannot definitively establish type 2 diabetes mellitus as either an immediate or contributory cause of death. This is because causes of death were not recorded and because disease diagnostic capabilities were largely absent. Genealogic studies of those who lived in Italy in the eighteenth and nineteenth centuries can at best provide data on approximate age at time of death. Early adult death in this era was not uncommon. However, its presence over several successive generations in a lineage raises the possibility of inherited diseases prominent among which is type 2 DM.

Mating type genes in the genus Neofusicoccum: Mating strategies and usefulness in species delimitation.

Science.gov (United States)

Lopes, Anabela; Phillips, Alan J L; Alves, Artur

2017-04-01

The genus Neofusicoccum includes species with wide geographical and plant host distribution, some of them of economic importance. The genus currently comprises 27 species that are difficult to identify based on morphological features alone. Thus, species differentiation is based on phylogenetic species recognition using multigene genealogies. In this study, we characterised the mating type genes of Neofusicoccum species. Specific primers were designed to amplify and sequence MAT genes in several species and a PCR-based mating type diagnostic assay was developed. Homothallism was the predominant mating strategy among the species tested. Furthermore, the potential of mating type gene sequences for species delimitation was evaluated. Phylogenetic analyses were performed on both MAT genes and compared with multigene genealogies using sequences of the ribosomal internal transcribed spacer region, translation elongation factor 1-alpha and beta-tubulin. Phylogenies based on mating type genes could discriminate between the species analysed and are in concordance with the results obtained with the more conventional multilocus phylogenetic analysis approach. Thus, MAT genes represent a powerful tool to delimit cryptic species in the genus Neofusicoccum. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Mitochondrial replacement techniques: egg donation, genealogy and eugenics.

Science.gov (United States)

Palacios-González, César

2016-03-01

Several objections against the morality of researching or employing mitochondrial replacement techniques have been advanced recently. In this paper, I examine three of these objections and show that they are found wanting. First I examine whether mitochondrial replacement techniques, research and clinical practice, should not be carried out because of possible harms to egg donors. Next I assess whether mitochondrial replacement techniques should be banned because they could affect the study of genealogical ancestry. Finally, I examine the claim that mitochondrial replacement techniques are not transferring mitochondrial DNA but nuclear DNA, and that this should be prohibited on ethical grounds.

Paradigma Kepariwisataan Bali Tahun 1930-An: Studi Genealogi Kepariwisataan Budaya

OpenAIRE

I Made Sendra

2016-01-01

This article analyses the connection between Baliseering discourse and the practice of Bali`s cultural tourism by applying the theory of hegemony from Gramsci and genealogy from Micheal Foucault as tools of analysis. It is very interesting topic to analyses especially in relation to the reconstruction of Baliseering discourse, the power knowledge emerged from Baliseering discourse, the articulation of it to open the space of Bali as historical cultural. Research shows that Baliseering is colo...

Genetic diversity of dog breeds: within-breed diversity comparing genealogical and molecular data.

Science.gov (United States)

Leroy, G; Verrier, E; Meriaux, J C; Rognon, X

2009-06-01

The genetic diversity of 61 dog breeds raised in France was investigated. Genealogical analyses were performed on the pedigree file of the French kennel club. A total of 1514 dogs were also genotyped using 21 microsatellite markers. For animals born from 2001 to 2005, the average coefficient of inbreeding ranged from 0.2% to 8.8% and the effective number of ancestors ranged from 9 to 209, according to the breed. The mean value of heterozygosity was 0.62 over all breeds (range 0.37-0.77). At the breed level, few correlations were found between genealogical and molecular parameters. Kinship coefficients and individual similarity estimators were, however, significantly correlated, with the best mean correlation being found for the Lynch & Ritland estimator (r = 0.43). According to both approaches, it was concluded that special efforts should be made to maintain diversity for three breeds, namely the Berger des Pyrénées, Braque Saint-Germain and Bull Terrier.

[Archaeology and genealogy as methodological options of nursing research].

Science.gov (United States)

Azevedo, Rosemeiry Capriata de Souza; Ramos, Flavia Regina Souza

2003-01-01

This article is based on the historical contextualization about the development of research in nursing, presents the categories/lines of interest that support the human knowledge applied in the Doctorate Thesis in Nursing in Brazil, points out the archeological and genealogical methods proposed by Michel Foucault, and their possibility to make more difficult the day-to-day tasks of the nursing profession Whether in Institutions, Public Policies, Health Reform, and Vocational Training, in the attempt to understand which strategies, challenges, knowledge base, and practices have influenced the building of the subjects.

[The importance of genealogy applied to genetic research in Costa Rica].

Science.gov (United States)

Meléndez Obando, Mauricio O

2004-09-01

The extensive development of genealogical studies based on archival documents has provided powerful support for genetic research in Costa Rica over the past quarter century. As a result, several questions of population history have been answered, such as those involving hereditary illnesses, suggesting additional avenues and questions as well. Similarly, the preservation of massive amounts of historical documentation highlights the major advantages that the Costa Rican population offers to genetic research.

Genealogy, morphology and fitness of spontaneous hybrids between wild and cultivated chicory (Cichorium intybus)

DEFF Research Database (Denmark)

Kiær, Lars Pødenphant; Philipp, M.; Bagger Jørgensen, Rikke

2007-01-01

Crop species are known to hybridize spontaneously with wild relatives, but few studies have characterized the performance of hybrids at various genealogies, life stages and environments. A group of cultivar-like individuals and potential hybrids were observed in a roadside population of wild chic...

Strong evidence for a genetic contribution to late-onset Alzheimer's disease mortality: a population-based study.

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.

Genealogy profiling through strain improvement by using metabolic network analysis: metabolic flux genealogy of several generations of lysine-producing corynebacteria.

Science.gov (United States)

Wittmann, Christoph; Heinzle, Elmar

2002-12-01

A comprehensive approach of metabolite balancing, (13)C tracer studies, gas chromatography-mass spectrometry, matrix-assisted laser desorption ionization-time of flight mass spectrometry, and isotopomer modeling was applied for comparative metabolic network analysis of a genealogy of five successive generations of lysine-producing Corynebacterium glutamicum. The five strains examined (C. glutamicum ATCC 13032, 13287, 21253, 21526, and 21543) were previously obtained by random mutagenesis and selection. Throughout the genealogy, the lysine yield in batch cultures increased markedly from 1.2 to 24.9% relative to the glucose uptake flux. Strain optimization was accompanied by significant changes in intracellular flux distributions. The relative pentose phosphate pathway (PPP) flux successively increased, clearly corresponding to the product yield. Moreover, the anaplerotic net flux increased almost twofold as a consequence of concerted regulation of C(3) carboxylation and C(4) decarboxylation fluxes to cover the increased demand for lysine formation; thus, the overall increase was a consequence of concerted regulation of C(3) carboxylation and C(4) decarboxylation fluxes. The relative flux through isocitrate dehydrogenase dropped from 82.7% in the wild type to 59.9% in the lysine-producing mutants. In contrast to the NADPH demand, which increased from 109 to 172% due to the increasing lysine yield, the overall NADPH supply remained constant between 185 and 196%, resulting in a decrease in the apparent NADPH excess through strain optimization. Extrapolated to industrial lysine producers, the NADPH supply might become a limiting factor. The relative contributions of PPP and the tricarboxylic acid cycle to NADPH generation changed markedly, indicating that C. glutamicum is able to maintain a constant supply of NADPH under completely different flux conditions. Statistical analysis by a Monte Carlo approach revealed high precision for the estimated fluxes, underlining the

Haim Yacobi, Israel and Africa: A Genealogy of Moral Geography

OpenAIRE

Levin, Ayala

2017-01-01

Haim Yacobi’s Israel and Africa: A Genealogy of Moral Geography boldly outlines the significant role the African continent has played in Israel’s political and cultural self-fashioning. Like its Middle Eastern setting, Africa’s geographic proximity and the web of ties this proximity entails are denied in the Israeli society, all the while the continent is produced as Israel’s “other.” Through its relationships with Africa, the author argues, Israel constitutes itself as Western, modern, enlig...

PPARγ partial agonist GQ-16 strongly represses a subset of genes in 3T3-L1 adipocytes

Energy Technology Data Exchange (ETDEWEB)

Milton, Flora Aparecida [Faculdade de Ciências da Saúde, Laboratório de Farmacologia Molecular, Universidade de Brasília (Brazil); Genomic Medicine, Houston Methodist Research Institute, Houston, TX (United States); Cvoro, Aleksandra [Genomic Medicine, Houston Methodist Research Institute, Houston, TX (United States); Amato, Angelica A. [Faculdade de Ciências da Saúde, Laboratório de Farmacologia Molecular, Universidade de Brasília (Brazil); Sieglaff, Douglas H.; Filgueira, Carly S.; Arumanayagam, Anithachristy Sigamani [Genomic Medicine, Houston Methodist Research Institute, Houston, TX (United States); Caro Alves de Lima, Maria do; Rocha Pitta, Ivan [Laboratório de Planejamento e Síntese de Fármacos – LPSF, Universidade Federal de Pernambuco (Brazil); Assis Rocha Neves, Francisco de [Faculdade de Ciências da Saúde, Laboratório de Farmacologia Molecular, Universidade de Brasília (Brazil); Webb, Paul, E-mail: pwebb@HoustonMethodist.org [Genomic Medicine, Houston Methodist Research Institute, Houston, TX (United States)

2015-08-28

Thiazolidinediones (TZDs) are peroxisome proliferator-activated receptor gamma (PPARγ) agonists that improve insulin resistance but trigger side effects such as weight gain, edema, congestive heart failure and bone loss. GQ-16 is a PPARγ partial agonist that improves glucose tolerance and insulin sensitivity in mouse models of obesity and diabetes without inducing weight gain or edema. It is not clear whether GQ-16 acts as a partial agonist at all PPARγ target genes, or whether it displays gene-selective actions. To determine how GQ-16 influences PPARγ activity on a gene by gene basis, we compared effects of rosiglitazone (Rosi) and GQ-16 in mature 3T3-L1 adipocytes using microarray and qRT-PCR. Rosi changed expression of 1156 genes in 3T3-L1, but GQ-16 only changed 89 genes. GQ-16 generally showed weak effects upon Rosi induced genes, consistent with partial agonist actions, but a subset of modestly Rosi induced and strongly repressed genes displayed disproportionately strong GQ-16 responses. PPARγ partial agonists MLR24 and SR1664 also exhibit disproportionately strong effects on transcriptional repression. We conclude that GQ-16 displays a continuum of weak partial agonist effects but efficiently represses some negatively regulated PPARγ responsive genes. Strong repressive effects could contribute to physiologic actions of GQ-16. - Highlights: • GQ-16 is an insulin sensitizing PPARγ ligand with reduced harmful side effects. • GQ-16 displays a continuum of weak partial agonist activities at PPARγ-induced genes. • GQ-16 exerts strong repressive effects at a subset of genes. • These inhibitor actions should be evaluated in models of adipose tissue inflammation.

PPARγ partial agonist GQ-16 strongly represses a subset of genes in 3T3-L1 adipocytes

International Nuclear Information System (INIS)

Milton, Flora Aparecida; Cvoro, Aleksandra; Amato, Angelica A.; Sieglaff, Douglas H.; Filgueira, Carly S.; Arumanayagam, Anithachristy Sigamani; Caro Alves de Lima, Maria do; Rocha Pitta, Ivan; Assis Rocha Neves, Francisco de; Webb, Paul

2015-01-01

Thiazolidinediones (TZDs) are peroxisome proliferator-activated receptor gamma (PPARγ) agonists that improve insulin resistance but trigger side effects such as weight gain, edema, congestive heart failure and bone loss. GQ-16 is a PPARγ partial agonist that improves glucose tolerance and insulin sensitivity in mouse models of obesity and diabetes without inducing weight gain or edema. It is not clear whether GQ-16 acts as a partial agonist at all PPARγ target genes, or whether it displays gene-selective actions. To determine how GQ-16 influences PPARγ activity on a gene by gene basis, we compared effects of rosiglitazone (Rosi) and GQ-16 in mature 3T3-L1 adipocytes using microarray and qRT-PCR. Rosi changed expression of 1156 genes in 3T3-L1, but GQ-16 only changed 89 genes. GQ-16 generally showed weak effects upon Rosi induced genes, consistent with partial agonist actions, but a subset of modestly Rosi induced and strongly repressed genes displayed disproportionately strong GQ-16 responses. PPARγ partial agonists MLR24 and SR1664 also exhibit disproportionately strong effects on transcriptional repression. We conclude that GQ-16 displays a continuum of weak partial agonist effects but efficiently represses some negatively regulated PPARγ responsive genes. Strong repressive effects could contribute to physiologic actions of GQ-16. - Highlights: • GQ-16 is an insulin sensitizing PPARγ ligand with reduced harmful side effects. • GQ-16 displays a continuum of weak partial agonist activities at PPARγ-induced genes. • GQ-16 exerts strong repressive effects at a subset of genes. • These inhibitor actions should be evaluated in models of adipose tissue inflammation

On the genealogy of branching random walks and of directed polymers

Science.gov (United States)

Derrida, Bernard; Mottishaw, Peter

2016-08-01

It is well known that the mean-field theory of directed polymers in a random medium exhibits replica symmetry breaking with a distribution of overlaps which consists of two delta functions. Here we show that the leading finite-size correction to this distribution of overlaps has a universal character which can be computed explicitly. Our results can also be interpreted as genealogical properties of branching Brownian motion or of branching random walks.

Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data.

Science.gov (United States)

Drummond, Alexei J; Nicholls, Geoff K; Rodrigo, Allen G; Solomon, Wiremu

2002-07-01

Molecular sequences obtained at different sampling times from populations of rapidly evolving pathogens and from ancient subfossil and fossil sources are increasingly available with modern sequencing technology. Here, we present a Bayesian statistical inference approach to the joint estimation of mutation rate and population size that incorporates the uncertainty in the genealogy of such temporally spaced sequences by using Markov chain Monte Carlo (MCMC) integration. The Kingman coalescent model is used to describe the time structure of the ancestral tree. We recover information about the unknown true ancestral coalescent tree, population size, and the overall mutation rate from temporally spaced data, that is, from nucleotide sequences gathered at different times, from different individuals, in an evolving haploid population. We briefly discuss the methodological implications and show what can be inferred, in various practically relevant states of prior knowledge. We develop extensions for exponentially growing population size and joint estimation of substitution model parameters. We illustrate some of the important features of this approach on a genealogy of HIV-1 envelope (env) partial sequences.

Erving Goffman: vida y genealogía intelectual

Directory of Open Access Journals (Sweden)

Urteaga, Eguzki

2010-06-01

Full Text Available What does happen when two or more persons are in a face to face situation? How the interaction develops when one of them commits an infamy, presents a physical disability or if he is considered as a mental patient? Erving Goffman (1922-1982, of Canadian origin, has tried to answer to this type of questions along his research life. It result an abundant, exciting but also controversial work because if some analysts see in Goffman the principal sociologist of the second half of the 20th century, others think that his analyses only constitute the reflection of a «petit bourgeois» point of view on the urban American society. This article presents both the life and the intellectual genealogy of this sociologist.

¿Qué sucede cuando dos o más personas se encuentran en una situación de cara a cara? ¿Cómo se desarrolla la interacción cuando una de ellas comete una torpeza o presenta una discapacidad física o si está considerada como una enferma mental? Erving Goffman (1922-1982, de origen canadiense, ha intentado contestar a ese tipo de preguntas a lo largo de su vida investigadora. Resulta de todo ello una obra abundante, apasionante pero también controvertida, puesto que algunos analistas ven en Goffman el mayor sociólogo de la segunda mitad del siglo XX mientras que otros consideran que sus análisis solo constituyen el reflejo de un punto de vista «pequeño-burgués» sobre la sociedad urbana americana. Este artículo presenta tanto la vida como la genealogía intelectual de ese sociólogo.

An academic genealogy on the history of American field primatologists.

Science.gov (United States)

Kelley, Elizabeth A; Sussman, Robert W

2007-03-01

In this paper, we present the academic genealogy of American field primatologists. The genealogy has been compiled to formally document the historical record of this young field. Data have been collected from three main sources: 1) e-mail surveys, 2) library and Internet research, and 3) verbal communication through forums such as American Association of Physical Anthropology meetings. Lineages of primatologists have been graphically displayed using Microsoft Visio. As of September 2005, 672 names and 239 affiliated universities, organizations and institutions have been recorded in 19 lineages. Five hundred and thirty-eight of the 672 names, 80.1%, are field primatologists. The Hooton/Washburn lineage is the largest; 60.6% of the recorded field primatologists are linked to this lineage. In addition, four of the five professors who have mentored a comparable number of field primatologists at American universities since Washburn are linked to the Hooton/Washburn lineage; and the school where Washburn mentored a majority of his students, UC-Berkeley, continues to have the highest overall graduation record for this subdiscipline. However, the field of primatology has been diversifying since the 1960s, and different universities are now responsible for graduating a substantial number of primatologists. We conclude that while the Hooton/Washburn lineage has remained remarkably homogenous in its anthropological focus, the field is also becoming increasingly enriched by primatologists who have had training in fields such as zoology, psychology, and ecology both in the United States and abroad. (c) 2006 Wiley-Liss, Inc.

The Promise of the New: Genealogies of Youth, Nation and Educational Reform in Australia

Science.gov (United States)

McLeod, Julie; Wright, Katie

2012-01-01

The promise of the new underpins much educational reform discourse, from utopian strands and grand gestures to more formulaic rhetoric found in declarations of new policies for new times. Informed by genealogical and feminist approaches, this essay introduces some conceptual frameworks for analysing such expressions of hopefulness and newness in…

Does having children extend life span? A genealogical study of parity and longevity in the Amish.

Science.gov (United States)

McArdle, Patrick F; Pollin, Toni I; O'Connell, Jeffrey R; Sorkin, John D; Agarwala, Richa; Schäffer, Alejandro A; Streeten, Elizabeth A; King, Terri M; Shuldiner, Alan R; Mitchell, Braxton D

2006-02-01

The relationship between parity and life span is uncertain, with evidence of both positive and negative relationships being reported previously. We evaluated this issue by using genealogical data from an Old Order Amish community in Lancaster, Pennsylvania, a population characterized by large nuclear families, homogeneous lifestyle, and extensive genealogical records. The analysis was restricted to the set of 2,015 individuals who had children, were born between 1749 and 1912, and survived until at least age 50 years. Pedigree structures and birth and death dates were extracted from Amish genealogies, and the relationship between parity and longevity was examined using a variance component framework. Life span of fathers increased in linear fashion with increasing number of children (0.23 years per additional child; p =.01), while life span of mothers increased linearly up to 14 children (0.32 years per additional child; p =.004) but decreased with each additional child beyond 14 (p =.0004). Among women, but not men, a later age at last birth was associated with longer life span (p =.001). Adjusting for age at last birth obliterated the correlation between maternal life span and number of children, except among mothers with ultrahigh (>14 children) parity. We conclude that high parity among men and later menopause among women may be markers for increased life span. Understanding the biological and/or social factors mediating these relationships may provide insights into mechanisms underlying successful aging.

Genealogías y molecular de los descendientes del Marquéz de Yavi

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Alfaro Gómez, Emma Laura

2007-01-01

Full Text Available El título nobiliario de Marqués del Valle del Toxo, conocido comúnmente como Marqués de Yavi, era el más importante en el territorio del virreinato del Río de la Plata y se extendía por toda la Puna argentina y diversos municipios de Bolivia. Hubo cuatro marqueses desde su creación en 1708 por la Real Cédula emitida por Felipe V, rey de España, hasta su disolución en 1820 luego del fallecimiento del cuarto marqués Juan José Feliciano Fernández Campero. La abundancia de referencias históricas sobre el Marquesado de Yavi, el reciente interés político por recuperar la figura histórica del último Marqués sumado al encuentro social de sus descendientes ofreció la extraordinaria posibilidad de realizar una reconstrucción detallada de la genealogía de la familia Campero y relacionarla con el estudio molecular de sus descendientes. Se analizaron muestras de 30 individuos Campero a través de 6 microsatélites del cromosoma Y (DYS:19, 389a y b, 390,392,393 Se encontraron 8 linajes paternos bien definidos, 16 muestras comparten un linaje único, el segundo linaje congrega a 5 individuos, el tercero y cuarto linaje cuentan con 2 individuos cada uno y en 5 muestras se encontraron linajes individuales no relacionados con los anteriores. De estos resultados se interpreta que en la Genealogía Campero coexisten linajes diferentes, de los cuales uno de ellos, el mayoritario, probablemente sea el linaje fundador de esta genealogía. Se discuten estos resultados a la luz de la información genealógica e histórica.

Evolutionary analyses of non-genealogical bonds produced by introgressive descent.

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Bapteste, Eric; Lopez, Philippe; Bouchard, Frédéric; Baquero, Fernando; McInerney, James O; Burian, Richard M

2012-11-06

All evolutionary biologists are familiar with evolutionary units that evolve by vertical descent in a tree-like fashion in single lineages. However, many other kinds of processes contribute to evolutionary diversity. In vertical descent, the genetic material of a particular evolutionary unit is propagated by replication inside its own lineage. In what we call introgressive descent, the genetic material of a particular evolutionary unit propagates into different host structures and is replicated within these host structures. Thus, introgressive descent generates a variety of evolutionary units and leaves recognizable patterns in resemblance networks. We characterize six kinds of evolutionary units, of which five involve mosaic lineages generated by introgressive descent. To facilitate detection of these units in resemblance networks, we introduce terminology based on two notions, P3s (subgraphs of three nodes: A, B, and C) and mosaic P3s, and suggest an apparatus for systematic detection of introgressive descent. Mosaic P3s correspond to a distinct type of evolutionary bond that is orthogonal to the bonds of kinship and genealogy usually examined by evolutionary biologists. We argue that recognition of these evolutionary bonds stimulates radical rethinking of key questions in evolutionary biology (e.g., the relations among evolutionary players in very early phases of evolutionary history, the origin and emergence of novelties, and the production of new lineages). This line of research will expand the study of biological complexity beyond the usual genealogical bonds, revealing additional sources of biodiversity. It provides an important step to a more realistic pluralist treatment of evolutionary complexity.

Determining Y-STR mutation rates in deep-routing genealogies: Identification of haplogroup differences.

Science.gov (United States)

Claerhout, Sofie; Vandenbosch, Michiel; Nivelle, Kelly; Gruyters, Leen; Peeters, Anke; Larmuseau, Maarten H D; Decorte, Ronny

2018-05-01

Knowledge of Y-chromosomal short tandem repeat (Y-STR) mutation rates is essential to determine the most recent common ancestor (MRCA) in familial searching or genealogy research. Up to now, locus-specific mutation rates have been extensively examined especially for commercially available forensic Y-STRs, while haplogroup specific mutation rates have not yet been investigated in detail. Through 450 patrilineally related namesakes distributed over 212 deep-rooting genealogies, the individual mutation rates of 42 Y-STR loci were determined, including 27 forensic Y-STR loci from the Yfiler ® Plus kit and 15 additional Y-STR loci (DYS388, DYS426, DYS442, DYS447, DYS454, DYS455, DYS459a/b, DYS549, DYS607, DYS643, DYS724a/b and YCAIIa/b). At least 726 mutations were observed over 148,596 meiosis and individual Y-STR mutation rates varied from 2.83 × 10 -4 to 1.86 × 10 -2 . The mutation rate was significantly correlated with the average allele size, the complexity of the repeat motif sequence and the age of the father. Significant differences in average Y-STR mutations rates were observed when haplogroup 'I & J' (4.03 × 10 -3 mutations/generation) was compared to 'R1b' (5.35 × 10 -3 mutations/generation) and to the overall mutation rate (5.03 × 10 -3 mutations/generation). A difference in allele size distribution was identified as the only cause for these haplogroup specific mutation rates. The haplogroup specific mutation rates were also present within the commercially available Y-STR kits (Yfiler ® , PowerPlex ® Y23 System and Yfiler ® Plus). This observation has consequences for applications where an average Y-STR mutation rate is used, e.g. tMRCA estimations in familial searching and genealogy research. Copyright © 2018 Elsevier B.V. All rights reserved.

A Genealogy of the "Future": Antipodean Trajectories and Travels of the "21st Century Learner"

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Williams, Carolyn; Gannon, Susanne; Sawyer, Wayne

2013-01-01

In this paper, from the particular positioning of educational researchers working in Australia, we unpack the figure of the "21st century learner" from both broad and specific perspectives. The paper begins with a policy genealogy that traces this figure through networks of documents, events and bodies that transcend borders and…

From Policies to Implementation of Open Distance Learning in Rwanda: A Genealogical and Governmentality Analysis

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Mukama, Evode

2018-01-01

The purpose of this paper is to analyse the interplay between policy formulation and implementation in terms of the historical practices of open distance learning (ODL) in Rwanda. This paper draws on the Foucauldian genealogical and governmentality analysis. The paper examines government aspirations as depicted in policy statements starting from…

Genealogy construction in a historically isolated population: application to genetic studies of rheumatoid arthritis in the Pima Indian.

Science.gov (United States)

Lin, J P; Hirsch, R; Jacobsson, L T; Scott, W W; Ma, L D; Pillemer, S R; Knowler, W C; Kastner, D L; Bale, S J

1999-01-01

Due to the characteristics of complex traits, many traits may not be amenable to traditional epidemiologic methods. We illustrate an approach that defines an isolated population as the "unit" for carrying out studies of complex disease. We provide an example using the Pima Indians, a relatively isolated population, in which the incidence and prevalence of Type 2 diabetes, gallbladder disease, and rheumatoid arthritis (RA) are significantly increased compared with the general U.S. population. A previous study of RA in the Pima utilizing traditional methods failed to detect a genetic effect on the occurrence of the disease. Our approach involved constructing a genealogy for this population and using a genealogic index to investigate familial aggregation. We developed an algorithm to identify biological relationships among 88 RA cases versus 4,000 subsamples of age-matched individuals from the same population. Kinship coefficients were calculated for all possible pairs of RA cases, and similarly for the subsamples. The sum of the kinship coefficient among all combination of RA pairs, 5.92, was significantly higher than the average of the 4,000 subsamples, 1.99 (p genealogy can be anticipated to provide valuable information for the genetic study of diseases other than RA. Defining an isolated population as the "unit" in which to assess familial aggregation may be advantageous, especially if there are a limited number of cases in the study population.

Sex and monstrosity. A genealogy of the sexual police

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Antón Fernández de Rota Irimia

2015-07-01

Full Text Available This essay outlines different forms of Western sexual police from the Seventeen Century to the present. The genealogy will approach the problem from the point of view of hermaphroditism and transvestism. By “sexual police” I mean the determinations, forms, norms and ethos that defines sex through times, as well as the categories of which it is composed, and what is permitted and is possible to do, see and say through these sexual categories. This essay, pays special attention to the fears and its embodiment in some paradigmatic figures. In particular, it analyzes the historical meaning of sexual “monstrosity”, key to understand the different polices, including the own sexual police of gender feminism.

Genealogy of Biopolitics: The Biology of the State

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Mikołaj Ratajczak

2013-01-01

Full Text Available The aim of the paper is to analyze a popular pseudo-scientific discoursein Germany in the twenties that developed an idea of a state as a living organism.The discourse was sometimes named “the biology of the state”. The aim ofthis analysis is to provide a genealogy of the term “biopolitics” that was first usedby a Swedish theoretician of the biology of the state Rudolf Kjellén and to showthe influence, that the idea of the biology of the state had on the development ofthe Nazi biopolitics. The paper reconstructs the main aspects of Michel Foucault’sgenealogy of the modern biopolitics and subsequently shows, how the idea of thebiology of the state constituted the extreme development of the naturalistic tendenciesdiagnosed by Foucault in the modern theories of (biopolitics.

Derin Paşaoǧlu D. Genealogy of the Crimean Khans according to “Umdet al-Akhbar” by Abdulgaffar Kyrymi

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Derya Derin Paşaoǧlu

2017-03-01

Full Text Available The article considers the genealogy of the Girayids contained in “Umdet al-Akhbar” by Abdulgaffar Kyrymi. Abdulgaffar Kyrymi was a great connoisseur of the Turkic-Tatar history. He wrote his historical work in 1747 according to the Ottoman-Turkish tradition, that is, the author gave detailed information about the history of the prophets since Adam, the history of Islam, Islamic Turkic states, the State of Seljuks and the Ottoman State, Chinggis Khan and his sons. Moreover, he collected most of the information from local sources of that period. But the main part of the work contains the history of Juchi Khan, his children and the history of the Crimea. It is for this reason that Abdulgaffar Kyrymi gives such a detailed genealogy of the Girayids and the sequence of their rules in the Crimean Khanate. Abdulgaffar Kyrymi’s genealogy begins with Chinggis Khan and his daughters (Kuchi Bike, Chechgan Bigim, Tumalyn Bigim, Elyatun Bigim, Turaly Bigim as well as with his 500 wives. But only five of them were respected: Borte Kuchin Biim, Kulan Bigim, Suyugan Khatun Bigim, Kökchi Bigim, Jeksulu Bigim. List of the Crimean dynasty of the Girayids is offered here to specialists, beginning with Haji Giray to Arslan Giray. Comparison of the list of the Girayid khans contained in “Umdet al-Akhbar” with researches on this topic reveals some differences. In the opinion of the author, to solve these problems, along with genealogical and other narrative sources, it is also necessary to use the numismatics data and a large corpus of letters of the Crimean khans to the rulers of various countries.

When Markers Meet Marketing: Ethnicity, Race, Hybridity, and Kinship in Genetic Genealogy Television Advertising

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Christine Scodari

2017-12-01

Full Text Available The essay explores issues pertaining to genetics vs. culture in understandings of kinship, hybridity as a disruptor of essentialist conceptions of race, the fetishization of ethnicity and culture, racist misuses of genetic science, processes of racialization, and counter-hegemonic resistance. Thirty- and sixty-second television advertisements airing in the U.S. from the 23andMe and AncestryDNA genetic genealogy testing services are analyzed in this context. The investigation demonstrates that genetic ancestry testing providers are well aware that their enterprise is premised on belief in the superiority of biological kinship and that hybridity is mobilized primarily as a marketing opportunity with ethnic components signified in shorthand by fetishized objects. Moreover, the categories of race and ethnicity presented in the ads give cover to racist abusers of genetic science, as the ads are consistent with socially constructed racial classifications. While maintaining this consistency, the categories are subject to adjustment based on the expectations of consumers. Resistance is possible in the use of genetic ancestry by descendants of African slaves to make localized connections to Africa, something that conventional genealogy seldom provides.

The Normalising Power of Marriage Law: An Irish Genealogy, 1945 – 2010

OpenAIRE

McGowan, Deirdre

2015-01-01

Marriage law is often conceptualised as an instrument of power that illegitimately imposes the will of the State on its citizens. Paradoxically, marriage law is also offered as a route to liberation. In this thesis, I question the efficacy of this type of analysis by investigating the actual power effects of marriage law. Using Michel Foucault’s concepts of bio-power and government, and his genealogical approach to history, I identify the role played by marriage law in governing the social do...

GENEALOGI DAN PENYEBARAN THARIQAH QADIRIYAH WA NAQSHABANDIYAH DI JAWA

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Aly Mashar

2016-11-01

Full Text Available This article investigates the geneology and spread of Thariqah Qadiriyah wa Naqshabandiyah in Java. Based on the previous literatures (Dhofier, Martin van Bruinessen, Zulkifli, and Mulyati, it was found out that in Java the genealogy of the thariqah formed by Syekh Ahmad Khatib Sambas directed to the three primary khalifah, i.e. Syekh Abdul Karim Banten, Syekh Ahmad Thalhah Cirebon, and Syekh Muhammad Hasbullah Madura, then spread out across Java Island through the four centers (on 1970s, such as Suryalaya, Rejoso, Mranggen, and Pangentongan. However, the writer found out that there were four khalifahs, including Syekhona Kholil Bangkalan Madura; with the nine dissemination centers (in 1970s including Berjan Purworejo, Sawah Pulo Surabaya, Cukir Jombang, Kencong Kediri, and Dawe Kudus.

Characterization of parasporin gene harboring Indian isolates of Bacillus thuringiensis

OpenAIRE

Lenina, N. K.; Naveenkumar, A.; Sozhavendan, A. E.; Balakrishnan, N.; Balasubramani, V.; Udayasuriyan, V.

2013-01-01

Bacillus thuringiensis (Bt) is popularly known as insecticidal bacterium. However, non-insecticidal Bt strains are more extensively available in natural environment than the insecticidal ones. Parasporin (PS) is a collection of genealogically heterogeneous Cry proteins synthesized in non-insecticidal isolates of Bt. An important character generally related with PS proteins is their strong cytocidal activity preferentially on human cancer cells of various origins. Identification and characteri...

Rare event computation in deterministic chaotic systems using genealogical particle analysis

International Nuclear Information System (INIS)

Wouters, J; Bouchet, F

2016-01-01

In this paper we address the use of rare event computation techniques to estimate small over-threshold probabilities of observables in deterministic dynamical systems. We demonstrate that genealogical particle analysis algorithms can be successfully applied to a toy model of atmospheric dynamics, the Lorenz ’96 model. We furthermore use the Ornstein–Uhlenbeck system to illustrate a number of implementation issues. We also show how a time-dependent objective function based on the fluctuation path to a high threshold can greatly improve the performance of the estimator compared to a fixed-in-time objective function. (paper)

Feminismos: teoría y práctica. Genealogía de una discordia

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Cristina Morales Saro

2015-12-01

Full Text Available Today, discord between feminist activism and academic feminism is evident. However it reproduced a pattern that is in the basis of Western metaphysics and yet continues unquestioned. We want here problematize the dispute between theory and praxis within feminism, and we will deepen the understanding of it, doing its genealogy, after which we will be able to assess its scope and consider its usefulness or not for feminisms.

Feminismos: teoría y práctica. Genealogía de una discordia

OpenAIRE

Cristina Morales Saro

2015-01-01

Today, discord between feminist activism and academic feminism is evident. However it reproduced a pattern that is in the basis of Western metaphysics and yet continues unquestioned. We want here problematize the dispute between theory and praxis within feminism, and we will deepen the understanding of it, doing its genealogy, after which we will be able to assess its scope and consider its usefulness or not for feminisms.

Host specificity and genealogy of Polyplax serrata on Apodemus species: a case of parasite duplication or colonisation?

Czech Academy of Sciences Publication Activity Database

Štefka, Jan; Hypša, Václav

2008-01-01

Roč. 38, č. 6 (2008), s. 731-741 ISSN 0020-7519 R&D Projects: GA MŠk LC06073 Institutional research plan: CEZ:AV0Z60220518 Keywords : parasite duplication * host specificity * genealogy * speciation * Polyplax * Apodemus Subject RIV: EH - Ecology, Behaviour Impact factor: 3.752, year: 2008

On the Political Genealogy of Trump after Foucault

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Bruce M. Knauft

2018-01-01

Full Text Available How would Foucault have viewed Trump as President, and Trumpism in the US more generally? More realistically, how can we discern and insightfully apply genealogical insights after Foucault to better comprehend and act in relation to our current political situation in the US? Questions of factuality across a base register of asserted falsehoods are now prominent in American politics in ways that put assertions of scholarly objectivity and interpretation in yet deeper question than previously. The extent, range, and vitriol of alt-Right assertions and their viral growth in American media provoke progressivist resistance and anxiety, but how can this opposition be most productively channeled? This paper examines a range of critical perspectives, timeframes, and topical optics with respect to Trump and Trumpism, including nationalist, racist, sexist, class-based, and oligarchical dimensions. These are considered in relation to media and the incitement of polarized subjectivity and dividing practices, and also in relation to Marxist political economy, neoliberalism/neoimperialism, and postcolonialism. I then address the limit points of Foucault, including with respect to engaged political activism and social protest movements, and I consider the relevance of these for the diverse optics that political genealogy as a form of analysis might pursue. Notwithstanding and indeed because of the present impetus to take organized political action, a Foucauldian perspective is useful in foregrounding the broader late modern formations of knowledge, power, and subjectivity within which both Rightist and Leftist political sensibilities in the US are presently cast. At larger issue are the values inscribed through contemporary late modernity that inform both sides of present divisive polarities—and which make the prognosis of tipping points or future political outcomes particularly difficult. As such, productive strategies of activist opposition are likely to

Species-Level Para- and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in European Lepidoptera.

Science.gov (United States)

Mutanen, Marko; Kivelä, Sami M; Vos, Rutger A; Doorenweerd, Camiel; Ratnasingham, Sujeevan; Hausmann, Axel; Huemer, Peter; Dincă, Vlad; van Nieukerken, Erik J; Lopez-Vaamonde, Carlos; Vila, Roger; Aarvik, Leif; Decaëns, Thibaud; Efetov, Konstantin A; Hebert, Paul D N; Johnsen, Arild; Karsholt, Ole; Pentinsaari, Mikko; Rougerie, Rodolphe; Segerer, Andreas; Tarmann, Gerhard; Zahiri, Reza; Godfray, H Charles J

2016-11-01

The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service "Monophylizer" to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ∼23%, but with operational factors still being included. Within the operational factors, we separately assessed the

A complex selection signature at the human AVPR1B gene

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Cagliani Rachele

2009-06-01

Full Text Available Abstract Background The vasopressin receptor type 1b (AVPR1B is mainly expressed by pituitary corticotropes and it mediates the stimulatory effects of AVP on ACTH release; common AVPR1B haplotypes have been involved in mood and anxiety disorders in humans, while rodents lacking a functional receptor gene display behavioral defects and altered stress responses. Results Here we have analyzed the two exons of the gene and the data we present suggest that AVPR1B has been subjected to natural selection in humans. In particular, analysis of exon 2 strongly suggests the action of balancing selection in African populations and Europeans: the region displays high nucleotide diversity, an excess of intermediate-frequency alleles, a higher level of within-species diversity compared to interspecific divergence and a genealogy with common haplotypes separated by deep branches. This relatively unambiguous situation coexists with unusual features across exon 1, raising the possibility that a nonsynonymous variant (Gly191Arg in this region has been subjected to directional selection. Conclusion Although the underlying selective pressure(s remains to be identified, we consider this to be among the first documented examples of a gene involved in mood disorders and subjected to natural selection in humans; this observation might add support to the long-debated idea that depression/low mood might have played an adaptive role during human evolution.

A complex selection signature at the human AVPR1B gene.

Science.gov (United States)

Cagliani, Rachele; Fumagalli, Matteo; Pozzoli, Uberto; Riva, Stefania; Cereda, Matteo; Comi, Giacomo P; Pattini, Linda; Bresolin, Nereo; Sironi, Manuela

2009-06-01

The vasopressin receptor type 1b (AVPR1B) is mainly expressed by pituitary corticotropes and it mediates the stimulatory effects of AVP on ACTH release; common AVPR1B haplotypes have been involved in mood and anxiety disorders in humans, while rodents lacking a functional receptor gene display behavioral defects and altered stress responses. Here we have analyzed the two exons of the gene and the data we present suggest that AVPR1B has been subjected to natural selection in humans. In particular, analysis of exon 2 strongly suggests the action of balancing selection in African populations and Europeans: the region displays high nucleotide diversity, an excess of intermediate-frequency alleles, a higher level of within-species diversity compared to interspecific divergence and a genealogy with common haplotypes separated by deep branches. This relatively unambiguous situation coexists with unusual features across exon 1, raising the possibility that a nonsynonymous variant (Gly191Arg) in this region has been subjected to directional selection. Although the underlying selective pressure(s) remains to be identified, we consider this to be among the first documented examples of a gene involved in mood disorders and subjected to natural selection in humans; this observation might add support to the long-debated idea that depression/low mood might have played an adaptive role during human evolution.

Redefinisi Kaum Paderi Melalui Metodologi Genealogis Foucauldian Sebagai Rekonsiliasi Etnis Minangkabau-Batak

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Alfi Arifian

2016-11-01

Full Text Available Redefinisi Kaum Paderi merupakan konsep pendefinisian Kaum Paderi berdasarkan metodologi genealogis yang menulis sejarah berdasarkan kerangka kekinian. Definisi ini berbeda dari definisi Kaum Paderi dalam pandangan sejarah umum. Redefinisi ini dimaksudkan untuk memetakan gerakan Paderi berdasarkan konsep kekuasaan berbasis keamiran melalui gelar Tuanku Imam Bonjol merujuk kerangka kekuasaan nagari (balad-dalam pemahaman imamah. Tujuan pemetaan gerakan Paderi adalah membuktikan (secara teori bahwa ada dikotomi di tubuh Paderi sebagai gerakan pemurni Islam serta yang bersifat radikal. Dikotomi inilah yang digunakan sebagai dalih untuk membangun wacana rekonsiliasi antara etnis Minangkabau-Batak lantaran konflik masa lalu "Perang Paderi" jilid I.

Frequency of the severe combined immunodeficiency disease gene among horses in Morocco.

Science.gov (United States)

Piro, M; Benjouad, A; Tligui, N S; El Allali, K; El Kohen, M; Nabich, A; Ouragh, L

2008-09-01

Severe combined immunodeficiency disease (SCID) of horses is an autosomal, recessive hereditary disease occurring among Arabian or crossbred Arabian horses. The genetic defect responsible was previously identified as a 5-base pair deletion in the gene encoding the catalytic subunit of the DNA dependant protein kinase (DNA-PKcs). This study was carried out to determine the frequency of SCID and identify horses carrying the gene for SCID among Arabian and Arabian crossbred stallions and mares in Morocco using a DNA-based test. Twenty-one horses were SCID carriers: 14 (7%) Arabians, 6 (4%) Arab-Barbs and one (33%) Anglo-Arab. After analysing their genealogy, 3 imported stallions were identified that disseminated the mutant gene of DNA-PKcs in Morocco.

Gene-Lifestyle Interactions in Complex Diseases: Design and Description of the GLACIER and VIKING Studies.

Science.gov (United States)

Kurbasic, Azra; Poveda, Alaitz; Chen, Yan; Agren, Asa; Engberg, Elisabeth; Hu, Frank B; Johansson, Ingegerd; Barroso, Ines; Brändström, Anders; Hallmans, Göran; Renström, Frida; Franks, Paul W

2014-12-01

Most complex diseases have well-established genetic and non-genetic risk factors. In some instances, these risk factors are likely to interact, whereby their joint effects convey a level of risk that is either significantly more or less than the sum of these risks. Characterizing these gene-environment interactions may help elucidate the biology of complex diseases, as well as to guide strategies for their targeted prevention. In most cases, the detection of gene-environment interactions will require sample sizes in excess of those needed to detect the marginal effects of the genetic and environmental risk factors. Although many consortia have been formed, comprising multiple diverse cohorts to detect gene-environment interactions, few robust examples of such interactions have been discovered. This may be because combining data across studies, usually through meta-analysis of summary data from the contributing cohorts, is often a statistically inefficient approach for the detection of gene-environment interactions. Ideally, single, very large and well-genotyped prospective cohorts, with validated measures of environmental risk factor and disease outcomes should be used to study interactions. The presence of strong founder effects within those cohorts might further strengthen the capacity to detect novel genetic effects and gene-environment interactions. Access to accurate genealogical data would also aid in studying the diploid nature of the human genome, such as genomic imprinting (parent-of-origin effects). Here we describe two studies from northern Sweden (the GLACIER and VIKING studies) that fulfill these characteristics.

What's in a name? Y chromosomes, surnames and the genetic genealogy revolution.

Science.gov (United States)

King, Turi E; Jobling, Mark A

2009-08-01

Heritable surnames are highly diverse cultural markers of coancestry in human populations. A patrilineal surname is inherited in the same way as the non-recombining region of the Y chromosome and there should, therefore, be a correlation between the two. Studies of Y haplotypes within surnames, mostly of the British Isles, reveal high levels of coancestry among surname cohorts and the influence of confounding factors, including multiple founders for names, non-paternities and genetic drift. Combining molecular genetics and surname analysis illuminates population structure and history, has potential applications in forensic studies and, in the form of 'genetic genealogy', is an area of rapidly growing interest for the public.

Interferon-β gene transfer induces a strong cytotoxic bystander effect on melanoma cells.

Science.gov (United States)

Rossi, Úrsula A; Gil-Cardeza, María L; Villaverde, Marcela S; Finocchiaro, Liliana M E; Glikin, Gerardo C

2015-05-01

A local gene therapy scheme for the delivery of type I interferons could be an alternative for the treatment of melanoma. We evaluated the cytotoxic effects of interferon-β (IFNβ) gene lipofection on tumor cell lines derived from three human cutaneous and four canine mucosal melanomas. The cytotoxicity of human IFNβ gene lipofection resulted higher or equivalent to that of the corresponding addition of the recombinant protein (rhIFNβ) to human cells. IFNβ gene lipofection was not cytotoxic for only one canine melanoma cell line. When cultured as monolayers, three human and three canine IFNβ-lipofected melanoma cell lines displayed a remarkable bystander effect. As spheroids, the same six cell lines were sensitive to IFNβ gene transfer, two displaying a significant multicell resistance phenotype. The effects of conditioned IFNβ-lipofected canine melanoma cell culture media suggested the release of at least one soluble thermolabile cytotoxic factor that could not be detected in human melanoma cells. By using a secretion signal-free truncated human IFNβ, we showed that its intracellular expression was enough to induce cytotoxicity in two human melanoma cell lines. The lower cytoplasmatic levels of reactive oxygen species detected after intracellular IFNβ expression could be related to the resistance displayed by one human melanoma cell line. As IFNβ gene transfer was effective against most of the assayed melanomas in a way not limited by relatively low lipofection efficiencies, the clinical potential of this approach is strongly supported. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

LAMMPS strong scaling performance optimization on Blue Gene/Q

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Coffman, Paul; Jiang, Wei; Romero, Nichols A.

2014-11-12

LAMMPS "Large-scale Atomic/Molecular Massively Parallel Simulator" is an open-source molecular dynamics package from Sandia National Laboratories. Significant performance improvements in strong-scaling and time-to-solution for this application on IBM's Blue Gene/Q have been achieved through computational optimizations of the OpenMP versions of the short-range Lennard-Jones term of the CHARMM force field and the long-range Coulombic interaction implemented with the PPPM (particle-particle-particle mesh) algorithm, enhanced by runtime parameter settings controlling thread utilization. Additionally, MPI communication performance improvements were made to the PPPM calculation by re-engineering the parallel 3D FFT to use MPICH collectives instead of point-to-point. Performance testing was done using an 8.4-million atom simulation scaling up to 16 racks on the Mira system at Argonne Leadership Computing Facility (ALCF). Speedups resulting from this effort were in some cases over 2x.

Identification, genealogical structure and population genetics of S-alleles in Malus sieversii, the wild ancestor of domesticated apple.

Science.gov (United States)

Ma, X; Cai, Z; Liu, W; Ge, S; Tang, L

2017-09-01

The self-incompatibility (SI) gene that is specifically expressed in pistils encodes the SI-associated ribonuclease (S-RNase), functioning as the female-specificity determinant of a gametophytic SI system. Despite extensive surveys in Malus domestica, the S-alleles have not been fully investigated for Malus sieversii, the primary wild ancestor of the domesticated apple. Here we screened the M. sieversii S-alleles via PCR amplification and sequencing, and identified 14 distinct alleles in this species. By contrast, nearly 40 are present in its close wild relative, Malus sylvestris. We further sequenced 8 nuclear genes to provide a neutral reference, and investigated the evolution of S-alleles via genealogical and population genetic analyses. Both shared ancestral polymorphism and an excess of non-synonymous substitution were detected in the S-RNases of the tribe Maleae in Rosaceae, indicating the action of long-term balancing selection. Approximate Bayesian Computations based on the reference neutral loci revealed a severe bottleneck in four of the six studied M. sieversii populations, suggesting that the low number of S-alleles found in this species is mainly the result of diversity loss due to a drastic population contraction. Such a bottleneck may lead to ambiguous footprints of ongoing balancing selection detected at the S-locus. This study not only elucidates the constituents and number of S-alleles in M. sieversii but also illustrates the potential utility of S-allele number shifts in demographic inference for self-incompatible plant species.

<strong>Genes Involved in Human Ribosome Biogenesis areTranscriptionally Upregulated in Colorectal Cancerstrong>

DEFF Research Database (Denmark)

Mansilla, Francisco; Lamy, Philippe; Ørntoft, Torben Falck

2009-01-01

Microarray gene expression profiling comprising 168 colorectal adenocarcinomas and 10 normal mucosas showed that over 79% of the genes involved in human ribosome biogenesis are significantly upregulated (log2>0.5, p<10-3) when compared to normal mucosa. Overexpression was independent of microsate......Microarray gene expression profiling comprising 168 colorectal adenocarcinomas and 10 normal mucosas showed that over 79% of the genes involved in human ribosome biogenesis are significantly upregulated (log2>0.5, p... of microsatellite status. The promoters of the genes studied showed a significant enrichment for several transcription factor binding sites. There was a significant correlation between the number of binding site targets for these transcription factors and the observed gene transcript upregulation. The upregulation...

"Father to no one": gender, genealogy, and storytelling in go down, Moses "Father to no one": gender, genealogy, and storytelling in go down, Moses

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Barbara Ladd

2008-04-01

Full Text Available "Was", the first story of Go Down, Moses, opens with the disclaimer that the protagonist Isaac McCaslin is "father to no one" and that the story to follow: was not something participated in or even seen by himself, but by his elder cousin, McCaslin Edmonds, grandson of Isaac's father's sister and so descended by the distaff, yet notwithstanding the inheritor, and in his time the bequestor, of that which some had thought then and some still thought should have been Isaac's, since his was the name in which the title to the land had first been granted from the Indian patent and which some of the descendants of his father's slaves still bore in the land. But Isaac was not one of these... (3. What is almost immediately clear is that the hook opens with issues of gender, genealogy, and inheritance foregrounded, and that these issues concern not merely the transmission of land from generation to generation but the transmission of stories, a kind of "naming" of one's relationship to the past that echoes the assigning of family names in the above passage. "Was", the first story of Go Down, Moses, opens with the disclaimer that the protagonist Isaac McCaslin is "father to no one" and that the story to follow: was not something participated in or even seen by himself, but by his elder cousin, McCaslin Edmonds, grandson of Isaac's father's sister and so descended by the distaff, yet notwithstanding the inheritor, and in his time the bequestor, of that which some had thought then and some still thought should have been Isaac's, since his was the name in which the title to the land had first been granted from the Indian patent and which some of the descendants of his father's slaves still bore in the land. But Isaac was not one of these... (3. What is almost immediately clear is that the hook opens with issues of gender, genealogy, and inheritance foregrounded, and that these issues concern not merely the transmission of land

Horizontal gene transfer in chromalveolates

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Bhattacharya Debashish

2007-09-01

Full Text Available Abstract Background Horizontal gene transfer (HGT, the non-genealogical transfer of genetic material between different organisms, is considered a potentially important mechanism of genome evolution in eukaryotes. Using phylogenomic analyses of expressed sequence tag (EST data generated from a clonal cell line of a free living dinoflagellate alga Karenia brevis, we investigated the impact of HGT on genome evolution in unicellular chromalveolate protists. Results We identified 16 proteins that have originated in chromalveolates through ancient HGTs before the divergence of the genera Karenia and Karlodinium and one protein that was derived through a more recent HGT. Detailed analysis of the phylogeny and distribution of identified proteins demonstrates that eight have resulted from independent HGTs in several eukaryotic lineages. Conclusion Recurring intra- and interdomain gene exchange provides an important source of genetic novelty not only in parasitic taxa as previously demonstrated but as we show here, also in free-living protists. Investigating the tempo and mode of evolution of horizontally transferred genes in protists will therefore advance our understanding of mechanisms of adaptation in eukaryotes.

Host specificity and genealogy of the louse Polyplax serrata on field mice, Apodemus species: a case of parasite duplication or colonisation?

Science.gov (United States)

Stefka, Jan; Hypsa, Václav

2008-05-01

The genealogy, population structure and population dynamics of the sucking louse Polyplax serrata were analysed across four host species of the genus Apodemus. An analysis of 126 sequences of cytochrome c oxidase subunit I using phylogenetic approaches and haplotype networking revealed a clear structure of European samples, forming three distinct and genetically distant clades with different host specificities. Although a clear connection was detected between the host and parasite genealogies/phylogenies, a uniform pattern of co-speciation was not found. For example, a dramatic shift in the degree of host specificity was demonstrated for two related louse lineages living in sympatry and sharing one of their host species. While one of the louse lineages frequently parasitised two different host taxa (Apodemus sylvaticus and Apodemus flavicollis), the other louse lineage was strictly specific to A. flavicollis. The estimate of divergence time between the two louse lineages indicates that they may have arisen due to parasite duplication on A. flavicollis.

Species-level para- and polyphyly in DNA barcode gene trees

DEFF Research Database (Denmark)

Mutanen, Marko; Kivelä, Sami M.; Vos, Rutger A.

2016-01-01

was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than...... between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service "Monophylizer......" to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention...

The Philosophical Genealogy of Taylor's Social Imaginaries: A Complex History of Ideas and Predecessors.

Science.gov (United States)

Vanheeswijck, Guido M

2017-01-01

The deepest sources of Charles Taylor's use of the concept "social imaginaries" are often related to political philosophy or social anthropology (Anderson, Castoriadis). The purpose of this article is to show that they also form part of Taylor's struggle to overcome the epistemological construal in modern philosophy and culture. Taylor locates the concept "social imaginaries" in the Kantian tradition, identifying their role to that of transcendental schemes. However, there remains a central difference between Kant's transcendental schemes and Taylor's social imaginaries. To elucidate that difference, this article will track the philosophical genealogy of Taylor's concept of "social imaginaries" in three steps.

Genetic variability within french race and riding horse breeds from genealogical data and blood marker polymorphisms

OpenAIRE

Moureaux, Sophie; Verrier, Etienne; Ricard, Anne; Meriaux, J-Claude

1996-01-01

The genetic variability of five horse breeds raised in France was analysed: Thoroughbred, Trotteur Français, Arab, Anglo-Arab and Selle Français. Genealogical data and genotypes at seven blood group and nine protein loci were used. Paternal family sizes were found to be unbalanced, especially in Trotteur français, Selle Franqais and Thoroughbred. Average coefficients of inbreeding for offspring born from 1989 to 1992 were 1.02 (Thoroughbred), 1.86 (Trotteur Français), 3.08 (Arab), 1.17 (...

Genealogical and molecular analysis of a family-based cohort of congenital heart disease patients from the São Miguel Island (Azores, Portugal).

Science.gov (United States)

Cabral, Rita; Pires, Renato; Anjos, Rui; Branco, Claudia C; Maciel, Paula; Mota-Vieira, Luisa

2016-11-01

Congenital heart disease (CHD) is one common birth malformation, accounting for ∼30% of total congenital abnormalities. Considering the unknown role of consanguinity in causing CHD, this study hypothesised that consanguineous unions and/or familial aggregation may be frequent in the Azorean Island of São Miguel (Portugal). To that end, a retrospective observational study was performed based on genealogical and molecular analyses. The study enrolled 112 CHD patients from São Miguel Island, which allowed the assessment of type of family (simplex or multiplex), parental consanguinity and grandparental endogamy. Based on 15 STR markers, inbreeding coefficients (F IS ) in the CHD cohort and healthy control group (n = 114) were estimated. Multiplex families were 37.6% (n = 41/109), a rate considerably higher than previously described in the literature (genealogical and genetic features related with CHD, revealing the presence of parental consanguinity and extensive familial aggregation in the CHD patients from São Miguel Island.

Michel Foucault and the genealogy as a criticism of the present

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Selvino José Assmann

2007-04-01

Full Text Available The main goal of this paper is to analyze the criticism to modernity that is in Foucault’s genealogy. First we discuss Focault’s analysis of Kant’s article on Aufklärung and Baudelaire’s concept of dandy. So, we focus gave emphasis the “truth analytic” and its ontextualization made by Foucault of the social role of an intellectual in the light of the great changes in knowledge and in the practices of power in the last decades. To conclude, we suggest that, by studying the Aufklärung investigating the excess of modern racionality, Foucault tries to reassess the possibilities of freedom practices, sustaining the criticism exercise as philosophical ethos. This is needed to redefine the governability and ethical and political commitments made by the agents in different social places.

Transformation of follicular lymphoma to plasmablastic lymphoma with c-myc gene rearrangement.

Science.gov (United States)

Ouansafi, Ihsane; He, Bing; Fraser, Cory; Nie, Kui; Mathew, Susan; Bhanji, Rumina; Hoda, Rana; Arabadjief, Melissa; Knowles, Daniel; Cerutti, Andrea; Orazi, Attilio; Tam, Wayne

2010-12-01

Follicular lymphoma (FL) is an indolent lymphoma that transforms to high-grade lymphoma, mostly diffuse large B-cell lymphoma, in about a third of patients. We present the first report of a case of FL that transformed to plasmablastic lymphoma (PBL). Clonal transformation of the FL to PBL was evidenced by identical IGH/BCL2 gene rearrangements and VDJ gene usage in rearranged IGH genes. IGH/ BCL2 translocation was retained in the PBL, which also acquired c-myc gene rearrangement. Genealogic analysis based on somatic hypermutation of the rearranged IGH genes of both FL and PBL suggests that transformation of the FL to PBL occurred most likely by divergent evolution from a common progenitor cell rather than direct evolution from the FL clone. Our study of this unusual case expands the histologic spectrum of FL transformation and increases our understanding of the pathogenetic mechanisms of transformation of indolent lymphomas to aggressive lymphomas.

Replication of genetic associations as pseudoreplication due to shared genealogy.

Science.gov (United States)

Rosenberg, Noah A; Vanliere, Jenna M

2009-09-01

The genotypes of individuals in replicate genetic association studies have some level of correlation due to shared descent in the complete pedigree of all living humans. As a result of this genealogical sharing, replicate studies that search for genotype-phenotype associations using linkage disequilibrium between marker loci and disease-susceptibility loci can be considered as "pseudoreplicates" rather than true replicates. We examine the size of the pseudoreplication effect in association studies simulated from evolutionary models of the history of a population, evaluating the excess probability that both of a pair of studies detect a disease association compared to the probability expected under the assumption that the two studies are independent. Each of nine combinations of a demographic model and a penetrance model leads to a detectable pseudoreplication effect, suggesting that the degree of support that can be attributed to a replicated genetic association result is less than that which can be attributed to a replicated result in a context of true independence.

History and Sociology: A genealogical perspective

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Ştefan UNGUREAN

2012-01-01

Full Text Available What could we possibly learn from a 70 year correspondence from the years of the Second World War, when the course of subsequent history has already been known? The sociologist is interested in seeing how an event unfolds, how it generates other actions, how the actors are driven by, what their strategies are and how they interact. The aim of the present essay is to identify those sociological concepts, that could lead us to explanations of the geopolitical, regarding the way Germany built up its hegemony, by starting from a genealogical perspective, that is, by identifying the logics of a situation and by understanding the reasoning behind individual decision while taking into consideration the analysis of the discourse. We take into account how enforcing a drastic peace treaty on Germany has lead to high surveillance costs that could not be sustained by the victors because of their path dependence, which ultimately led to the fact of the ‘good’ being sacrificed for the sake of the ‘comfortable’. We understand how military successes represent the test of truth for an ideology and provide the Nazi leaders with their legitimacy, inciting a group phantasm. We discern, in the relations between Germany, Soviet Union and the French-English duo, all the elements of a triad and, implicitly, all elements of power that are generated by a game based on imposing and accepting uncertainties. All of the above bare evidence to the fact that sociological notions and concepts can produce revelations when taken into new domains, such as geopolitics and war.

SiRNAs conjugated with aromatic compounds induce RISC-mediated antisense strand selection and strong gene-silencing activity

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Kubo, Takanori, E-mail: kubo-t@yasuda-u.ac.jp [Faculty of Pharmacy, Yasuda Women' s University, 6-13-1 Yasuhigashi, Asaminami-ku, Hiroshima 731-0153 (Japan); Yanagihara, Kazuyoshi [Faculty of Pharmacy, Yasuda Women' s University, 6-13-1 Yasuhigashi, Asaminami-ku, Hiroshima 731-0153 (Japan); Division of Genetics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 (Japan); Takei, Yoshifumi [Department of Biochemistry, Nagoya University Graduate School of Medicine, 65 Tsurumi-cho, Showa-ku, Nagoya 466-8550 (Japan); Mihara, Keichiro [Department of Hematology and Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553 (Japan); Sato, Yuichiro; Seyama, Toshio [Faculty of Pharmacy, Yasuda Women' s University, 6-13-1 Yasuhigashi, Asaminami-ku, Hiroshima 731-0153 (Japan)

2012-10-05

Highlights: Black-Right-Pointing-Pointer SiRNAs conjugated with aromatic compounds (Ar-siRNAs) at 5 Prime -sense strand were synthesized. Black-Right-Pointing-Pointer Ar-siRNAs increased resistance against nuclease degradation. Black-Right-Pointing-Pointer Ar-siRNAs were thermodynamically stable compared with the unmodified siRNA. Black-Right-Pointing-Pointer High levels of cellular uptake and cytoplasmic localization were found. Black-Right-Pointing-Pointer Strong gene-silencing efficacy was exhibited in the Ar-siRNAs. -- Abstract: Short interference RNA (siRNA) is a powerful tool for suppressing gene expression in mammalian cells. In this study, we focused on the development of siRNAs conjugated with aromatic compounds in order to improve the potency of RNAi and thus to overcome several problems with siRNAs, such as cellular delivery and nuclease stability. The siRNAs conjugated with phenyl, hydroxyphenyl, naphthyl, and pyrenyl derivatives showed strong resistance to nuclease degradation, and were thermodynamically stable compared with unmodified siRNA. A high level of membrane permeability in HeLa cells was also observed. Moreover, these siRNAs exhibited enhanced RNAi efficacy, which exceeded that of locked nucleic acid (LNA)-modified siRNAs, against exogenous Renilla luciferase in HeLa cells. In particular, abundant cytoplasmic localization and strong gene-silencing efficacy were found in the siRNAs conjugated with phenyl and hydroxyphenyl derivatives. The novel siRNAs conjugated with aromatic compounds are promising candidates for a new generation of modified siRNAs that can solve many of the problems associated with RNAi technology.

Genealogy and the Consecration of the Biopolitics Term. Interchanges Between Esposito, Arendt and Foucault

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Lara Emanuele da Luz

2017-11-01

Full Text Available The present article intends, on the one hand, to study the genealogy of the term biopolitics, passing through the term bíos. To support this reflection, the first part of the book by Roberto Esposito, Bíos, will be used. The term biopolitics undergoes a mutation since its first use in 1905. On the other hand, based on the data presented in the first part of the chapter, an analysis of the consecration of the term made by Michel Foucault will be made. In the course of the article, besides Foucault and Esposito, a connection will be made to the Arendtian work

Divergent and nonuniform gene expression patterns in mouse brain

Science.gov (United States)

Morris, John A.; Royall, Joshua J.; Bertagnolli, Darren; Boe, Andrew F.; Burnell, Josh J.; Byrnes, Emi J.; Copeland, Cathy; Desta, Tsega; Fischer, Shanna R.; Goldy, Jeff; Glattfelder, Katie J.; Kidney, Jolene M.; Lemon, Tracy; Orta, Geralyn J.; Parry, Sheana E.; Pathak, Sayan D.; Pearson, Owen C.; Reding, Melissa; Shapouri, Sheila; Smith, Kimberly A.; Soden, Chad; Solan, Beth M.; Weller, John; Takahashi, Joseph S.; Overly, Caroline C.; Lein, Ed S.; Hawrylycz, Michael J.; Hohmann, John G.; Jones, Allan R.

2010-01-01

Considerable progress has been made in understanding variations in gene sequence and expression level associated with phenotype, yet how genetic diversity translates into complex phenotypic differences remains poorly understood. Here, we examine the relationship between genetic background and spatial patterns of gene expression across seven strains of mice, providing the most extensive cellular-resolution comparative analysis of gene expression in the mammalian brain to date. Using comprehensive brainwide anatomic coverage (more than 200 brain regions), we applied in situ hybridization to analyze the spatial expression patterns of 49 genes encoding well-known pharmaceutical drug targets. Remarkably, over 50% of the genes examined showed interstrain expression variation. In addition, the variability was nonuniformly distributed across strain and neuroanatomic region, suggesting certain organizing principles. First, the degree of expression variance among strains mirrors genealogic relationships. Second, expression pattern differences were concentrated in higher-order brain regions such as the cortex and hippocampus. Divergence in gene expression patterns across the brain could contribute significantly to variations in behavior and responses to neuroactive drugs in laboratory mouse strains and may help to explain individual differences in human responsiveness to neuroactive drugs. PMID:20956311

Pareto genealogies arising from a Poisson branching evolution model with selection.

Science.gov (United States)

Huillet, Thierry E

2014-02-01

We study a class of coalescents derived from a sampling procedure out of N i.i.d. Pareto(α) random variables, normalized by their sum, including β-size-biasing on total length effects (β Poisson-Dirichlet (α, -β) Ξ-coalescent (α ε[0, 1)), or to a family of continuous-time Beta (2 - α, α - β)Λ-coalescents (α ε[1, 2)), or to the Kingman coalescent (α ≥ 2). We indicate that this class of coalescent processes (and their scaling limits) may be viewed as the genealogical processes of some forward in time evolving branching population models including selection effects. In such constant-size population models, the reproduction step, which is based on a fitness-dependent Poisson Point Process with scaling power-law(α) intensity, is coupled to a selection step consisting of sorting out the N fittest individuals issued from the reproduction step.

Genetics, Gene Flow, and Glaciation: The Case of the South American Limpet Nacella mytilina.

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Claudio A González-Wevar

Full Text Available Glacial episodes of the Quaternary, and particularly the Last Glacial Maximum (LGM drastically altered the distribution of the Southern-Hemisphere biota, principally at higher latitudes. The irregular coastline of Patagonia expanding for more than 84.000 km constitutes a remarkable area to evaluate the effect of Quaternary landscape and seascape shifts over the demography of near-shore marine benthic organisms. Few studies describing the biogeographic responses of marine species to the LGM have been conducted in Patagonia, but existing data from coastal marine species have demonstrated marked genetic signatures of post-LGM recolonization and expansion. The kelp-dweller limpet Nacella mytilina is broadly distributed along the southern tip of South America and at the Falkland/Malvinas Islands. Considering its distribution, abundance, and narrow bathymetry, N. mytilina represents an appropriate model to infer how historical and contemporary processes affected the distribution of intraspecific genetic diversity and structure along the southern tip of South America. At the same time, it will be possible to determine how life history traits and the ecology of the species are responsible for the current pattern of gene flow and connectivity across the study area. We conducted phylogeographic and demographic inference analyses in N. mytilina from 12 localities along Pacific Patagonia (PP and one population from the Falkland/Malvinas Islands (FI. Analyses of the mitochondrial gene COI in 300 individuals of N. mytilina revealed low levels of genetic polymorphism and the absence of genetic differentiation along PP. In contrast, FI showed a strong and significant differentiation from Pacific Patagonian populations. Higher levels of genetic diversity were also recorded in the FI population, together with a more expanded genealogy supporting the hypothesis of glacial persistence of the species in these islands. Haplotype genealogy, and mismatch analyses in

Genetics, Gene Flow, and Glaciation: The Case of the South American Limpet Nacella mytilina

Science.gov (United States)

González-Wevar, Claudio A.; Rosenfeld, Sebastián; Segovia, Nicolás I.; Hüne, Mathias; Gérard, Karin; Ojeda, Jaime; Mansilla, Andrés; Brickle, Paul; Díaz, Angie; Poulin, Elie

2016-01-01

Glacial episodes of the Quaternary, and particularly the Last Glacial Maximum (LGM) drastically altered the distribution of the Southern-Hemisphere biota, principally at higher latitudes. The irregular coastline of Patagonia expanding for more than 84.000 km constitutes a remarkable area to evaluate the effect of Quaternary landscape and seascape shifts over the demography of near-shore marine benthic organisms. Few studies describing the biogeographic responses of marine species to the LGM have been conducted in Patagonia, but existing data from coastal marine species have demonstrated marked genetic signatures of post-LGM recolonization and expansion. The kelp-dweller limpet Nacella mytilina is broadly distributed along the southern tip of South America and at the Falkland/Malvinas Islands. Considering its distribution, abundance, and narrow bathymetry, N. mytilina represents an appropriate model to infer how historical and contemporary processes affected the distribution of intraspecific genetic diversity and structure along the southern tip of South America. At the same time, it will be possible to determine how life history traits and the ecology of the species are responsible for the current pattern of gene flow and connectivity across the study area. We conducted phylogeographic and demographic inference analyses in N. mytilina from 12 localities along Pacific Patagonia (PP) and one population from the Falkland/Malvinas Islands (FI). Analyses of the mitochondrial gene COI in 300 individuals of N. mytilina revealed low levels of genetic polymorphism and the absence of genetic differentiation along PP. In contrast, FI showed a strong and significant differentiation from Pacific Patagonian populations. Higher levels of genetic diversity were also recorded in the FI population, together with a more expanded genealogy supporting the hypothesis of glacial persistence of the species in these islands. Haplotype genealogy, and mismatch analyses in the FI population

Divorcing China: The Swing from the Patrilineal Genealogy of China to the Matrilineal Genealogy of Taiwan in Taiwan’s National Imagination

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Yin C. Chuang

2011-01-01

Full Text Available This paper explores the popular concept of the relationship between Taiwan and China as a feminine/ masculine dichotomy which has been constructed within Taiwan’s national imagination. First, I will focus on how this dichotomy has been created within the process of identity-shifting in Taiwan since the 1990s as manifested in Taiwanese pop songs. Second, I will demonstrate how it has been appropriated within the process of nation-building. Two primary questions will be addressed: How is the national imagination of Taiwan in Taiwanese pop songs constructed through maternal and feminine images? How is the matrilineal genealogy in Taiwanese pop songs appropriated by the opposition camp, namely the Democratic Progressive Party (DPP, to mobilize voters? I will investigate, from a cultural studies perspective, how cultural imagination has come to serve as the vehicle to formulate resistance, mobilize voters, gain power and, most importantly, reconstruct Taiwanese nationalism within Taiwan’s political limbo for decades. Furthermore, Margaret Somers’ discussion (1993, 1994, 1995a, 1995b, 1995c; Somers and Gibson 1994 of narrative identity is adopted as the framework for this paper in order to look at how identities are constructed within and across multiple realms. My research methods consist of conducting in-depth interviews and analysing texts.

Genealogía hipnótica del mito del zombi: The Magic Island (1929

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Carcavilla Puey, Lorenzo

2013-06-01

Full Text Available This is the first of series of articles that aims to study the history and psychological significance of the “myth of the zombie” through the analysis of its allegorical and symbolic elements, based on a myth’s conceptualization extracted from the notions of Jung’s analytical psychology and Eliade’s history of religions. Here, we’ll look deeply into the symbolic genealogy that comes before and it’s inserted in zombie conception in Seabrook’s The magic island (first text where zombie appears as living dead through a comparative analysis with the somnambulist in literature and filmography of “the dark side of animal magnetism and hypnosis” and its connection with the automaton.Este es el primero de una serie de artículos en los que se pretende estudiar la historia y la significación psicológica del “mito del zombi” a través del análisis de sus elementos alegóricos y simbólicos partiendo de una conceptualización de “mito” extraída de las nociones de la psicología analítica de Jung y de la historia de las religiones de Eliade. Aquí profundizaremos en la genealogía simbólica que antecede y se inserta en la concepción del zombi en The Magic Island de Seabrook (primer texto donde aparece el zombi como muerto viviente a través del análisis comparativo con el sonámbulo de la literatura y cinematografía del “lado oscuro del magnetismo animal y la hipnosis” y su relación con el autómata.

ACADEMIC GENEALOGIES WITH RESPECT TO NARRATIVE IN HUMAN AND SOCIAL SCIENCES AND THEIR IMPLICATION FOR PUBLIC POLICIES

Science.gov (United States)

Fujii, Satoshi; Hasegawa, Taiki; Nakano, Takeshi; Hatori, Tsuyoshi

In human and society science, narrative is regarded as an important issue to understand dynamic actions of human being and society. Therefore, narrative is also expected to be important for public policies that try to improve dynamic actions of human being and society. In th is study, we review academic genealogies with respect to narratives including western philosophy, hermeneutics, historical science, historical philosophy, literary criticism, clinical psychology and sociology, narrative psychology and folklore. Then we discuss how narrative can be pragmatically applied for public policies.

High chlorpyrifos resistance in Culex pipiens mosquitoes: strong synergy between resistance genes

Science.gov (United States)

Alout, H; Labbé, P; Berthomieu, A; Makoundou, P; Fort, P; Pasteur, N; Weill, M

2016-01-01

We investigated the genetic determinism of high chlorpyrifos resistance (HCR), a phenotype first described in 1999 in Culex pipiens mosquitoes surviving chlorpyrifos doses ⩾1 mg l−1 and more recently found in field samples from Tunisia, Israel or Indian Ocean islands. Through chlorpyrifos selection, we selected several HCR strains that displayed over 10 000-fold resistance. All strains were homozygous for resistant alleles at two main loci: the ace-1 gene, with the resistant ace-1R allele expressing the insensitive G119S acetylcholinesterase, and a resistant allele of an unknown gene (named T) linked to the sex and ace-2 genes. We constructed a strain carrying only the T-resistant allele and studied its resistance characteristics. By crossing this strain with strains harboring different alleles at the ace-1 locus, we showed that the resistant ace-1R and the T alleles act in strong synergy, as they elicited a resistance 100 times higher than expected from a simple multiplicative effect. This effect was specific to chlorpyrifos and parathion and was not affected by synergists. We also examined how HCR was expressed in strains carrying other ace-1-resistant alleles, such as ace-1V or the duplicated ace-1D allele, currently spreading worldwide. We identified two major parameters that influenced the level of resistance: the number and the nature of the ace-1-resistant alleles and the number of T alleles. Our data fit a model that predicts that the T allele acts by decreasing chlorpyrifos concentration in the compartment targeted in insects. PMID:26463842

Lineage divergence and historical gene flow in the Chinese horseshoe bat (Rhinolophus sinicus.

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Xiuguang Mao

Full Text Available Closely related taxa living in sympatry provide good opportunities to investigate the origin of barriers to gene flow as well as the extent of reproductive isolation. The only two recognized subspecies of the Chinese rufous horseshoe bat Rhinolophus sinicus are characterized by unusual relative distributions in which R. s. septentrionalis is restricted to a small area within the much wider range of its sister taxon R. s. sinicus. To determine the history of lineage divergence and gene flow between these taxa, we applied phylogenetic, demographic and coalescent analyses to multi-locus datasets. MtDNA gene genealogies and microsatellite-based clustering together revealed three divergent lineages of sinicus, corresponding to Central China, East China and the offshore Hainan Island. However, the central lineage of sinicus showed a closer relationship with septentrionalis than with other lineages of R. s. sinicus, in contrary to morphological data. Paraphyly of sinicus could result from either past asymmetric mtDNA introgression between these two taxa, or could suggest septentrionalis evolved in situ from its more widespread sister subspecies. To test between these hypotheses, we applied coalescent-based phylogenetic reconstruction and Approximate Bayesian Computation (ABC. We found that septentrionalis is likely to be the ancestral taxon and therefore a recent origin of this subspecies can be ruled out. On the other hand, we found a clear signature of asymmetric mtDNA gene flow from septentrionalis into central populations of sinicus yet no nuclear gene flow, thus strongly pointing to historical mtDNA introgression. We suggest that the observed deeply divergent lineages within R. sinicus probably evolved in isolation in separate Pleistocene refugia, although their close phylogeographic correspondence with distinct eco-environmental zones suggests that divergent selection might also have promoted broad patterns of population genetic structure.

Genealogical Analysis of the North-American Spring Wheat Varieties with Different Resistance to Pre-harvest Sprouting

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Martynov Sergey

2016-12-01

Full Text Available A comparative analysis of genetic diversity of North American spring wheat varieties differing in resistance to pre-harvest sprouting was carried out. For identification of sources of resistance the genealogical profiles of 148 red-grained and 63 white-grained North-American spring wheat varieties with full pedigrees were calculated and estimates were made of pre-harvest sprouting. The cluster structure of the populations of red-grained and white-grained varieties was estimated. Analysis of variance revealed significant differences between the average contributions of landraces in the groups of resistant and susceptible varieties. Distribution of the putative sources of resistance in the clusters indicated that varieties having different genetic basis may have different sources of resistance. For red-grained varieties the genetic sources of resistance to pre-harvest sprouting are landraces Crimean, Hard Red Calcutta, and Iumillo, or Button, Kenya 9M-1A-3, and Kenya-U, or Red Egyptian and Kenya BF4-3B-10V1. Tracking of pedigrees showed these landraces contributed to the pedigrees, respectively, via Thatcher, Kenya-Farmer, and Kenya-58, which were likely donors of resistance for red-grained varieties. For white-grained varieties the sources of resistance were landraces Crimean, Hard Red Calcutta, Ostka Galicyjska, Iumillo, Akakomugi, Turco, Hybrid English, Rough Chaff White and Red King, and putative donors of resistance — Thatcher, RL2265, and Frontana. The genealogical profile of accession RL4137, the most important donor of resistance to pre-harvest sprouting in North American spring wheat breeding programmes, contains almost all identified sources of resistance.

Berber genealogy and the politics of prehistoric archaeology and craniology in French Algeria (1860s-1880s).

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Effros, Bonnie

2017-03-01

Following the conquest of Algiers and its surrounding territory by the French army in 1830, officers noted an abundance of standing stones in this region of North Africa. Although they attracted considerably less attention among their cohort than more familiar Roman monuments such as triumphal arches and bridges, these prehistoric remains were similar to formations found in Brittany and other parts of France. The first effort to document these remains occurred in 1863, when Laurent-Charles Féraud, a French army interpreter, recorded thousands of dolmens and stone formations south-west of Constantine. Alleging that these constructions were Gallic, Féraud hypothesized the close affinity of the French, who claimed descent from the ancient Gauls, with the early inhabitants of North Africa. After Féraud's claims met with scepticism among many prehistorians, French scholars argued that these remains were constructed by the ancestors of the Berbers (Kabyles in contemporary parlance), whom they hypothesized had been dominated by a blond race of European origin. Using craniometric statistics of human remains found in the vicinity of the standing stones to propose a genealogy of the Kabyles, French administrators in Algeria thereafter suggested that their mixed origins allowed them to adapt more easily than the Arab population to French colonial governance. This case study at the intersection of prehistoric archaeology, ancient history and craniology exposes how genealogical (and racial) classification made signal contributions to French colonial ideology and policy between the 1860s and 1880s.

Phylogeny and evolution of Digitulati ground beetles (Coleoptera, Carabidae) inferred from mitochondrial ND5 gene sequences.

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Su, Zhi-Hui; Imura, Yûki; Okamoto, Munehiro; Kim, Choong-Gon; Zhou, Hong-Zhang; Paik, Jong-Cheol; Osawa, Syozo

2004-01-01

Genealogical trees have been constructed using mitochondrial ND5 gene sequences of 87 specimens consisting of 32 species which have been believed to belong to the division Digitulati (one of the lineages of the subtribe Carabina) of the world. There have been recognized six lineages, which are well separated from each other. Each lineage contains the following genus: (1) the lineage A: Ohomopterus from Japan; (2) the lineage B: Isiocarabus from eastern Eurasian Continent; (3) the lineage C: Carabus from China which are further subdivided into three sublineages; (4) the lineage D: Carabus from USA; (5) the lineage E: Carabus from the Eurasian Continent, Japan and North America; and (6) the lineage F: Eucarabus from the Eurasian Continent. Additionally, the genus Acrocarabus which had been treated as a constituent of the division Archicarabomorphi has been recognized to be the 7th lineage of the division Digitulati from the ND5 genealogical analysis as well as morphology. These lineages are assumed to have radiated within a short period and are largely linked to their geographic distribution.

Genealogy Composition in Response to Trauma: Gender and Memory in 1 Chronicles 1–9 and the Documentary Film "My Life Part 2”

NARCIS (Netherlands)

Löwisch, I.S.

2013-01-01

The thesis asks which characteristics of the biblical genealogies turn them into a form of cultural memory that has the potential to make sense of traumatic and fractured pasts, and to integrate them into present conceptions of identity and agency. Specifically, it asks which role gender plays in

Immune gene expression in Bombus terrestris: signatures of infection despite strong variation among populations, colonies, and sister workers.

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Franziska S Brunner

Full Text Available Ecological immunology relies on variation in resistance to parasites. Colonies of the bumblebee Bombus terrestris vary in their susceptibility to the trypanosome gut parasite Crithidia bombi, which reduces colony fitness. To understand the possible origin of this variation in resistance we assayed the expression of 28 immunologically important genes in foraging workers. We deliberately included natural variation of the host "environment" by using bees from colonies collected in two locations and sampling active foraging workers that were not age controlled. Immune gene expression patterns in response to C. bombi showed remarkable variability even among genetically similar sisters. Nevertheless, expression varied with parasite exposure, among colonies and, perhaps surprisingly, strongly among populations (collection sites. While only the antimicrobial peptide abaecin is universally up regulated upon exposure, linear discriminant analysis suggests that the overall exposure effect is driven by a combination of several immune pathways and further immune functions such as ROS regulation. Also, the differences among colonies in their immune gene expression profiles provide clues to the mechanistic basis of well-known inter-colony variation in susceptibility to this parasite. Our results show that transcriptional responses to parasite exposure can be detected in ecologically heterogeneous groups despite strong background noise.

Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta.

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McNeal, Joel R; Kuehl, Jennifer V; Boore, Jeffrey L; de Pamphilis, Claude W

2007-10-24

Plastid genome content and protein sequence are highly conserved across land plants and their closest algal relatives. Parasitic plants, which obtain some or all of their nutrition through an attachment to a host plant, are often a striking exception. Heterotrophy can lead to relaxed constraint on some plastid genes or even total gene loss. We sequenced plastid genomes of two species in the parasitic genus Cuscuta along with a non-parasitic relative, Ipomoea purpurea, to investigate changes in the plastid genome that may result from transition to the parasitic lifestyle. Aside from loss of all ndh genes, Cuscuta exaltata retains photosynthetic and photorespiratory genes that evolve under strong selective constraint. Cuscuta obtusiflora has incurred substantially more change to its plastid genome, including loss of all genes for the plastid-encoded RNA polymerase. Despite extensive change in gene content and greatly increased rate of overall nucleotide substitution, C. obtusiflora also retains all photosynthetic and photorespiratory genes with only one minor exception. Although Epifagus virginiana, the only other parasitic plant with its plastid genome sequenced to date, has lost a largely overlapping set of transfer-RNA and ribosomal genes as Cuscuta, it has lost all genes related to photosynthesis and maintains a set of genes which are among the most divergent in Cuscuta. Analyses demonstrate photosynthetic genes are under the highest constraint of any genes within the plastid genomes of Cuscuta, indicating a function involving RuBisCo and electron transport through photosystems is still the primary reason for retention of the plastid genome in these species.

Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta

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Kuehl Jennifer V

2007-10-01

Full Text Available Abstract Background Plastid genome content and protein sequence are highly conserved across land plants and their closest algal relatives. Parasitic plants, which obtain some or all of their nutrition through an attachment to a host plant, are often a striking exception. Heterotrophy can lead to relaxed constraint on some plastid genes or even total gene loss. We sequenced plastid genomes of two species in the parasitic genus Cuscuta along with a non-parasitic relative, Ipomoea purpurea, to investigate changes in the plastid genome that may result from transition to the parasitic lifestyle. Results Aside from loss of all ndh genes, Cuscuta exaltata retains photosynthetic and photorespiratory genes that evolve under strong selective constraint. Cuscuta obtusiflora has incurred substantially more change to its plastid genome, including loss of all genes for the plastid-encoded RNA polymerase. Despite extensive change in gene content and greatly increased rate of overall nucleotide substitution, C. obtusiflora also retains all photosynthetic and photorespiratory genes with only one minor exception. Conclusion Although Epifagus virginiana, the only other parasitic plant with its plastid genome sequenced to date, has lost a largely overlapping set of transfer-RNA and ribosomal genes as Cuscuta, it has lost all genes related to photosynthesis and maintains a set of genes which are among the most divergent in Cuscuta. Analyses demonstrate photosynthetic genes are under the highest constraint of any genes within the plastid genomes of Cuscuta, indicating a function involving RuBisCo and electron transport through photosystems is still the primary reason for retention of the plastid genome in these species.

OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations.

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Diaz-Uriarte, Ramon

2017-06-15

OncoSimulR implements forward-time genetic simulations of biallelic loci in asexual populations with special focus on cancer progression. Fitness can be defined as an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, restrictions in the order of accumulation of mutations, and order effects. Mutation rates can differ among genes, and can be affected by (anti)mutator genes. Also available are sampling from simulations (including single-cell sampling), plotting the genealogical relationships of clones and generating and plotting fitness landscapes. Implemented in R and C ++, freely available from BioConductor for Linux, Mac and Windows under the GNU GPL license. Version 2.5.9 or higher available from: http://www.bioconductor.org/packages/devel/bioc/html/OncoSimulR.html . GitHub repository at: https://github.com/rdiaz02/OncoSimul. ramon.diaz@iib.uam.es. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Local genealogies in a linear mixed model for genome-wide association mapping in complex pedigreed populations.

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Goutam Sahana

Full Text Available INTRODUCTION: The state-of-the-art for dealing with multiple levels of relationship among the samples in genome-wide association studies (GWAS is unified mixed model analysis (MMA. This approach is very flexible, can be applied to both family-based and population-based samples, and can be extended to incorporate other effects in a straightforward and rigorous fashion. Here, we present a complementary approach, called 'GENMIX (genealogy based mixed model' which combines advantages from two powerful GWAS methods: genealogy-based haplotype grouping and MMA. SUBJECTS AND METHODS: We validated GENMIX using genotyping data of Danish Jersey cattle and simulated phenotype and compared to the MMA. We simulated scenarios for three levels of heritability (0.21, 0.34, and 0.64, seven levels of MAF (0.05, 0.10, 0.15, 0.20, 0.25, 0.35, and 0.45 and five levels of QTL effect (0.1, 0.2, 0.5, 0.7 and 1.0 in phenotypic standard deviation unit. Each of these 105 possible combinations (3 h(2 x 7 MAF x 5 effects of scenarios was replicated 25 times. RESULTS: GENMIX provides a better ranking of markers close to the causative locus' location. GENMIX outperformed MMA when the QTL effect was small and the MAF at the QTL was low. In scenarios where MAF was high or the QTL affecting the trait had a large effect both GENMIX and MMA performed similarly. CONCLUSION: In discovery studies, where high-ranking markers are identified and later examined in validation studies, we therefore expect GENMIX to enrich candidates brought to follow-up studies with true positives over false positives more than the MMA would.

Clinical-genealogical and cytogenetic peculiarities of children born to fathers-liquidators of the Chernobyl accident

International Nuclear Information System (INIS)

Korenev, N.M.; Kovaleva, V.I.; Bagatskaya, N.V.

2004-01-01

Clinical-genealogical and cytogenetic peculiarities were studied in children, born to fathers who took part in liquidation the Chernobyl nuclear accident consequences for 1999-2002 at the Institute of Children and Adolescents' Health Care of AMS of Ukraine. Dynamic study (from 3 to 3.5 years) of cytogenetic influence in such children showed a certain decrease in chromosomal disorders incidence (from 1.26% to 0.53%, p<0.001). Together with decrease in the chromosomal aberrations incidence in children, it was established an increase in numerical chromosomal disorders (polyploidy). The rate of polyploidy in the group under investigation was up to 2.01% that exceeded the data of the preliminary examination (0.09%, p<0.001)

G1738R is a BRCA1 founder mutation in Greek breast/ovarian cancer patients: evaluation of its pathogenicity and inferences on its genealogical history.

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Anagnostopoulos, Theodore; Pertesi, Maroulio; Konstantopoulou, Irene; Armaou, Sofia; Kamakari, Smaragda; Nasioulas, George; Athanasiou, Athanassios; Dobrovic, Alex; Young, Mary-Anne; Goldgar, David; Fountzilas, George; Yannoukakos, Drakoulis

2008-07-01

We have performed screening in 287 breast/ovarian cancer families in Greece which has revealed that approximately 12% (8/65) of all index patients-carriers of a deleterious mutation in BRCA1 and BRCA2 genes, contain the base substitution G to A at position 5331 of BRCA1 gene. This generates the amino acid change G1738R for which based on a combination of genetic, in silico and histopathological analysis there are strong suggestions that it is a causative mutation. In this paper, we present further evidence suggesting the pathogenicity of this variant. Forty breast/ovarian cancer patients were reported in 11 Greek families: the above eight living in Greece, two living in Australia and one in USA, all containing G1738R. Twenty of these patients were screened and were all found to be carriers of the same base substitution. In addition, we have detected the same base change in five breast/ovarian cancer patients after screening 475 unselected patient samples with no apparent family history. The mean age of onset for all the above patients was 39.4 and 53.6 years for breast and ovarian cancer cases, respectively. A multi-factorial likelihood model for classification of unclassified variants in BRCA1 and BRCA2 developed previously was applied on G1738R and the odds of it being a deleterious mutation was estimated to be 11470:1. In order to explain the prevalence of this mutation mainly in the Greek population, its genealogical history was examined. DNA samples were collected from 11 carrier families living in Greece, Australia and USA. Screening of eight intragenic SNPs, three intragenic and seven extragenic microsatellite markers and comparison with control individuals, suggested a common origin for the mutation while the time to its most recent common ancestor was estimated to be 11 generations (about 275 years assuming a generational interval of 25 years) with a 1-lod support interval of 4-24 generations (100-600 years). Considering the large degree of genetic

Development of Nuclear R and D Man-power Genealogy DB and preparation of Guiding Principle in Assets Application for Nuclear R and D Fund

Energy Technology Data Exchange (ETDEWEB)

Lee, Dong Uk; Song, Seung Hyun; Kim, Hak Jun; Chung, Chul Eun

2007-08-15

Information search for nuclear professional man-power, technology genealogy search, project participation history etc. is serviced, and present limits to KAERI additionally, but constructed Site-Based DB that service is embodied as well as subject responsible person's pedigree. Information of professional man-power include origin school, last degree, distinction of sex, age etc. and technology genealogy consist of NuTRM classification, national science technology classification, and technology tree system classified in KAERI. Technology possession present condition for professional man-power of only KAERI is included within DB. Hereafter, professional manpower of the other nuclear energy company should be strengthened on the basis of DB structure that is developed. Technology tree system classified in KAERI also required to be strengthened on the man-power DB that has effectiveness for long-term as that embody by technology tree system which can represent nuclear energy through the verification of the other nuclear energy company. By applying readying guiding principle in assets application for nuclear R and D fund, secure lucency of assets application.

Development of Nuclear R and D Man-power Genealogy DB and preparation of Guiding Principle in Assets Application for Nuclear R and D Fund

International Nuclear Information System (INIS)

Lee, Dong Uk; Song, Seung Hyun; Kim, Hak Jun; Chung, Chul Eun

2007-08-01

Information search for nuclear professional man-power, technology genealogy search, project participation history etc. is serviced, and present limits to KAERI additionally, but constructed Site-Based DB that service is embodied as well as subject responsible person's pedigree. Information of professional man-power include origin school, last degree, distinction of sex, age etc. and technology genealogy consist of NuTRM classification, national science technology classification, and technology tree system classified in KAERI. Technology possession present condition for professional man-power of only KAERI is included within DB. Hereafter, professional manpower of the other nuclear energy company should be strengthened on the basis of DB structure that is developed. Technology tree system classified in KAERI also required to be strengthened on the man-power DB that has effectiveness for long-term as that embody by technology tree system which can represent nuclear energy through the verification of the other nuclear energy company. By applying readying guiding principle in assets application for nuclear R and D fund, secure lucency of assets application

Molecular Genealogy of a Mongol Queen's Family and Her Possible Kinship with Genghis Khan.

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Lkhagvasuren, Gavaachimed; Shin, Heejin; Lee, Si Eun; Tumen, Dashtseveg; Kim, Jae-Hyun; Kim, Kyung-Yong; Kim, Kijeong; Park, Ae Ja; Lee, Ho Woon; Kim, Mi Jin; Choi, Jaesung; Choi, Jee-Hye; Min, Na Young; Lee, Kwang-Ho

2016-01-01

Members of the Mongol imperial family (designated the Golden family) are buried in a secret necropolis; therefore, none of their burial grounds have been found. In 2004, we first discovered 5 graves belonging to the Golden family in Tavan Tolgoi, Eastern Mongolia. To define the genealogy of the 5 bodies and the kinship among them, SNP and/or STR profiles of mitochondria, autosomes, and Y chromosomes were analyzed. Four of the 5 bodies were determined to carry the mitochondrial DNA haplogroup D4, while the fifth carried haplogroup CZ, indicating that this individual had no kinship with the others. Meanwhile, Y-SNP and Y-STR profiles indicate that the males examined belonged to the R1b-M343 haplogroup. Thus, their East Asian D4 or CZ matrilineal and West Eurasian R1b-M343 patrilineal origins reveal genealogical admixture between Caucasoid and Mongoloid ethnic groups, despite a Mongoloid physical appearance. In addition, Y chromosomal and autosomal STR profiles revealed that the four D4-carrying bodies bore the relationship of either mother and three sons or four full siblings with almost the same probability. Moreover, the geographical distribution of R1b-M343-carrying modern-day individuals demonstrates that descendants of Tavan Tolgoi bodies today live mainly in Western Eurasia, with a high frequency in the territories of the past Mongol khanates. Here, we propose that Genghis Khan and his family carried Y-haplogroup R1b-M343, which is prevalent in West Eurasia, rather than the Y-haplogroup C3c-M48, which is prevalent in Asia and which is widely accepted to be present in the family members of Genghis Khan. Additionally, Tavan Tolgoi bodies may have been the product of marriages between the lineage of Genghis Khan's Borjigin clan and the lineage of either the Ongud or Hongirad clans, indicating that these individuals were members of Genghis Khan's immediate family or his close relatives.

The Astronomy Genealogy Project: It's more than just tracing your ancestry

Science.gov (United States)

Tenn, Joseph S.; AstroGen Team

2017-01-01

The Astronomy Genealogy Project ("AstroGen"), a project of the Historical Astronomy Division (HAD), will soon appear on the AAS website (https://astrogen.aas.org/). Ultimately, it will list the world's astronomers with their highest degrees, titles of theses for those who wrote them, academic advisors, universities, and links to the astronomers or their obituaries, their theses when online, and more. At present the AstroGen team is working on those who earned doctorates with astronomy-related theses. We show what can be learned already, with twelve countries essentially complete and about 19,000 theses recorded. For the twelve countries—Australia, Canada, Chile, Ireland, the Netherlands, New Zealand, Norway, South Africa, Spain, Sweden, the United Kingdom, and the United States—half of the theses have been submitted since 1999, and more than 60% are online. We will present information comparing countries, universities, and eras. Nearly all information has been gathered online, and there is much more available. We are seeking people with knowledge of the languages and academic cultures of other countries to join us.

La extraña idea del desarrollo. Genealogía de un concepto

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Carlos Eduardo Maldonado

2017-01-01

Full Text Available Este artículo elabora una genealogía del concepto de desarrollo. Formulado originalmente por R. Prebisch (1950, el con- cepto sufre varias traducciones, extensiones y modi caciones que terminan asimilándolo a una idea perfectamente distinta. El sentido y el contexto originarios terminan transformándose. Así, el desarrollo termina siendo una apología del capitalismo. Después de una introducción histórica y cientí ca, el artículo desarrolla cuatro argumentos, así: el modelo de desarrollo es una idea extraña; esta idea se ve ampliada y extendida en términos de sostenibilidad; varias críticas, sin embargo, emergen y se ha- cen necesarias; consiguientemente, se hace posible e imperativo un modelo alternativo al desarrollo. Cada una de las secciones mencionadas son justi cadas en cada paso. Al nal se extraen algunas conclusiones, y el artículo termina con una idea fuerte que vincula bancarización y control ciudadano. Palabras clave: Historia de la economía, filosofía de la economía, capitalismo, economía política Abstract This paper carries out a genealogy of the concept of development. Originally stated out by R. Prebisch (1950, the concept su ers a number of translations, extension, and changes that end up with a quite di erent idea than it was originally thought. Both the meaning and framework end up being radically changed. us, development ends as an apology to capitalism. A er a short historical and philosophical introduction, this paper develops four arguments, as follows: the model of economic de- velopment is a weird idea; such an idea is both extended and widened in terms of sustainability; a number of critiques merge, though, that are necessary and feasible; therea er, an alternative model of development becomes at the same time possible and compulsory. Each one of the mentioned paragraphs are justi ed in due time. At the end some conclusions are drawn, ad the paper ends with a string idea that

Theories of Population Variation in Genes and Genomes

DEFF Research Database (Denmark)

Christiansen, Freddy

This textbook provides an authoritative introduction to both classical and coalescent approaches to population genetics. Written for graduate students and advanced undergraduates by one of the world’s leading authorities in the field, the book focuses on the theoretical background of population...... genetics, while emphasizing the close interplay between theory and empiricism. Traditional topics such as genetic and phenotypic variation, mutation, migration, and linkage are covered and advanced by contemporary coalescent theory, which describes the genealogy of genes in a population, ultimately...... connecting them to a single common ancestor. Effects of selection, particularly genomic effects, are discussed with reference to molecular genetic variation. The book is designed for students of population genetics, bioinformatics, evolutionary biology, molecular evolution, and theoretical biology—as well...

HACIA UNA GENEALOGÍA DE LA EDUCACIÓN Y LA PEDAGOGÍA | TOWARDS A GENEALOGY OF EDUCATION AND PEDAGOGY

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Héctor Rodríguez García

2016-11-01

Full Text Available This inquiry is a theoretical approach to various epistemological constructions which are in the historical development of Education and Pedagogy. It is the incursion in a variety of cultural places to decipher the epochal and discursive signs that account for different positions that show various training programs and conceptions of humanity. This is why the genealogical trip to the scene of invention of Paideia in Ancient Greece is considered essential. Especially because it is an opportunity to find the enunciations of sophistry, maieutics and dialectics. This itinerary also includes the opening of the educational ideas of the European Enlightenment. It is an emerging time marked by great social transformations that have an important influence on the processes of Revolution of Independence and political and educational ideals that were born from Latin America. Thus, from a documentary view, unfolds a methodological approach based on critical hermeneutics that enables to understand the currents of ideas in this part of the continent that give rise to intellectual liberation. In this regard, it is underlined that genealogy as an epistemological strategy gives the opportunity to discover the diatribes and controversies that arise in historical events. That is why it is convenient to include in the conclusions the need to assume the historicity of pedagogical knowledge, the epochal and discursive changes, the rotation of globalization and the irreverent gesture that feeds the utopia and the liberating Latin American pedagogical thinking.

Molecular Genealogy of a Mongol Queen’s Family and Her Possible Kinship with Genghis Khan

Science.gov (United States)

Lkhagvasuren, Gavaachimed; Shin, Heejin; Lee, Si Eun; Tumen, Dashtseveg; Kim, Jae-Hyun; Kim, Kyung-Yong; Kim, Kijeong; Park, Ae Ja; Lee, Ho Woon; Kim, Mi Jin; Choi, Jaesung; Choi, Jee-Hye; Min, Na Young

2016-01-01

Members of the Mongol imperial family (designated the Golden family) are buried in a secret necropolis; therefore, none of their burial grounds have been found. In 2004, we first discovered 5 graves belonging to the Golden family in Tavan Tolgoi, Eastern Mongolia. To define the genealogy of the 5 bodies and the kinship among them, SNP and/or STR profiles of mitochondria, autosomes, and Y chromosomes were analyzed. Four of the 5 bodies were determined to carry the mitochondrial DNA haplogroup D4, while the fifth carried haplogroup CZ, indicating that this individual had no kinship with the others. Meanwhile, Y-SNP and Y-STR profiles indicate that the males examined belonged to the R1b-M343 haplogroup. Thus, their East Asian D4 or CZ matrilineal and West Eurasian R1b-M343 patrilineal origins reveal genealogical admixture between Caucasoid and Mongoloid ethnic groups, despite a Mongoloid physical appearance. In addition, Y chromosomal and autosomal STR profiles revealed that the four D4-carrying bodies bore the relationship of either mother and three sons or four full siblings with almost the same probability. Moreover, the geographical distribution of R1b-M343-carrying modern-day individuals demonstrates that descendants of Tavan Tolgoi bodies today live mainly in Western Eurasia, with a high frequency in the territories of the past Mongol khanates. Here, we propose that Genghis Khan and his family carried Y-haplogroup R1b-M343, which is prevalent in West Eurasia, rather than the Y-haplogroup C3c-M48, which is prevalent in Asia and which is widely accepted to be present in the family members of Genghis Khan. Additionally, Tavan Tolgoi bodies may have been the product of marriages between the lineage of Genghis Khan’s Borjigin clan and the lineage of either the Ongud or Hongirad clans, indicating that these individuals were members of Genghis Khan’s immediate family or his close relatives. PMID:27627454

Origin and diversification of hindwingless Damaster ground beetles within the Japanese islands as deduced from mitochondrial ND5 gene sequences (Coleoptera, Carabidae).

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Su, Z H; Tominaga, O; Okamoto, M; Osawa, S

1998-08-01

Genealogical trees have been constructed using mitochondrial ND5 gene sequences of 78 Damaster (s. str.) specimens from all over the Japanese Islands. Eight lineages (called races in this paper) have been recognized. The races are tightly linked to geography with sharp distribution boundaries between them. The races and their distribution ranges do not coincide with those of classical morphology. Based on the observed distribution of the mitochondrial DNA haplotypes and the geohistorical data, we propose a diversification scenario of Damaster.

Periodificación en arqueología peruana: genealogía y aporía

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2005-01-01

Full Text Available Périodisation en archéologie péruvienne : généalogie et aporie Résumé: La périodisation est un point stratégique d’intersection entre la théorie et la recherche empirique. Son histoire au Pérou résume bien les débats expérimentés par l’archéologie péruvienne. La variété des périodisations postulées et pratiquées dans les Andes l’a transformée en un champ d’étude privilégié. Une fois assumée la réciprocit nécessaire entre le développement d’une discipline et la connaissance de son histoire, l’auteur se livre à cette enquête sur les principaux systèmes de periodisation, les affrontements entre les tendances et le panorama actuel. Ce n’est pas un travail théorique, mais plutôt historiographique sur un aspect spécifique de l’archeologie péruvienne. L’objectif est de faire une généalogie critique et fonctionnelle, c’est-à-dire présenter la genèse des schémas conceptuels utilisés aujourd’hui, leurs liens et leurs limites. La periodificación es un estratégico punto de intersección entre la propuesta teórica y la investigación empírica. Su historia resume bien los debates por los que ha atravesado la arqueología peruana. La variedad de periodificaciones postuladas y/o practicadas en el área central andina, las convierte en un privilegiado campo de estudio. Asumida la necesaria reciprocidad entre el avance de toda disciplina y el conocimiento de su historia, se plantea este recorrido por los principales sistemas de periodificación, los enfrentamientos entre tendencias y el panorama actual. No se trata de un enfoque teórico, antes bien historiográfico de un aspecto específico de la arqueología peruana. El objetivo es hacer una genealogía crítica y funcional, es decir presentar la génesis de los esquemas conceptuales actualmente utilizados, sus conexiones y límites. Periodization in Peruvian archaeology: genealogy and apory Abstract: Periodization is a strategic point of intersection

How Ending Impunity for Conflict-Related Sexual Violence Overwhelmed the UN Women, Peace, and Security Agenda: A Discursive Genealogy.

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Reilly, Niamh

2018-05-01

The recent unprecedented focus on ending impunity for conflict-related sexual violence (CRSV) is positive in many respects. However, it has narrowed the scope of Security Council Resolution 1325 and the women, peace, and security (WPS) agenda it established in 2000. Through a critical discursive genealogy of the interrelation of two UN agendas-protection of civilians in armed conflict and women, peace, and security-the author traces how CRSV emerged as the defining issue of the latter while the transformative imperative of making women's participation central to every UN endeavor for peace and security has failed to gain traction.

Evolution of the complementary sex-determination gene of honey bees: balancing selection and trans-species polymorphisms.

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Cho, Soochin; Huang, Zachary Y; Green, Daniel R; Smith, Deborah R; Zhang, Jianzhi

2006-11-01

The mechanism of sex determination varies substantively among evolutionary lineages. One important mode of genetic sex determination is haplodiploidy, which is used by approximately 20% of all animal species, including >200,000 species of the entire insect order Hymenoptera. In the honey bee Apis mellifera, a hymenopteran model organism, females are heterozygous at the csd (complementary sex determination) locus, whereas males are hemizygous (from unfertilized eggs). Fertilized homozygotes develop into sterile males that are eaten before maturity. Because homozygotes have zero fitness and because common alleles are more likely than rare ones to form homozygotes, csd should be subject to strong overdominant selection and negative frequency-dependent selection. Under these selective forces, together known as balancing selection, csd is expected to exhibit a high degree of intraspecific polymorphism, with long-lived alleles that may be even older than the species. Here we sequence the csd genes as well as randomly selected neutral genomic regions from individuals of three closely related species, A. mellifera, Apis cerana, and Apis dorsata. The polymorphic level is approximately seven times higher in csd than in the neutral regions. Gene genealogies reveal trans-species polymorphisms at csd but not at any neutral regions. Consistent with the prediction of rare-allele advantage, nonsynonymous mutations are found to be positively selected in csd only in early stages after their appearances. Surprisingly, three different hypervariable repetitive regions in csd are present in the three species, suggesting variable mechanisms underlying allelic specificities. Our results provide a definitive demonstration of balancing selection acting at the honey bee csd gene, offer insights into the molecular determinants of csd allelic specificities, and help avoid homozygosity in bee breeding.

Hairpin RNA Targeting Multiple Viral Genes Confers Strong Resistance to Rice Black-Streaked Dwarf Virus

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Fangquan Wang

2016-05-01

Full Text Available Rice black-streaked dwarf virus (RBSDV belongs to the genus Fijivirus in the family of Reoviridae and causes severe yield loss in rice-producing areas in Asia. RNA silencing, as a natural defence mechanism against plant viruses, has been successfully exploited for engineering virus resistance in plants, including rice. In this study, we generated transgenic rice lines harbouring a hairpin RNA (hpRNA construct targeting four RBSDV genes, S1, S2, S6 and S10, encoding the RNA-dependent RNA polymerase, the putative core protein, the RNA silencing suppressor and the outer capsid protein, respectively. Both field nursery and artificial inoculation assays of three generations of the transgenic lines showed that they had strong resistance to RBSDV infection. The RBSDV resistance in the segregating transgenic populations correlated perfectly with the presence of the hpRNA transgene. Furthermore, the hpRNA transgene was expressed in the highly resistant transgenic lines, giving rise to abundant levels of 21–24 nt small interfering RNA (siRNA. By small RNA deep sequencing, the RBSDV-resistant transgenic lines detected siRNAs from all four viral gene sequences in the hpRNA transgene, indicating that the whole chimeric fusion sequence can be efficiently processed by Dicer into siRNAs. Taken together, our results suggest that long hpRNA targeting multiple viral genes can be used to generate stable and durable virus resistance in rice, as well as other plant species.

Hairpin RNA Targeting Multiple Viral Genes Confers Strong Resistance to Rice Black-Streaked Dwarf Virus.

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Wang, Fangquan; Li, Wenqi; Zhu, Jinyan; Fan, Fangjun; Wang, Jun; Zhong, Weigong; Wang, Ming-Bo; Liu, Qing; Zhu, Qian-Hao; Zhou, Tong; Lan, Ying; Zhou, Yijun; Yang, Jie

2016-05-11

Rice black-streaked dwarf virus (RBSDV) belongs to the genus Fijivirus in the family of Reoviridae and causes severe yield loss in rice-producing areas in Asia. RNA silencing, as a natural defence mechanism against plant viruses, has been successfully exploited for engineering virus resistance in plants, including rice. In this study, we generated transgenic rice lines harbouring a hairpin RNA (hpRNA) construct targeting four RBSDV genes, S1, S2, S6 and S10, encoding the RNA-dependent RNA polymerase, the putative core protein, the RNA silencing suppressor and the outer capsid protein, respectively. Both field nursery and artificial inoculation assays of three generations of the transgenic lines showed that they had strong resistance to RBSDV infection. The RBSDV resistance in the segregating transgenic populations correlated perfectly with the presence of the hpRNA transgene. Furthermore, the hpRNA transgene was expressed in the highly resistant transgenic lines, giving rise to abundant levels of 21-24 nt small interfering RNA (siRNA). By small RNA deep sequencing, the RBSDV-resistant transgenic lines detected siRNAs from all four viral gene sequences in the hpRNA transgene, indicating that the whole chimeric fusion sequence can be efficiently processed by Dicer into siRNAs. Taken together, our results suggest that long hpRNA targeting multiple viral genes can be used to generate stable and durable virus resistance in rice, as well as other plant species.

Genealogía del código pedagógico del entorno

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Julio MATEOS MONTERO

2009-11-01

Full Text Available RESUMEN: El Conocimiento del Medio, área que se incorpora al curriculum de la Enseñanza Primaria en el contexto reformista de la LOGSE (Ley Orgánica de Ordenación del Sistema Educativo, tiene tras de sí una larga y compleja genealogía que transciende con mucho las explicaciones de la historiografía idealista y las justificaciones de carácter técnico o psicopedagógico.En este artículo planteo ciertas perspectivas teóricas que orientan una investigación destinada a desvelar la génesis sociohistórica del código pedagógico del entorno. A modo ilustrativo se expone una muestra de los discursos, las prácticas, las normas y otros ingredientes que intervinieron en el largo proceso de codificación de la didáctica del medio o entorno; ingredientes originalmente inventados y sedimentados en contextos pedagógicos en estrecha relación con los modos de educación. Por otra parte, mi indagación, de la que el lector obtendrá aquí una panorámica significativa, responde a un interés intelectual, compartido y socializado en un colectivo que tiene el ambicioso proyecto de contribuir elocuentemente a desvelar los discursos y las prácticas de los sistemas de enseñanza en la era del capitalismo.ABSTRACT: The knowledge of environment, subject incorporated in the curriculum of Primary School in the reforming context of the LOGSE (Organic Law of General Planning of the Educational System, has behind it a long and complex genealogy which by far goes beyond the explanations of the idealistic historiography and the justifications of technical or psychopedagogical nature. In this article I raise certain theoretical prospectives which orientate an investigation meant to unveil the sociohistorical genesis of the pedagogical code of environment. In an illustrative way an example of the discourses, the practices, norms and other ingredients is displayed/shown, which took part in the long process of codification of the environmental didactics

Multiple gene genealogies and phenotypic characters differentiate several novel species of Mycosphaerella and related anamorphs on banana.

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Arzanlou, M; Groenewald, J Z; Fullerton, R A; Abeln, E C A; Carlier, J; Zapater, M-F; Buddenhagen, I W; Viljoen, A; Crous, P W

2008-06-01

Three species of Mycosphaerella, namely M. eumusae, M. fijiensis, and M. musicola are involved in the Sigatoka disease complex of bananas. Besides these three primary pathogens, several additional species of Mycosphaerella or their anamorphs have been described from Musa. However, very little is known about these taxa, and for the majority of these species no culture or DNA is available for study. In the present study, we collected a global set of Mycosphaerella strains from banana, and compared them by means of morphology and a multi-gene nucleotide sequence data set. The phylogeny inferred from the ITS region and the combined data set containing partial gene sequences of the actin gene, the small subunit mitochondrial ribosomal DNA and the histone H3 gene revealed a rich diversity of Mycosphaerella species on Musa. Integration of morphological and molecular data sets confirmed more than 20 species of Mycosphaerella (incl. anamorphs) to occur on banana. This study reconfirmed the previously described presence of Cercospora apii, M. citri and M. thailandica, and also identified Mycosphaerella communis, M. lateralis and Passalora loranthi on this host. Moreover, eight new species identified from Musa are described, namely Dissoconium musae, Mycosphaerella mozambica, Pseudocercospora assamensis, P. indonesiana, P. longispora, Stenella musae, S. musicola, and S. queenslandica.

Bears in a forest of gene trees: phylogenetic inference is complicated by incomplete lineage sorting and gene flow.

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Kutschera, Verena E; Bidon, Tobias; Hailer, Frank; Rodi, Julia L; Fain, Steven R; Janke, Axel

2014-08-01

Ursine bears are a mammalian subfamily that comprises six morphologically and ecologically distinct extant species. Previous phylogenetic analyses of concatenated nuclear genes could not resolve all relationships among bears, and appeared to conflict with the mitochondrial phylogeny. Evolutionary processes such as incomplete lineage sorting and introgression can cause gene tree discordance and complicate phylogenetic inferences, but are not accounted for in phylogenetic analyses of concatenated data. We generated a high-resolution data set of autosomal introns from several individuals per species and of Y-chromosomal markers. Incorporating intraspecific variability in coalescence-based phylogenetic and gene flow estimation approaches, we traced the genealogical history of individual alleles. Considerable heterogeneity among nuclear loci and discordance between nuclear and mitochondrial phylogenies were found. A species tree with divergence time estimates indicated that ursine bears diversified within less than 2 My. Consistent with a complex branching order within a clade of Asian bear species, we identified unidirectional gene flow from Asian black into sloth bears. Moreover, gene flow detected from brown into American black bears can explain the conflicting placement of the American black bear in mitochondrial and nuclear phylogenies. These results highlight that both incomplete lineage sorting and introgression are prominent evolutionary forces even on time scales up to several million years. Complex evolutionary patterns are not adequately captured by strictly bifurcating models, and can only be fully understood when analyzing multiple independently inherited loci in a coalescence framework. Phylogenetic incongruence among gene trees hence needs to be recognized as a biologically meaningful signal. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Genetic genealogy reveals true Y haplogroup of House of Bourbon contradicting recent identification of the presumed remains of two French Kings.

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Larmuseau, Maarten H D; Delorme, Philippe; Germain, Patrick; Vanderheyden, Nancy; Gilissen, Anja; Van Geystelen, Anneleen; Cassiman, Jean-Jacques; Decorte, Ronny

2014-05-01

Genetic analysis strongly increases the opportunity to identify skeletal remains or other biological samples from historical figures. However, validation of this identification is essential and should be done by DNA typing of living relatives. Based on the similarity of a limited set of Y-STRs, a blood sample and a head were recently identified as those belonging respectively to King Louis XVI and his paternal ancestor King Henry IV. Here, we collected DNA samples from three living males of the House of Bourbon to validate the since then controversial identification of these remains. The three living relatives revealed the Bourbon's Y-chromosomal variant on a high phylogenetic resolution for several members of the lineage between Henry IV and Louis XVI. This 'true' Bourbon's variant is different from the published Y-STR profiles of the blood as well as of the head. The earlier identifications of these samples can therefore not be validated. Moreover, matrilineal genealogical data revealed that the published mtDNA sequence of the head was also different from the one of a series of relatives. This therefore leads to the conclusion that the analyzed samples were not from the French kings. Our study once again demonstrated that in order to realize an accurate genetic identification of historical remains DNA typing of living persons, who are paternally or maternally related with the presumed donor of the samples, is required.

[Ethics and medicine in Michel Foucault: the humanistic dimension of medicine derived from a genealogy of morality].

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Gomes, Benjamim

2005-01-01

The article presents the results of a doctoral dissertation defended at the Universidad de Salamanca, based on Foucault's final decade of writings. If Foucault's goal in writing The History of Sexuality was to fashion a genealogy of ethics, my goal in analyzing this book, along with his other writings, is to demonstrate his last contribution to the history of medicine. He moves from a conception of power over others towards a conception of power over oneself, an exclusive terrain of ancient Greek morality. As a thinker who tries to understand today's problems by going to their roots, Foucault develops less a history than a philosophy of history. Considered an anti-humanist, he leaves us with a portrait of a wholly ethical-humanistic medicine.

Empirical and genealogical analysis of non-vocational adult education in Europe

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Manninen, Jyri

2017-06-01

Non-formal, non-vocational adult education (NFNVAE) is a low-cost, low-threshold learning activity that generates many benefits for individuals and society, and it should play a more central role in educational policy. NFNVAE's challenge is that it lacks clear concepts and definitions and is, therefore, less systematically covered in statistics, research and surveys. This article seeks to tackle these problems by providing (1) a mapping of NFNVAE courses in 10 European countries and (2) a conceptual framework for NFNVAE. The mapping is based on survey data ( n = 8,646) that contain information on 14,063 courses, which were coded into 24 categories and three general types: civic, liberal and basic skills education. Popular adult education courses (in the radical meaning of the term) were not found among these data; therefore, further mapping is needed. The genealogical analysis shows that ideological discourses and cultural practices should be taken into account when different concepts are used to describe NFNVAE. Especially the concept "popular" needs more clarification, since it is frequently used to refer to several different traditions, for example the Nordic " folkbildning", which is a civic education system, and therefore differs from Latin American popular adult education, which is a radical, non-governmental movement.[Figure not available: see fulltext.

Neurotree: a collaborative, graphical database of the academic genealogy of neuroscience.

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David, Stephen V; Hayden, Benjamin Y

2012-01-01

Neurotree is an online database that documents the lineage of academic mentorship in neuroscience. Modeled on the tree format typically used to describe biological genealogies, the Neurotree web site provides a concise summary of the intellectual history of neuroscience and relationships between individuals in the current neuroscience community. The contents of the database are entirely crowd-sourced: any internet user can add information about researchers and the connections between them. As of July 2012, Neurotree has collected information from 10,000 users about 35,000 researchers and 50,000 mentor relationships, and continues to grow. The present report serves to highlight the utility of Neurotree as a resource for academic research and to summarize some basic analysis of its data. The tree structure of the database permits a variety of graphical analyses. We find that the connectivity and graphical distance between researchers entered into Neurotree early has stabilized and thus appears to be mostly complete. The connectivity of more recent entries continues to mature. A ranking of researcher fecundity based on their mentorship reveals a sustained period of influential researchers from 1850-1950, with the most influential individuals active at the later end of that period. Finally, a clustering analysis reveals that some subfields of neuroscience are reflected in tightly interconnected mentor-trainee groups.

Genealogía de la difícil relación entre antropología social y turismo

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Antonio Miguel Nogués Pedregal

2009-01-01

Full Text Available En el texto se transforma el proceso de conocimiento antropológico sobre turismo en el objeto de conocimiento mismo. Para ello se aborda de manera sintética una genealogía de la aparición del turismo como objeto de estudio fenoménico, expuesta en los tres momentos epistemológicos que se han dado en la relación entre antropología y turismo. En ésta se trasluce un progresivo abandono de los sistemas discretos y dialécticos de análisis, hacia modelos más contextuales en los que predomina la metáfora del continuo y la dialógica.

The strong selective sweep candidate gene ADRA2C does not explain domestication related changes in the stress response of chickens.

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Magnus Elfwing

Full Text Available Analysis of selective sweeps to pinpoint causative genomic regions involved in chicken domestication has revealed a strong selective sweep on chromosome 4 in layer chickens. The autoregulatory α-adrenergic receptor 2C (ADRA2C gene is the closest to the selective sweep and was proposed as an important gene in the domestication of layer chickens. The ADRA2C promoter region was also hypermethylated in comparison to the non-selected ancestor of all domesticated chicken breeds, the Red Junglefowl, further supporting its relevance. In mice the receptor is involved in the fight-or-flight response as it modulates epinephrine release from the adrenals. To investigate the involvement of ADRA2C in chicken domestication, we measured gene expression in the adrenals and radiolabeled receptor ligand in three brain regions comparing the domestic White Leghorn strain with the wild ancestor Red Junglefowl. In adrenals ADRA2C was twofold greater expressed than the related receptor gene ADRA2A, indicating that ADRA2C is the predominant modulator of epinephrine release but no strain differences were measured. In hypothalamus and amygdala, regions associated with the stress response, and in striatum, receptor binding pIC50 values ranged between 8.1-8.4, and the level was not influenced by the genotyped allele. Because chicken strains differ in morphology, physiology and behavior, differences attributed to a single gene may be lost in the noise caused by the heterogeneous genetic background. Therefore an F10 advanced intercross strain between White Leghorn and Red Junglefowl was used to investigate effects of ADRA2C alleles on fear related behaviors and fecundity. We did not find compelling genotype effects in open field, tonic immobility, aerial predator, associative learning or fecundity. Therefore we conclude that ADRA2C is probably not involved in the domestication of the stress response in chicken, and the strong selective sweep is probably caused by selection

GENDER GENEALOGY OF READING AS CULTURAL PRACTICE

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N. Yu. Kryvda

2017-06-01

Full Text Available Purpose. The article is devoted to the cultural aspect of texts using in European culture. The paper found out methodological basis of correctly interpreting the term "practice" in the philosophical and sociological discourses. In the first case the concept reveals human nature; appealing to the field of ethics and intersubjective interactions. In sociological approach the term practice is contrasted to institutional life. It seems to be an organic; vital relevance of actions for contrast to the mechanically regulated community life. Methodology. The paper considered the typology of human intellectual conditions according to Kant’s divided into pure and practical reason. The last one directs action-willed individual efforts so as to meet the universal relevance and ethical coherence. Gottlieb Fichte interpreted practice reason as the way to combine intellectual intentions and material conditions of human being. G. W. F. Hegel enriched the concept with terms of "objectification" and "alienation” of labour. Karl Marx formulated the main features of activity approach to the human nature exploring. In sociological discourse the term practice is opposed to mechanically done actions (according to institutional normativity. Given the philosophical and sociological methodological contexts the reading is studied as activity that aimed emotional and volitional contact with sense. Originality. The paper analysed the genealogy of reading practices. There were selected two types of text perception – rapid "masculine" and prudent "women's" reading. Women salon environment of the XVIII-th century capitalistic Europe was the main condition for the forming of literary-aware public. The authors analysed the process of reading of the text-as-satisfaction and text-as-pleasure (R. Barthes. The work presents the overview of classical studies of sociocultural field: Thorstein Veblen; Vladimir Toporov; Rolan Barthes and contemporary researchers such as T. Markova

Maternal genealogical patterns of chicken breeds sampled in Europe.

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Lyimo, C M; Weigend, A; Msoffe, P L; Hocking, P M; Simianer, H; Weigend, S

2015-08-01

The aim of this study was to investigate the maternal genealogical pattern of chicken breeds sampled in Europe. Sequence polymorphisms of 1256 chickens of the hypervariable region (D-loop) of mitochondrial DNA (mtDNA) were used. Median-joining networks were constructed to establish evolutionary relationships among mtDNA haplotypes of chickens, which included a wide range of breeds with different origin and history. Chicken breeds which have had their roots in Europe for more than 3000 years were categorized by their founding regions, encompassing Mediterranean type, East European type and Northwest European type. Breeds which were introduced to Europe from Asia since the mid-19th century were classified as Asian type, and breeds based on crossbreeding between Asian breeds and European breeds were classified as Intermediate type. The last group, Game birds, included fighting birds from Asia. The classification of mtDNA haplotypes was based on Liu et al.'s (2006) nomenclature. Haplogroup E was the predominant clade among the European chicken breeds. The results showed, on average, the highest number of haplotypes, highest haplotype diversity, and highest nucleotide diversity for Asian type breeds, followed by Intermediate type chickens. East European and Northwest European breeds had lower haplotype and nucleotide diversity compared to Mediterranean, Intermediate, Game and Asian type breeds. Results of our study support earlier findings that chicken breeds sampled in Europe have their roots in the Indian subcontinent and East Asia. This is consistent with historical and archaeological evidence of chicken migration routes to Europe. © 2015 Stichting International Foundation for Animal Genetics.

The structured ancestral selection graph and the many-demes limit.

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Slade, Paul F; Wakeley, John

2005-02-01

We show that the unstructured ancestral selection graph applies to part of the history of a sample from a population structured by restricted migration among subpopulations, or demes. The result holds in the limit as the number of demes tends to infinity with proportionately weak selection, and we have also made the assumptions of island-type migration and that demes are equivalent in size. After an instantaneous sample-size adjustment, this structured ancestral selection graph converges to an unstructured ancestral selection graph with a mutation parameter that depends inversely on the migration rate. In contrast, the selection parameter for the population is independent of the migration rate and is identical to the selection parameter in an unstructured population. We show analytically that estimators of the migration rate, based on pairwise sequence differences, derived under the assumption of neutrality should perform equally well in the presence of weak selection. We also modify an algorithm for simulating genealogies conditional on the frequencies of two selected alleles in a sample. This permits efficient simulation of stronger selection than was previously possible. Using this new algorithm, we simulate gene genealogies under the many-demes ancestral selection graph and identify some situations in which migration has a strong effect on the time to the most recent common ancestor of the sample. We find that a similar effect also increases the sensitivity of the genealogy to selection.

A genealogical map of the concept of habit.

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Barandiaran, Xabier E; Di Paolo, Ezequiel A

2014-01-01

The notion of information processing has dominated the study of the mind for over six decades. However, before the advent of cognitivism, one of the most prominent theoretical ideas was that of Habit. This is a concept with a rich and complex history, which is again starting to awaken interest, following recent embodied, enactive critiques of computationalist frameworks. We offer here a very brief history of the concept of habit in the form of a genealogical network-map. This serves to provide an overview of the richness of this notion and as a guide for further re-appraisal. We identify 77 thinkers and their influences, and group them into seven schools of thought. Two major trends can be distinguished. One is the associationist trend, starting with the work of Locke and Hume, developed by Hartley, Bain, and Mill to be later absorbed into behaviorism through pioneering animal psychologists (Morgan and Thorndike). This tradition conceived of habits atomistically and as automatisms (a conception later debunked by cognitivism). Another historical trend we have called organicism inherits the legacy of Aristotle and develops along German idealism, French spiritualism, pragmatism, and phenomenology. It feeds into the work of continental psychologists in the early 20th century, influencing important figures such as Merleau-Ponty, Piaget, and Gibson. But it has not yet been taken up by mainstream cognitive neuroscience and psychology. Habits, in this tradition, are seen as ecological, self-organizing structures that relate to a web of predispositions and plastic dependencies both in the agent and in the environment. In addition, they are not conceptualized in opposition to rational, volitional processes, but as transversing a continuum from reflective to embodied intentionality. These are properties that make habit a particularly attractive idea for embodied, enactive perspectives, which can now re-evaluate it in light of dynamical systems theory and complexity research.

A genealogical map of the concept of habit

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Xabier E Barandiaran

2014-07-01

Full Text Available The notion of information processing has dominated the study of the mind for over six decades. However, before the advent of cognitivism, one of the most prominent theoretical ideas was that of Habit. This is a concept with a rich and complex history, which is again starting to awaken interest, following recent embodied, enactive critiques of computationalist frameworks. We offer here a very brief history of the concept of habit in the form of a genealogical network-map. This serves to provide an overview of the richness of this notion and as a guide for further re-appraisal. We identify 77 thinkers and their influences, and group them into seven schools of thought. Two major trends can be distinguished. One is the associationist trend, starting with the work of Locke and Hume, developed by Hartley, Bain and Mill to be later absorbed into behaviourism through pioneering animal psychologists (Morgan and Thorndike. This tradition conceived of habits atomistically and as automatisms (a conception later debunked by cognitivism. Another historical trend we have called organicism inherits the legacy of Aristotle and develops along German idealism, French spiritualism, pragmatism, and phenomenology. It feeds into the work of continental psychologists in the early 20th century, influencing important figures such as Merleau-Ponty, Piaget, and Gibson. But it has not yet been taken up by mainstream cognitive neuroscience and psychology. Habits, in this tradition, are seen as ecological, self-organizing structures that relate to a web of predispositions and plastic dependencies both in the agent and in the environment. In addition, they are not conceptualized in opposition to rational, volitional processes, but as transversing a continuum from reflective to embodied intentionality. These are properties that make habit a particularly attractive idea for embodied, enactive perspectives, which can now re-evaluate it in light of dynamical systems theory and

Ética y medicina en Michel Foucault: la dimensión humanística de la medicina a partir de una genealogía de la moral Ethics and medicine in Michel Foucault: the humanistic dimension of medicine derived from a genealogy of morality

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Benjamim Gomes

2005-12-01

Full Text Available Este trabajo presenta una tesis doctoral leída en la Universidad de Salamanca y basada en los escritos de la última década de Foucault. Si escribiendo la Historia de la sexualidad su objetivo fue hacer una genealogía de la ética, analizándola, junto con los demás escritos suyos, mi objetivo es enseñar su última aportación a la historia de la medicina. Él parte de una concepción de poder sobre los demás hacia una concepción de poder sobre uno mismo, espacio exclusivo de la antigua moral griega. Como pensador que busca comprender los problemas de hoy yendo a sus raíces, más que historia Foucault hace filosofía de la historia. Considerado un antihumanista, él nos deja el retrato de una medicina absolutamente ético-humanística.The article presents the results of a doctoral dissertation defended at the Universidad de Salamanca, based on Foucault's final decade of writings. If Foucault's goal in writing The History of Sexuality was to fashion a genealogy of ethics, my goal in analyzing this book, along with his other writings, is to demonstrate his last contribution to the history of medicine. He moves from a conception of power over others towards a conception of power over oneself, an exclusive terrain of ancient Greek morality. As a thinker who tries to understand today's problems by going to their roots, Foucault develops less a history than a philosophy of history. Considered an anti-humanist, he leaves us with a portrait of a wholly ethical-humanistic medicine.

Madness, Monstrosity and Writing: Towards a Genealogical Analysis in 'El obsceno pájaro de la noche'

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Santiago Juan-Navarro

2016-06-01

Full Text Available Drawing on Foucault’s concept of “genealogy,” this article explores madness, monstrosity and writing in José Donoso´s The Obscene Bird of Night(1970. Like Foucault, Donoso is interested in studying the body as “the inscribed surface of events,” the locus of a dissociated self (adopting the illusion of a substantial unity, and a mass in perpetual disintegration. Like Donoso, Foucault assaults enlightened reason and the principle of reality in order to subvert and transgress the instrumental rationality and normalcy of bourgeois culture. This essay analyzes Donoso’s novel in light of these concepts in order to open a new path for understanding one of the most obscure texts in modern Latin American fiction.

Do orthologous gene phylogenies really support tree-thinking?

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Leigh J

2005-05-01

Full Text Available Abstract Background Since Darwin's Origin of Species, reconstructing the Tree of Life has been a goal of evolutionists, and tree-thinking has become a major concept of evolutionary biology. Practically, building the Tree of Life has proven to be tedious. Too few morphological characters are useful for conducting conclusive phylogenetic analyses at the highest taxonomic level. Consequently, molecular sequences (genes, proteins, and genomes likely constitute the only useful characters for constructing a phylogeny of all life. For this reason, tree-makers expect a lot from gene comparisons. The simultaneous study of the largest number of molecular markers possible is sometimes considered to be one of the best solutions in reconstructing the genealogy of organisms. This conclusion is a direct consequence of tree-thinking: if gene inheritance conforms to a tree-like model of evolution, sampling more of these molecules will provide enough phylogenetic signal to build the Tree of Life. The selection of congruent markers is thus a fundamental step in simultaneous analysis of many genes. Results Heat map analyses were used to investigate the congruence of orthologues in four datasets (archaeal, bacterial, eukaryotic and alpha-proteobacterial. We conclude that we simply cannot determine if a large portion of the genes have a common history. In addition, none of these datasets can be considered free of lateral gene transfer. Conclusion Our phylogenetic analyses do not support tree-thinking. These results have important conceptual and practical implications. We argue that representations other than a tree should be investigated in this case because a non-critical concatenation of markers could be highly misleading.

Mythological Recuperation and Performance as Agency for Genealogical Return in Djanet Sears’s Afrika Solo

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Lekan Balogun

2018-04-01

Full Text Available This paper is an examination of Djanet Sears’s Afrika Solo (1990 as a unique example of how Blacks in the global diaspora trace their genealogical roots back to Africa. Drawing from research in anthropology, cultural studies, and performance, the paper purports that Sears’s African-Canadian identity is underlined by her recuperation of a heritage, epistemes and performative aesthetics, and, real or imagined, practices that are not just Afrocentric but specifically Yoruba. Essentially, the paper examines Afrika Solo in the context of Black Aesthetic and more significantly as “text” in a Yoruba sense, which constitutes her own way of “going back to get it.” The paper is divided into two parts: the first part presents a general argument about Sears’s journey back to Africa and the culturally-rooted nature of the performance as opposed to feminist/gender readings of same, while the second part explores ways of understanding the play through the lens of Yoruba ritual and its aesthetics.

Candidate genes detected in transcriptome studies are strongly dependent on genetic background.

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Pernille Sarup

2011-01-01

Full Text Available Whole genome transcriptomic studies can point to potential candidate genes for organismal traits. However, the importance of potential candidates is rarely followed up through functional studies and/or by comparing results across independent studies. We have analysed the overlap of candidate genes identified from studies of gene expression in Drosophila melanogaster using similar technical platforms. We found little overlap across studies between putative candidate genes for the same traits in the same sex. Instead there was a high degree of overlap between different traits and sexes within the same genetic backgrounds. Putative candidates found using transcriptomics therefore appear very sensitive to genetic background and this can mask or override effects of treatments. The functional importance of putative candidate genes emerging from transcriptome studies needs to be validated through additional experiments and in future studies we suggest a focus on the genes, networks and pathways affecting traits in a consistent manner across backgrounds.

Beyond Discourse: A Genealogical Analysis of an Intersubjective Transformation Process of Gender

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Patricia Amigot Leache

2007-05-01

Full Text Available This article presents a genealogical analysis of a specific process of transformation of gender. It analyses the shifts of a group of Spanish working-class women in the context of the final years of Franco's dictatorship and the transition to democracy. These women took part in the activities of the so-called Centros de Promoción de la Mujer y Cultura Popular [Centres for Women's Promotion and Popular Culture]. I identify the elements of the transformation processes through in-depth interviews with a sample of women. Through these narrations and the documents of the Centres I show the road that goes from a state of domination (in FOUCAULT's words to a more flexible and mobile situation in which not only are the practical possibilities for these women wider, but also we can witness the transformation of the institution itself. The analysis is made with a FOUCAULTian toolbox, using especially FOUCAULT's analysis of power, his theoretical construction of practices of self and the link he posits between such practices and identity games of truth. The analysis shows the intersubjective nature of the processes and of the practices involved in such transformations. URN: urn:nbn:de:0114-fqs070295

Problematizing special observation in psychiatry: Foucault, archaeology, genealogy, discourse and power/knowledge.

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Stevenson, C; Cutcliffe, J

2006-12-01

Special observation by mental health professionals is the recommended approach for those people deemed as at risk or risky. Recent research and academic writing have challenged the benefits of observing people/patients who are defined as 'at risk', and a more human engagement process is being recommended. Despite this assault, practice has not changed substantively, suggesting a need for a thorough exploration and questioning of the practices and process. The paper outlines three Foucaultian approaches to historical analysis. It applies aspects of Foucault's archaeology/genealogy, discourse and power/knowledge to explore the practices of special observation as a means of controlling risk, especially suicide risk. We identify the regulatory function of the 'gaze', professional codes and government policy in relation to restricting professional practices. We argue that observation can be related to moral therapy, wherein the person relinquishes madness for responsibility through a disciplinary process and, in governing risk, a 'professional industry' is created. The regulation of statements about people with mental health issues are exposed and related to what can be said and done by professionals. Finally, we look at productive power in relation to observation, and how it is intimately related to resistance. We conclude with 'soft' recommendations for practice discursively produced through the writing of the paper.

La genealogía de los reglamentos escolares en México: análisis de la obra de Rafael Ramírez

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Ana Cecilia Valencia Aguirre

2011-01-01

Full Text Available Este trabajo es resultado de un análisis cuya pregunta central es ¿Cuál es la genealogía de los reglamentos en las escuelas de educación primaria en México? el objetivo es analizar la obra de Rafael Ramírez, a través de la literatura formativa de los profesores, considerada un elemento fundacional de los mandatos institucionales de la escuela primaria, ya que genera un discurso que instituye la normatividad en la escuela básica mexicana. El método utilizado es el análisis crítico del discurso de Van Dijk, los actos de habla de Searle y la perspectiva de las metáforas de la vida cotidiana de Lakoff. La hipótesis que orienta la indagación plantea que los primeros pasos de la institucionalización del control escolar estuvieron atravesados por el discurso cristiano-católico expresado en diversos interdiscursos de la época y fundamentalmente en los reglamentos escolares que comenzaron a aparecer como parte de la literatura formativa de los profesores de escuelas primarias. Dicho análisis permite concluir que esta literatura refleja gran parte del imaginario de los profesores de escuelas públicas, ya que expresa un nacionalismobasado en el imaginario de la familia nuclear cristiana, elemento clave que configuró una de las imágenes más vivas en la conformación del estado mexicano posrevolucionario.

A comparative genomics screen identifies a Sinorhizobium meliloti 1021 sodM-like gene strongly expressed within host plant nodules

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Queiroux Clothilde

2012-05-01

Full Text Available Abstract Background We have used the genomic data in the Integrated Microbial Genomes system of the Department of Energy’s Joint Genome Institute to make predictions about rhizobial open reading frames that play a role in nodulation of host plants. The genomic data was screened by searching for ORFs conserved in α-proteobacterial rhizobia, but not conserved in closely-related non-nitrogen-fixing α-proteobacteria. Results Using this approach, we identified many genes known to be involved in nodulation or nitrogen fixation, as well as several new candidate genes. We knocked out selected new genes and assayed for the presence of nodulation phenotypes and/or nodule-specific expression. One of these genes, SMc00911, is strongly expressed by bacterial cells within host plant nodules, but is expressed minimally by free-living bacterial cells. A strain carrying an insertion mutation in SMc00911 is not defective in the symbiosis with host plants, but in contrast to expectations, this mutant strain is able to out-compete the S. meliloti 1021 wild type strain for nodule occupancy in co-inoculation experiments. The SMc00911 ORF is predicted to encode a “SodM-like” (superoxide dismutase-like protein containing a rhodanese sulfurtransferase domain at the N-terminus and a chromate-resistance superfamily domain at the C-terminus. Several other ORFs (SMb20360, SMc01562, SMc01266, SMc03964, and the SMc01424-22 operon identified in the screen are expressed at a moderate level by bacteria within nodules, but not by free-living bacteria. Conclusions Based on the analysis of ORFs identified in this study, we conclude that this comparative genomics approach can identify rhizobial genes involved in the nitrogen-fixing symbiosis with host plants, although none of the newly identified genes were found to be essential for this process.

The characterization of six auxin-induced tomato GH3 genes uncovers a member, SlGH3.4, strongly responsive to arbuscular mycorrhizal symbiosis.

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Liao, Dehua; Chen, Xiao; Chen, Aiqun; Wang, Huimin; Liu, Jianjian; Liu, Junli; Gu, Mian; Sun, Shubin; Xu, Guohua

2015-04-01

In plants, the GH3 gene family is widely considered to be involved in a broad range of plant physiological processes, through modulation of hormonal homeostasis. Multiple GH3 genes have been functionally characterized in several plant species; however, to date, limited works to study the GH3 genes in tomato have been reported. Here, we characterize the expression and regulatory profiles of six tomato GH3 genes, SlGH3.2, SlGH3.3, SlGH3.4, SlGH3.7, SlGH3.9 and SlGH3.15, in response to different phytohormone applications and arbuscular mycorrhizal (AM) fungal colonization. All six GH3 genes showed inducible responses to external IAA, and three members were significantly up-regulated in response to AM symbiosis. In particular, SlGH3.4, the transcripts of which were barely detectable under normal growth conditions, was strongly activated in the IAA-treated and AM fungal-colonized roots. A comparison of the SlGH3.4 expression in wild-type plants and M161, a mutant with a defect in AM symbiosis, confirmed that SlGH3.4 expression is highly correlated to mycorrhizal colonization. Histochemical staining demonstrated that a 2,258 bp SlGH3.4 promoter fragment could drive β-glucuronidase (GUS) expression strongly in root tips, steles and cortical cells of IAA-treated roots, but predominantly in the fungal-colonized cells of mycorrhizal roots. A truncated 654 bp promoter failed to direct GUS expression in IAA-treated roots, but maintained the symbiosis-induced activity in mycorrhizal roots. In summary, our results suggest that a mycorrhizal signaling pathway that is at least partially independent of the auxin signaling pathway has evolved for the co-regulation of the auxin- and mycorrhiza-activated GH3 genes in plants. © The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Genealogías feministas: sobre mujeres, revoluciones e ilustración: una mirada desde el sur Feminist genealogies: on women, revolution & enlightment: a point of view from the south

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Alejandra Ciriza Jofré

2012-12-01

Full Text Available Este trabajo apunta a la esbozar y reconstruir genealogías feministas desde el sur, procurando articular la reflexión filosófica sobre el pasado político de las mujeres y los fragmentos dispersos de la historia de las mujeres en Nuestra América. La lectura que me propongo realizar se halla ligada a una perspectiva sobre la relación entre pasado y presente vinculada a la inspiración benjaminiana. Desde ese punto de vista, el pasado que interesa a los y las subalternas es el tiempo ahora, esto es, un tiempo que se nutre del pasado, de la mirada hacia atrás, hacia ese momento significativo en la historia de Nuestra América - el de las guerras de independencia - y el presente. En aquel tiempo se abría un horizonte entonces anticipado como de inauguración de un nuevo tiempo y de un orden político nuevo. Esta reflexión está centrada en las relaciones entre cuerpo, política e historia desde un punto de vista que busca construir conocimiento situado, y producir una crítica a la tendencia a retornar sobre la idea del carácter a-histórico de la subordinación de las mujeres, a transformarla en lo que Geneviève Fraisse denomina una 'querella', un debate sin tiempo en el que se juega la eterna repetición de lo mismo. Una operación que, desde el punto de vista que sostengo, se duplica en el caso de las mujeres del sur.The goal of this work is to sketch and reconstruct Feminist Genealogies from a southern perspective. It aims to articulate a philosophical reflection on women's political past and the disperse fragments of the history of women (herstory in Our America. This reading will be based on the Benjaminian thought about the relationship between past and present. From this point of view, the past that concerns subalterns is the jetzt zeit, a present time that is fed from the regard to the past. Namely, in this case, the relationship between a significant time of the History of Our America - the time of the Independence Wars during

"Bildung" and the Historical and Genealogical Critique of Contemporary Culture: Wilhelm von Humboldt's Neo-Humanistic Theory of "Bildung" and Nietzsche's Critique of Neo-Humanistic Ideas in Classical Philology and Education

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Zelic, Tomislav

2018-01-01

To answer the question as to the relation of the idea of "Bildung" and the historical and genealogical critique of contemporary culture, this article takes a detour through nineteenth-century German thought to recall the primary ideas, institutions, and processes such as the university, knowledge/scholarship ("Wissenschaft"),…

Inferring contemporary levels of gene flow and demographic history in a local population of the leaf beetle Gonioctena olivacea from mitochondrial DNA sequence variation.

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Mardulyn, Patrick; Milinkovitch, Michel C

2005-05-01

We have studied mitochondrial DNA variation in a local population of the leaf beetle species Gonioctena olivacea, to check whether its apparent low dispersal behaviour affects its pattern of genetic variation at a small geographical scale. We have sampled 10 populations of G. olivacea within a rectangle of 5 x 2 km in the Belgian Ardennes, as well as five populations located approximately along a straight line of 30 km and separated by distances of 3-12 km. For each sampled individual (8-19 per population), a fragment of the mtDNA control region was polymerase chain reaction-amplified and sequenced. Sequence data were analysed to test whether significant genetic differentiation could be detected among populations separated by such relatively short distances. The reconstructed genealogy of the mitochondrial haplotypes was also used to investigate the demographic history of these populations. Computer simulations of the evolution of populations were conducted to assess the minimum amount of gene flow that is necessary to explain the observed pattern of variation in the samples. Results show that migration among populations included in the rectangle of 5 x 2 km is substantial, and probably involves the occurrence of dispersal flights. This appears difficult to reconcile with the results of a previous ecological field study that concluded that most of this species dispersal occurs by walking. While sufficient migration to homogenize genetic diversity occurs among populations separated by distances of a few hundred metres to a few kilometres, distances greater than 5 km results in contrast in strong differentiation among populations, suggesting that migration is drastically reduced on such distances. Finally, the results of coalescent simulations suggest that the star-like genealogy inferred from the mtDNA sequence data is fully compatible with a past demographic expansion. However, a metapopulation structure alone (without the need to invoke a population expansion

Genome-wide estimates of coancestry and inbreeding in a closed herd of ancient Iberian pigs.

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María Saura

Full Text Available Maintaining genetic variation and controlling the increase in inbreeding are crucial requirements in animal conservation programs. The most widely accepted strategy for achieving these objectives is to maximize the effective population size by minimizing the global coancestry obtained from a particular pedigree. However, for most natural or captive populations genealogical information is absent. In this situation, microsatellites have been traditionally the markers of choice to characterize genetic variation, and several estimators of genealogical coefficients have been developed using marker data, with unsatisfactory results. The development of high-throughput genotyping techniques states the necessity of reviewing the paradigm that genealogical coancestry is the best parameter for measuring genetic diversity. In this study, the Illumina PorcineSNP60 BeadChip was used to obtain genome-wide estimates of rates of coancestry and inbreeding and effective population size for an ancient strain of Iberian pigs that is now in serious danger of extinction and for which very accurate genealogical information is available (the Guadyerbas strain. Genome-wide estimates were compared with those obtained from microsatellite and from pedigree data. Estimates of coancestry and inbreeding computed from the SNP chip were strongly correlated with genealogical estimates and these correlations were substantially higher than those between microsatellite and genealogical coefficients. Also, molecular coancestry computed from SNP information was a better predictor of genealogical coancestry than coancestry computed from microsatellites. Rates of change in coancestry and inbreeding and effective population size estimated from molecular data were very similar to those estimated from genealogical data. However, estimates of effective population size obtained from changes in coancestry or inbreeding differed. Our results indicate that genome-wide information represents a

Stereotypy in the Portrayal of Female Characters in Genealogical Cycles of William Faulkner and Miroslav Krleža : Eula Varner Snopes and Charlotta Castelli -Glembay

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Biljana Oklopčić

2008-01-01

Full Text Available Defined as genealogies, Faulkner’s Snopes trilogy (The Hamlet, The Town, The Mansion and Krleža’s Glembay trilogy (Gospoda Glembajevi, U agoniji, Leda, together with corresponding short stories and novels, share a whole array of common characteristics. One of them is the stereotypical characterization of women characters. This point of view is justified by the appearance of Eula Varner Snopes as the ravished Southern belle and the rehabilitated Dixie Madonna and Charlotta Castelli-Glembay as the Nietzschean cat woman and femme fatale.

Some Reflections on the Origin of Reason Through an Outline of the Genealogy of Language in the Light of Homonymity, Analogy, and Metaphor

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Kirkeby, Ole Fogh

2016-01-01

The origin of reason through an outline of the genealogy of language in the light of homonymity, analogy, and metaphor. In this chapter, I try to show that reason as a cognitive capacity primarily functions through the use of homonyms. The argument is based on the fact that experience is created...... relating to their value basis, because reason also is involved as their principle of origin—qua practical reason—through which this metaphorical richness was originally coined. These principles of construction and deconstruction may also be applied to the analysis of reason itself since it also has...

[Chromosome as a chronicler: Genetic dating, historical events, and DNA-genealogic temptation].

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Balanovsky, O P; Zaporozhchenko, V V

2016-07-01

Nonrecombinant portions of the genome, Y chromosome and mitochondrial DNA, are widely used for research on human population gene pools and reconstruction of their history. These systems allow the genetic dating of clusters of emerging haplotypes. The main method for age estimations is ρ statistics, which is an average number of mutations from founder haplotype to all modern-day haplotypes. A researcher can estimate the age of the cluster by multiplying this number by the mutation rate. The second method of estimation, ASD, is used for STR haplotypes of the Y chromosome and is based on the squared difference in the number of repeats. In addition to the methods of calculation, methods of Bayesian modeling assume a new significance. They have greater computational cost and complexity, but they allow obtaining an a posteriori distribution of the value of interest that is the most consistent with experimental data. The mutation rate must be known for both calculation methods and modeling methods. It can be determined either during the analysis of lineages or by providing calibration points based on populations with known formation time. These two approaches resulted in rate estimations for Y-chromosomal STR haplotypes with threefold difference. This contradiction was only recently refuted through the use of sequence data for the complete Y chromosome; “whole-genomic” rates of single nucleotide mutations obtained by both methods are mutually consistent and mark the area of application for different rates of STR markers. An issue even more crucial than that of the rates is correlation of the reconstructed history of the haplogroup (a cluster of haplotypes) and the history of the population. Although the need for distinguishing “lineage history” and “population history” arose in the earliest days of phylogeographic research, reconstructing the population history using genetic dating requires a number of methods and conditions. It is known that population

CADM1 is a strong neuroblastoma candidate gene that maps within a 3.72 Mb critical region of loss on 11q23

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Michels, Evi; Speleman, Frank; Hoebeeck, Jasmien; De Preter, Katleen; Schramm, Alexander; Brichard, Bénédicte; De Paepe, Anne; Eggert, Angelika; Laureys, Geneviève; Vandesompele, Jo

2008-01-01

Recurrent loss of part of the long arm of chromosome 11 is a well established hallmark of a subtype of aggressive neuroblastomas. Despite intensive mapping efforts to localize the culprit 11q tumour suppressor gene, this search has been unsuccessful thus far as no sufficiently small critical region could be delineated for selection of candidate genes. To refine the critical region of 11q loss, the chromosome 11 status of 100 primary neuroblastoma tumours and 29 cell lines was analyzed using a BAC array containing a chromosome 11 tiling path. For the genes mapping within our refined region of loss, meta-analysis on published neuroblastoma mRNA gene expression datasets was performed for candidate gene selection. The DNA methylation status of the resulting candidate gene was determined using re-expression experiments by treatment of neuroblastoma cells with the demethylating agent 5-aza-2'-deoxycytidine and bisulphite sequencing. Two small critical regions of loss within 11q23 at chromosomal band 11q23.1-q23.2 (1.79 Mb) and 11q23.2-q23.3 (3.72 Mb) were identified. In a first step towards further selection of candidate neuroblastoma tumour suppressor genes, we performed a meta-analysis on published expression profiles of 692 neuroblastoma tumours. Integration of the resulting candidate gene list with expression data of neuroblastoma progenitor cells pinpointed CADM1 as a compelling candidate gene. Meta-analysis indicated that CADM1 expression has prognostic significance and differential expression for the gene was noted in unfavourable neuroblastoma versus normal neuroblasts. Methylation analysis provided no evidence for a two-hit mechanism in 11q deleted cell lines. Our study puts CADM1 forward as a strong candidate neuroblastoma suppressor gene. Further functional studies are warranted to elucidate the role of CADM1 in neuroblastoma development and to investigate the possibility of CADM1 haploinsufficiency in neuroblastoma

Candidate Genes Detected in Transcriptome Studies are Strongly Dependent on Genetic Background

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Sarup, Pernille Merete; Sørensen, Jesper Givskov; Kristensen, Torsten Nygård

2011-01-01

identified from studies of gene expression in Drosophila melanogaster using similar technical platforms. We found little overlap across studies between putative candidate genes for the same traits in the same sex. Instead there was a high degree of overlap between different traits and sexes within the same...

Gene expression during different periods of the handling-stress response in Pampus argenteus

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Sun, Peng; Tang, Baojun; Yin, Fei

2017-11-01

Common aquaculture practices subject fish to a variety of acute and chronic stressors. Such stressors are inherent in aquaculture production but can adversely affect survival, growth, immune response, reproductive capacity, and behavior. Understanding the biological mechanisms underlying stress responses helps with methods to alleviate the negative effects through better aquaculture practices, resulting in improved animal welfare and production efficiency. In the present study, transcriptome sequencing of liver and kidney was performed in silver pomfret (Pampus argenteus) subjected to handling stress versus controls. A total of 162.19 million clean reads were assembled to 30 339 unigenes. The quality of the assembly was high, with an N50 length of 2 472 bases. For function classification and pathway assignment, the unigenes were categorized into three GO (gene ontology) categories, twenty-six clusters of eggNOG (evolutionary genealogy of genes: non-supervised orthologous groups) function categories, and thirty-eight KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. Stress affected different functional groups of genes in the tissues studied. Differentially expressed genes were mainly involved in metabolic pathways (carbohydrate metabolism, lipid metabolism, amino-acid metabolism, uptake of cofactors and vitamins, and biosynthesis of other secondary metabolites), environmental information processing (signaling molecules and their interactions), organismal systems (endocrine system, digestive system), and disease (immune, neurodegenerative, endocrine and metabolic diseases). This is the first reported analysis of genome-wide transcriptome in P. argenteus, and the findings expand our understanding of the silver pomfret genome and gene expression in association with stress. The results will be useful to future analyses of functional genes and studies of healthy artificial breeding in P. argenteus and other related fish species.

Data Resources for Biodemographic Studies on Familial Clustering of Human Longevity

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1999-09-01

Full Text Available The main cause that hampered many previous biodemographic studies of human longevity is the lack of appropriate data. At the same time, many existing data resources (millions of genealogical records are under-utilized, because their very existence is not widely known, let alone the quality and scientific value of these data sets are not yet validated. The purpose of this work is to review the data resources that could be used in familial studies of human longevity. This is an extended and supplemented version of the previous study made by the authors upon the request of the National Institute on Aging (1998 NIH Professional Service Contract. The review describes: (1 data resources developed for biodemographic studies, (2 data collected in the projects on historical demography, (3 data resources for long lived individuals and their families, (4 publicly available computerized genealogical data resources, (5 published genealogical and family history data. The review also contains the description of databases developed by the participants of the Research Workshops "Genes, Genealogies, and Longevity" organized by the Max Planck Institute for Demographic Research.

Isolation of a strong Arabidopsis guard cell promoter and its potential as a research tool

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Yang, Yingzhen; Costa, Alex; Leonhardt, Nathalie; Siegel, Robert S; Schroeder, Julian I

2008-01-01

Background A common limitation in guard cell signaling research is that it is difficult to obtain consistent high expression of transgenes of interest in Arabidopsis guard cells using known guard cell promoters or the constitutive 35S cauliflower mosaic virus promoter. An additional drawback of the 35S promoter is that ectopically expressing a gene throughout the organism could cause pleiotropic effects. To improve available methods for targeted gene expression in guard cells, we isolated strong guard cell promoter candidates based on new guard cell-specific microarray analyses of 23,000 genes that are made available together with this report. Results A promoter, pGC1(At1g22690), drove strong and relatively specific reporter gene expression in guard cells including GUS (beta-glucuronidase) and yellow cameleon YC3.60 (GFP-based calcium FRET reporter). Reporter gene expression was weaker in immature guard cells. The expression of YC3.60 was sufficiently strong to image intracellular Ca2+ dynamics in guard cells of intact plants and resolved spontaneous calcium transients in guard cells. The GC1 promoter also mediated strong reporter expression in clustered stomata in the stomatal development mutant too-many-mouths (tmm). Furthermore, the same promoter::reporter constructs also drove guard cell specific reporter expression in tobacco, illustrating the potential of this promoter as a method for high level expression in guard cells. A serial deletion of the promoter defined a guard cell expression promoter region. In addition, anti-sense repression using pGC1 was powerful for reducing specific GFP gene expression in guard cells while expression in leaf epidermal cells was not repressed, demonstrating strong cell-type preferential gene repression. Conclusion The pGC1 promoter described here drives strong reporter expression in guard cells of Arabidopsis and tobacco plants. It provides a potent research tool for targeted guard cell expression or gene silencing. It is also

Genetic diversity and natural selection of Plasmodium knowlesi merozoite surface protein 1 paralog gene in Malaysia.

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Ahmed, Md Atique; Fauzi, Muh; Han, Eun-Taek

2018-03-14

Human infections due to the monkey malaria parasite Plasmodium knowlesi is on the rise in most Southeast Asian countries specifically Malaysia. The C-terminal 19 kDa domain of PvMSP1P is a potential vaccine candidate, however, no study has been conducted in the orthologous gene of P. knowlesi. This study investigates level of polymorphisms, haplotypes and natural selection of full-length pkmsp1p in clinical samples from Malaysia. A total of 36 full-length pkmsp1p sequences along with the reference H-strain and 40 C-terminal pkmsp1p sequences from clinical isolates of Malaysia were downloaded from published genomes. Genetic diversity, polymorphism, haplotype and natural selection were determined using DnaSP 5.10 and MEGA 5.0 software. Genealogical relationships were determined using haplotype network tree in NETWORK software v5.0. Population genetic differentiation index (F ST ) and population structure of parasite was determined using Arlequin v3.5 and STRUCTURE v2.3.4 software. Comparison of 36 full-length pkmsp1p sequences along with the H-strain identified 339 SNPs (175 non-synonymous and 164 synonymous substitutions). The nucleotide diversity across the full-length gene was low compared to its ortholog pvmsp1p. The nucleotide diversity was higher toward the N-terminal domains (pkmsp1p-83 and 30) compared to the C-terminal domains (pkmsp1p-38, 33 and 19). Phylogenetic analysis of full-length genes identified 2 distinct clusters of P. knowlesi from Malaysian Borneo. The 40 pkmsp1p-19 sequences showed low polymorphisms with 16 polymorphisms leading to 18 haplotypes. In total there were 10 synonymous and 6 non-synonymous substitutions and 12 cysteine residues were intact within the two EGF domains. Evidence of strong purifying selection was observed within the full-length sequences as well in all the domains. Shared haplotypes of 40 pkmsp1p-19 were identified within Malaysian Borneo haplotypes. This study is the first to report on the genetic diversity and natural

The number of genes encoding repeat domain-containing proteins positively correlates with genome size in amoebal giant viruses

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Shukla, Avi; Chatterjee, Anirvan

2018-01-01

Abstract Curiously, in viruses, the virion volume appears to be predominantly driven by genome length rather than the number of proteins it encodes or geometric constraints. With their large genome and giant particle size, amoebal viruses (AVs) are ideally suited to study the relationship between genome and virion size and explore the role of genome plasticity in their evolutionary success. Different genomic regions of AVs exhibit distinct genealogies. Although the vertically transferred core genes and their functions are universally conserved across the nucleocytoplasmic large DNA virus (NCLDV) families and are essential for their replication, the horizontally acquired genes are variable across families and are lineage-specific. When compared with other giant virus families, we observed a near–linear increase in the number of genes encoding repeat domain-containing proteins (RDCPs) with the increase in the genome size of AVs. From what is known about the functions of RDCPs in bacteria and eukaryotes and their prevalence in the AV genomes, we envisage important roles for RDCPs in the life cycle of AVs, their genome expansion, and plasticity. This observation also supports the evolution of AVs from a smaller viral ancestor by the acquisition of diverse gene families from the environment including RDCPs that might have helped in host adaption. PMID:29308275

Novel strong tissue specific promoter for gene expression in human germ cells

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Kuzmin Denis

2010-08-01

Full Text Available Abstract Background Tissue specific promoters may be utilized for a variety of applications, including programmed gene expression in cell types, tissues and organs of interest, for developing different cell culture models or for use in gene therapy. We report a novel, tissue-specific promoter that was identified and engineered from the native upstream regulatory region of the human gene NDUFV1 containing an endogenous retroviral sequence. Results Among seven established human cell lines and five primary cultures, this modified NDUFV1 upstream sequence (mNUS was active only in human undifferentiated germ-derived cells (lines Tera-1 and EP2102, where it demonstrated high promoter activity (~twice greater than that of the SV40 early promoter, and comparable to the routinely used cytomegaloviral promoter. To investigate the potential applicability of the mNUS promoter for biotechnological needs, a construct carrying a recombinant cytosine deaminase (RCD suicide gene under the control of mNUS was tested in cell lines of different tissue origin. High cytotoxic effect of RCD with a cell-death rate ~60% was observed only in germ-derived cells (Tera-1, whereas no effect was seen in a somatic, kidney-derived control cell line (HEK293. In further experiments, we tested mNUS-driven expression of a hyperactive Sleeping Beauty transposase (SB100X. The mNUS-SB100X construct mediated stable transgene insertions exclusively in germ-derived cells, thereby providing further evidence of tissue-specificity of the mNUS promoter. Conclusions We conclude that mNUS may be used as an efficient promoter for tissue-specific gene expression in human germ-derived cells in many applications. Our data also suggest that the 91 bp-long sequence located exactly upstream NDUFV1 transcriptional start site plays a crucial role in the activity of this gene promoter in vitro in the majority of tested cell types (10/12, and an important role - in the rest two cell lines.

Familial aggregation of childhood and adult cancer in the Utah genealogy.

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Neale, Rachel E; Stiller, Charles A; Bunch, Kathryn J; Milne, Elizabeth; Mineau, Geraldine P; Murphy, Michael F G

2013-12-15

A small proportion of childhood cancer is attributable to known hereditary syndromes, but whether there is any familial component to the remainder remains uncertain. We explored familial aggregation of cancer in a population-based case-control study using genealogical record linkage and designed to overcome limitations of previous studies. Subjects were selected from the Utah Population Database. We compared risk of cancer in adult first-degree relatives of children who were diagnosed with cancer with the risk in relatives of children who had not had a cancer diagnosed. We identified 1,894 childhood cancer cases and 3,788 controls; 7,467 relatives of cases and 14,498 relatives of controls were included in the analysis. Relatives of children with cancer had a higher risk of cancer in adulthood than relatives of children without cancer [odds ratio (OR) 1.31, 95% confidence interval (CI) 1.11-1.56]; this was restricted to mothers and siblings and was not evident in fathers. Familial aggregation appeared stronger among relatives of cases diagnosed before 5 years of age (OR 1.48, 95% CI 1.13-1.95) than among relatives of cases who were older when diagnosed (OR 1.22, 95% CI 0.98-1.51). These findings provide evidence of a generalized excess of cancer in the mothers and siblings of children with cancer. The tendency for risk to be higher in the relatives of children who were younger at cancer diagnosis should be investigated in other large data sets. The excesses of thyroid cancer in parents of children with cancer and of any cancer in relatives of children with leukemia merit further investigation. Copyright © 2013 UICC.

Identification of strong promoters based on the transcriptome of Bacillus licheniformis.

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Liu, Xin; Yang, Haiyan; Zheng, Junwei; Ye, Yanrui; Pan, Li

2017-06-01

To expand the repertoire of strong promoters for high level expression of proteins based on the transcriptome of Bacillus licheniformis. The transcriptome of B. licheniformis ATCC14580 grown to the early stationary phase was analyzed and the top 10 highly expressed genes/operons out of the 3959 genes and 1249 operons identified were chosen for study promoter activity. Using beta-galactosidase gene as a reporter, the candidate promoter pBL9 exhibited the strongest activity which was comparable to that of the widely used strong promoter p43. Furthermore, the pro-transglutaminase from Streptomyces mobaraensis (pro-MTG) was expressed under the control of promoter pBL9 and the activity of pro-MTG reached 82 U/ml after 36 h, which is 23% higher than that of promoter p43 (66.8 U/ml). In our analyses of the transcriptome of B. licheniformis, we have identified a strong promoter pBL9, which could be adapted for high level expression of proteins in the host Bacillus subtilis.

Sequence variation at the phenylalanine hydroxylase gene in the British Isles

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Tyfield, L.A. [Southmead Hospital, Bristol (United Kingdom)]|[Univ. of Bristol (United Kingdom); Stephenson, A. [Southmead Hospital, Bristol (United Kingdom); Cockburn, F. [Royal Hospital for Sick Children, Glasgow (United Kingdom)] [and others

1997-02-01

Using mutation and haplotype analysis, we have examined the phenylalanine hydroxylase gene in the phenylketonuria populations of four geographical areas of the British Isles: the west of Scotland, southern Wales, and southwestern and southeastern England. The enormous genetic diversity of this locus within the British Isles is demonstrated in the large number of different mutations characterized and in the variety of genetic backgrounds on which individual mutations are found. Allele frequencies of the more common mutations exhibited significant nonrandom distribution in a north/south differentiation. Differences between the west of Scotland and southwestern England may be related to different events in the recent and past histories of their respective populations. Similarities between southern Wales and southeastern England are likely to reflect the heterogeneity that is seen in and around two large capital cities. Finally, comparison with more recently colonized areas of the world corroborates the genealogical origin by range expansion of several mutations. 38 refs., 2 tabs.

Gene expression profiling for human iPS-derived motor neurons from sporadic ALS patients reveals a strong association between mitochondrial functions and neurodegeneration

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Alves, Chrystian J.; Dariolli, Rafael; Jorge, Frederico M.; Monteiro, Matheus R.; Maximino, Jessica R.; Martins, Roberto S.; Strauss, Bryan E.; Krieger, José E.; Callegaro, Dagoberto; Chadi, Gerson

2015-01-01

Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease that leads to widespread motor neuron death, general palsy and respiratory failure. The most prevalent sporadic ALS form is not genetically inherited. Attempts to translate therapeutic strategies have failed because the described mechanisms of disease are based on animal models carrying specific gene mutations and thus do not address sporadic ALS. In order to achieve a better approach to study the human disease, human induced pluripotent stem cell (hiPSC)-differentiated motor neurons were obtained from motor nerve fibroblasts of sporadic ALS and non-ALS subjects using the STEMCCA Cre-Excisable Constitutive Polycistronic Lentivirus system and submitted to microarray analyses using a whole human genome platform. DAVID analyses of differentially expressed genes identified molecular function and biological process-related genes through Gene Ontology. REVIGO highlighted the related functions mRNA and DNA binding, GTP binding, transcription (co)-repressor activity, lipoprotein receptor binding, synapse organization, intracellular transport, mitotic cell cycle and cell death. KEGG showed pathways associated with Parkinson's disease and oxidative phosphorylation, highlighting iron homeostasis, neurotrophic functions, endosomal trafficking and ERK signaling. The analysis of most dysregulated genes and those representative of the majority of categorized genes indicates a strong association between mitochondrial function and cellular processes possibly related to motor neuron degeneration. In conclusion, iPSC-derived motor neurons from motor nerve fibroblasts of sporadic ALS patients may recapitulate key mechanisms of neurodegeneration and may offer an opportunity for translational investigation of sporadic ALS. Large gene profiling of differentiated motor neurons from sporadic ALS patients highlights mitochondrial participation in the establishment of autonomous mechanisms associated with sporadic ALS

Genetic signature of strong recent positive selection at interleukin-32 gene in goat

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Akhtar Rasool Asif

2017-07-01

Full Text Available Objective Identification of the candidate genes that play key roles in phenotypic variations can provide new information about evolution and positive selection. Interleukin (IL-32 is involved in many biological processes, however, its role for the immune response against various diseases in mammals is poorly understood. Therefore, the current investigation was performed for the better understanding of the molecular evolution and the positive selection of single nucleotide polymorphisms in IL-32 gene. Methods By using fixation index (FST based method, IL-32 (9375 gene was found to be outlier and under significant positive selection with the provisional combined allocation of mean heterozygosity and FST. Using nucleotide sequences of 11 mammalian species from National Center for Biotechnology Information database, the evolutionary selection of IL-32 gene was determined using Maximum likelihood model method, through four models (M1a, M2a, M7, and M8 in Codeml program of phylogenetic analysis by maximum liklihood. Results IL-32 is detected under positive selection using the FST simulations method. The phylogenetic tree revealed that goat IL-32 was in close resemblance with sheep IL-32. The coding nucleotide sequences were compared among 11 species and it was found that the goat IL-32 gene shared identity with sheep (96.54%, bison (91.97%, camel (58.39%, cat (56.59%, buffalo (56.50%, human (56.13%, dog (50.97%, horse (54.04%, and rabbit (53.41% respectively. Conclusion This study provides evidence for IL-32 gene as under significant positive selection in goat.

Isolation of a strong Arabidopsis guard cell promoter and its potential as a research tool

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Siegel Robert S

2008-02-01

Full Text Available Abstract Background A common limitation in guard cell signaling research is that it is difficult to obtain consistent high expression of transgenes of interest in Arabidopsis guard cells using known guard cell promoters or the constitutive 35S cauliflower mosaic virus promoter. An additional drawback of the 35S promoter is that ectopically expressing a gene throughout the organism could cause pleiotropic effects. To improve available methods for targeted gene expression in guard cells, we isolated strong guard cell promoter candidates based on new guard cell-specific microarray analyses of 23,000 genes that are made available together with this report. Results A promoter, pGC1(At1g22690, drove strong and relatively specific reporter gene expression in guard cells including GUS (beta-glucuronidase and yellow cameleon YC3.60 (GFP-based calcium FRET reporter. Reporter gene expression was weaker in immature guard cells. The expression of YC3.60 was sufficiently strong to image intracellular Ca2+ dynamics in guard cells of intact plants and resolved spontaneous calcium transients in guard cells. The GC1 promoter also mediated strong reporter expression in clustered stomata in the stomatal development mutant too-many-mouths (tmm. Furthermore, the same promoter::reporter constructs also drove guard cell specific reporter expression in tobacco, illustrating the potential of this promoter as a method for high level expression in guard cells. A serial deletion of the promoter defined a guard cell expression promoter region. In addition, anti-sense repression using pGC1 was powerful for reducing specific GFP gene expression in guard cells while expression in leaf epidermal cells was not repressed, demonstrating strong cell-type preferential gene repression. Conclusion The pGC1 promoter described here drives strong reporter expression in guard cells of Arabidopsis and tobacco plants. It provides a potent research tool for targeted guard cell expression or

Resveratrol strongly enhances the retinoic acid-induced superoxide generating activity via up-regulation of gp91-phox gene expression in U937 cells.

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Kikuchi, Hidehiko; Mimuro, Hitomi; Kuribayashi, Futoshi

2018-01-01

The membrane bound cytochrome b 558 composed of gp91-phox and p22-phox proteins, and cytosolic proteins p40-, p47-and p67-phox are important components of superoxide (O 2 - )-generating system in phagocytes. Here, we describe that resveratrol, a pleiotropic phytochemical belonging to the stilbenoids, dramatically activates the O 2 - -generating system during retinoic acid (RA)-induced differentiation of human monoblastic leukemia U937 cells to macrophage-like cells. When U937 cells were cultured in the presence of RA and resveratrol, the O 2 - -generating activity increased more than 5-fold compared with that in the absence of the latter. Semiquantitative RT-PCR showed that co-treatment with RA and resveratrol strongly enhanced transcription of the gp91-phox compared with those of the RA-treatment only. On the other hand, immunoblot analysis revealed that co-treatment with RA and resveratrol caused remarkable accumulation of protein levels of gp91-phox (to 4-fold), p22-phox (to 5-fold) and p47-phox (to 4-fold) compared with those of the RA-treatment alone. In addition, ChIP assay suggested that resveratrol participates in enhancing the gene expression of gp91-phox via promoting acetylation of Lys-9 residues and Lys-14 residues of histone H3 within chromatin around the promoter regions of the gene. These results suggested that resveratrol strongly enhances the RA-induced O 2 - -generating activity via up-regulation of gp91-phox gene expression in U937 cells. Copyright © 2017 Elsevier Inc. All rights reserved.

The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography.

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Lapierre, Marguerite; Blin, Camille; Lambert, Amaury; Achaz, Guillaume; Rocha, Eduardo P C

2016-07-01

Recent studies have linked demographic changes and epidemiological patterns in bacterial populations using coalescent-based approaches. We identified 26 studies using skyline plots and found that 21 inferred overall population expansion. This surprising result led us to analyze the impact of natural selection, recombination (gene conversion), and sampling biases on demographic inference using skyline plots and site frequency spectra (SFS). Forward simulations based on biologically relevant parameters from Escherichia coli populations showed that theoretical arguments on the detrimental impact of recombination and especially natural selection on the reconstructed genealogies cannot be ignored in practice. In fact, both processes systematically lead to spurious interpretations of population expansion in skyline plots (and in SFS for selection). Weak purifying selection, and especially positive selection, had important effects on skyline plots, showing patterns akin to those of population expansions. State-of-the-art techniques to remove recombination further amplified these biases. We simulated three common sampling biases in microbiological research: uniform, clustered, and mixed sampling. Alone, or together with recombination and selection, they further mislead demographic inferences producing almost any possible skyline shape or SFS. Interestingly, sampling sub-populations also affected skyline plots and SFS, because the coalescent rates of populations and their sub-populations had different distributions. This study suggests that extreme caution is needed to infer demographic changes solely based on reconstructed genealogies. We suggest that the development of novel sampling strategies and the joint analyzes of diverse population genetic methods are strictly necessary to estimate demographic changes in populations where selection, recombination, and biased sampling are present. © The Author 2016. Published by Oxford University Press on behalf of the Society for

Genealogia feminina: diálogo silencioso entre gerações - Female genealogy: silent dialogue between generations

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Flávia Obino Corrêa Werle, Brasil

2014-05-01

Full Text Available Este artigo, desenvolvido na linha da História Cultural, adota como metodologia uma abordagem biográfico-narrativa. Discute, dentre outros conceitos, os de tradição, inovação, genealogia feminina na perspectiva de novos enfoques para a História da Educação. Considera a memória, tanto como um discurso, quanto como uma presença nos objetos e cultura material. Analisa um objeto guardado e presenteado de gerações em gerações a ser usado pelas mulheres de uma mesma família na hora do parto. Problematiza o tema da formação humana em espaços de relações familiares e em modalidades não escolarizadas e questiona o que as irmãs ensinam umas às outras, que aprendizagens ocorrem nas relações entre mulheres que são vizinhas, amigas, primas, tias, sobrinhas.Palavras-chave: história da educação, tradição, memória.FEMALE GENEALOGY: SILENT DIALOGUE BETWEEN GENERATIONSAbstractThe methodology of this article, developed along the lines of Cultural History, is a biographical-narrative approach. Among other concepts, it discusses tradition, innovation, female genealogy from the perspective of new ways to focus on History of Education. It considers memory both as a discourse and as a presence in objects and material culture. An object stored and gifted from generation to generation, to be used by the women of a same family at the time of childbirth is analyzed. It problematizes tthe topic of human formation in spaces of family relations and in non-schooled modes, and asks what the sisters teach each other, what learnings occur in the relationships between women who are neighbors, friends, cousins, sisters, nieces.Key-words: history of education, tradition, memory.GENEALOGIA FEMENINA: DIALOGO SILENCIOSO ENTRE GENERACIONESResumen Este artículo, desarrollado en el contexto dela Historia Cultural, adopta como metodología una temática biográfica-narrativa. Trata los conceptos de tradición, inovación, genealogía femenina desde la

Reconstructing genealogies of serial samples under the assumption of a molecular clock using serial-sample UPGMA.

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Drummond, A; Rodrigo, A G

2000-12-01

Reconstruction of evolutionary relationships from noncontemporaneous molecular samples provides a new challenge for phylogenetic reconstruction methods. With recent biotechnological advances there has been an increase in molecular sequencing throughput, and the potential to obtain serial samples of sequences from populations, including rapidly evolving pathogens, is fast being realized. A new method called the serial-sample unweighted pair grouping method with arithmetic means (sUPGMA) is presented that reconstructs a genealogy or phylogeny of sequences sampled serially in time using a matrix of pairwise distances. The resulting tree depicts the terminal lineages of each sample ending at a different level consistent with the sample's temporal order. Since sUPGMA is a variant of UPGMA, it will perform best when sequences have evolved at a constant rate (i.e., according to a molecular clock). On simulated data, this new method performs better than standard cluster analysis under a variety of longitudinal sampling strategies. Serial-sample UPGMA is particularly useful for analysis of longitudinal samples of viruses and bacteria, as well as ancient DNA samples, with the minimal requirement that samples of sequences be ordered in time.

American Uncles and Aunts: Generations, Genealogies, Bildungs in 1930s Novels

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Cinzia Scarpino

2013-05-01

Full Text Available The essay focuses on the characters of uncles and aunts as they emerge in four novels written in the 1930s by two second-generation immigrant novelists and two American women writers: Henry Roth’s Call It Sleep (1934, Pietro di Donato’s Christ in Concrete (1939, Josephine Herbst’s Pity Is Not Enough (1933, and Catherine Anne Porter’s Old Mortality (1937. In their portrayal of a growing-up young male and female protagonist sharing many autobiographical traits with the authors, these works can be considered late versions of American Bildungsromans in which the presence of uncles and aunts seem to function as an alternative – or complementary – model to the parental one and to play a pivotal role in the (possible or impossible Bildungs of nephews and nieces.    Starting with a brief survey on the rediscovery and mapping of anthropological, ethnological and folkloric genealogies (including recent immigrants’ stories and their unprecedented entrance into  official national narratives during the Great Depression, the essay attempts to show how the figures of uncles and aunts play strategic roles in both the working-class and immigrant Bildungs (or “anti-Bildungs represented in Call It Sleep and Christ in Concrete, and the female middle-class Bildungs (or “awakenings” evoked in Pity Is Not Enough and Old Mortality. Whereas Roth and di Donato simultaneously mark the coming of age and the modern watershed of the hyphenated literary tradition of Jewish-American and Italian-American novels by creating impossible narratives of “development” built around ghetto children, Herbst and Porters’ works seem to stem from the genre of the sentimental novel and the novel of “awakening” and to twist them into a modernist version of possible female Bildungs.

The genealogical decomposition of a matrix population model with applications to the aggregation of stages.

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Bienvenu, François; Akçay, Erol; Legendre, Stéphane; McCandlish, David M

2017-06-01

Matrix projection models are a central tool in many areas of population biology. In most applications, one starts from the projection matrix to quantify the asymptotic growth rate of the population (the dominant eigenvalue), the stable stage distribution, and the reproductive values (the dominant right and left eigenvectors, respectively). Any primitive projection matrix also has an associated ergodic Markov chain that contains information about the genealogy of the population. In this paper, we show that these facts can be used to specify any matrix population model as a triple consisting of the ergodic Markov matrix, the dominant eigenvalue and one of the corresponding eigenvectors. This decomposition of the projection matrix separates properties associated with lineages from those associated with individuals. It also clarifies the relationships between many quantities commonly used to describe such models, including the relationship between eigenvalue sensitivities and elasticities. We illustrate the utility of such a decomposition by introducing a new method for aggregating classes in a matrix population model to produce a simpler model with a smaller number of classes. Unlike the standard method, our method has the advantage of preserving reproductive values and elasticities. It also has conceptually satisfying properties such as commuting with changes of units. Copyright © 2017 Elsevier Inc. All rights reserved.

The genealogy and genetic viability of reintroduced Yellowstone grey wolves.

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Vonholdt, Bridgett M; Stahler, Daniel R; Smith, Douglas W; Earl, Dent A; Pollinger, John P; Wayne, Robert K

2008-01-01

The recovery of the grey wolf in Yellowstone National Park is an outstanding example of a successful reintroduction. A general question concerning reintroduction is the degree to which genetic variation has been preserved and the specific behavioural mechanisms that enhance the preservation of genetic diversity and reduce inbreeding. We have analysed 200 Yellowstone wolves, including all 31 founders, for variation in 26 microsatellite loci over the 10-year reintroduction period (1995-2004). The population maintained high levels of variation (1995 H(0) = 0.69; 2004 H(0) = 0.73) with low levels of inbreeding (1995 F(IS) = -0.063; 2004 F(IS) = -0.051) and throughout, the population expanded rapidly (N(1995) = 21; N(2004) = 169). Pedigree-based effective population size ratios did not vary appreciably over the duration of population expansion (1995 N(e)/N(g) = 0.29; 2000 N(e)/N(g) = 0.26; 2004 N(e)/N(g) = 0.33). We estimated kinship and found only two of 30 natural breeding pairs showed evidence of being related (average r = -0.026, SE = 0.03). We reconstructed the genealogy of 200 wolves based on genetic and field data and discovered that they avoid inbreeding through a wide variety of behavioural mechanisms including absolute avoidance of breeding with related pack members, male-biased dispersal to packs where they breed with nonrelatives, and female-biased subordinate breeding. We documented a greater diversity of such population assembly patterns in Yellowstone than previously observed in any other natural wolf population. Inbreeding avoidance is nearly absolute despite the high probability of within-pack inbreeding opportunities and extensive interpack kinship ties between adjacent packs. Simulations showed that the Yellowstone population has levels of genetic variation similar to that of a population managed for high variation and low inbreeding, and greater than that expected for random breeding within packs or across the entire breeding pool. Although short

Moorean tree snail survival revisited: a multi-island genealogical perspective.

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Lee, Taehwan; Burch, John B; Coote, Trevor; Pearce-Kelly, Paul; Hickman, Carole; Meyer, Jean-Yves; O Foighil, Diarmaid

2009-08-18

The mass extirpation of the island of Moorea's endemic partulid tree snail fauna, following the deliberate introduction of the alien predator Euglandina rosea, represents one of the highest profile conservation crises of the past thirty years. All of the island's partulids were thought to be extirpated by 1987, with five species persisting in zoos, but intensive field surveys have recently detected a number of surviving wild populations. We report here a mitochondrial (mt) phylogenetic estimate of Moorean partulid wild and captive lineage survival calibrated with a reference museum collection that pre-dates the predator's introduction and that also includes a parallel dataset from the neighboring island of Tahiti. Although severe winnowing of Moorea's mt lineage diversity has occurred, seven of eight (six Partula; two Samoana) partulid tip clades remain extant. The extinct mt clade occurred predominantly in the P. suturalis species complex and it represented a major component of Moorea's endemic partulid treespace. Extant Moorean mt clades exhibited a complex spectrum of persistence on Moorea, in captivity, and (in the form of five phylogenetically distinct sister lineages) on Tahiti. Most notably, three Partula taxa, bearing two multi-island mt lineages, have survived decades of E. rosea predation on Moorea (P. taeniata) and in the valleys of Tahiti (P. hyalina and P. clara). Their differential persistence was correlated with intrinsic attributes, such as taxonomy and mt lineages, rather than with their respective within-island distribution patterns. Conservation efforts directed toward Moorean and Tahitian partulids have typically operated within a single island frame of reference, but our discovery of robust genealogical ties among survivors on both islands implies that a multi-island perspective is required. Understanding what genetic and/or ecological factors have enabled Partula taeniata, P. hyalina and P. clara to differentially survive long-term direct

Moorean tree snail survival revisited: a multi-island genealogical perspective

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Meyer Jean-Yves

2009-08-01

Full Text Available Abstract Background The mass extirpation of the island of Moorea's endemic partulid tree snail fauna, following the deliberate introduction of the alien predator Euglandina rosea, represents one of the highest profile conservation crises of the past thirty years. All of the island's partulids were thought to be extirpated by 1987, with five species persisting in zoos, but intensive field surveys have recently detected a number of surviving wild populations. We report here a mitochondrial (mt phylogenetic estimate of Moorean partulid wild and captive lineage survival calibrated with a reference museum collection that pre-dates the predator's introduction and that also includes a parallel dataset from the neighboring island of Tahiti. Results Although severe winnowing of Moorea's mt lineage diversity has occurred, seven of eight (six Partula; two Samoana partulid tip clades remain extant. The extinct mt clade occurred predominantly in the P. suturalis species complex and it represented a major component of Moorea's endemic partulid treespace. Extant Moorean mt clades exhibited a complex spectrum of persistence on Moorea, in captivity, and (in the form of five phylogenetically distinct sister lineages on Tahiti. Most notably, three Partula taxa, bearing two multi-island mt lineages, have survived decades of E. rosea predation on Moorea (P. taeniata and in the valleys of Tahiti (P. hyalina and P. clara. Their differential persistence was correlated with intrinsic attributes, such as taxonomy and mt lineages, rather than with their respective within-island distribution patterns. Conclusion Conservation efforts directed toward Moorean and Tahitian partulids have typically operated within a single island frame of reference, but our discovery of robust genealogical ties among survivors on both islands implies that a multi-island perspective is required. Understanding what genetic and/or ecological factors have enabled Partula taeniata, P. hyalina and P

A BAYESIAN NONPARAMETRIC MIXTURE MODEL FOR SELECTING GENES AND GENE SUBNETWORKS.

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Zhao, Yize; Kang, Jian; Yu, Tianwei

2014-06-01

It is very challenging to select informative features from tens of thousands of measured features in high-throughput data analysis. Recently, several parametric/regression models have been developed utilizing the gene network information to select genes or pathways strongly associated with a clinical/biological outcome. Alternatively, in this paper, we propose a nonparametric Bayesian model for gene selection incorporating network information. In addition to identifying genes that have a strong association with a clinical outcome, our model can select genes with particular expressional behavior, in which case the regression models are not directly applicable. We show that our proposed model is equivalent to an infinity mixture model for which we develop a posterior computation algorithm based on Markov chain Monte Carlo (MCMC) methods. We also propose two fast computing algorithms that approximate the posterior simulation with good accuracy but relatively low computational cost. We illustrate our methods on simulation studies and the analysis of Spellman yeast cell cycle microarray data.

Global spread and genetic variants of the two CYP9M10 haplotype forms associated with insecticide resistance in Culex quinquefasciatus Say.

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Itokawa, K; Komagata, O; Kasai, S; Kawada, H; Mwatele, C; Dida, G O; Njenga, S M; Mwandawiro, C; Tomita, T

2013-09-01

Insecticide resistance develops as a genetic factor (allele) conferring lower susceptibility to insecticides proliferates within a target insect population under strong positive selection. Intriguingly, a resistance allele pre-existing in a population often bears a series of further adaptive allelic variants through new mutations. This phenomenon occasionally results in replacement of the predominating resistance allele by fitter new derivatives, and consequently, development of greater resistance at the population level. The overexpression of the cytochrome P450 gene CYP9M10 is associated with pyrethroid resistance in the southern house mosquito Culex quinquefasciatus. Previously, we have found two genealogically related overexpressing CYP9M10 haplotypes, which differ in gene copy number (duplicated and non-duplicated). The duplicated haplotype was derived from the non-duplicated overproducer probably recently. In the present study, we investigated allelic series of CYP9M10 involved in three C. quinquefasciatus laboratory colonies recently collected from three different localities. Duplicated and non-duplicated overproducing haplotypes coexisted in African and Asian colonies indicating a global distribution of both haplotype lineages. The duplicated haplotypes both in the Asian and African colonies were associated with higher expression levels and stronger resistance than non-duplicated overproducing haplotypes. There were slight variation in expression level among the non-duplicated overproducing haplotypes. The nucleotide sequences in coding and upstream regions among members of this group also showed a little diversity. Non-duplicated overproducing haplotypes with relatively higher expression were genealogically closer to the duplicated haplotypes than the other non-duplicated overproducing haplotypes, suggesting multiple cis-acting mutations before duplication.

Strong Migration Limit for Games in Structured Populations: Applications to Dominance Hierarchy and Set Structure

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Dhaker Kroumi

2015-09-01

Full Text Available In this paper, we deduce a condition for a strategy S1 to be more abundant on average at equilibrium under weak selection than another strategy S2 in a population structured into a finite number of colonies of fixed proportions as the population size tends to infinity. It is assumed that one individual reproduces at a time with some probability depending on the payoff received in pairwise interactions within colonies and between colonies and that the offspring replaces one individual chosen at random in the colony into which the offspring migrates. It is shown that an expected weighted average equilibrium frequency of S1 under weak symmetric strategy mutation between S1 and S2 is increased by weak selection if an expected weighted payoff of S1 near neutrality exceeds the corresponding expected weighted payoff of S2. The weights are given in terms of reproductive values of individuals in the different colonies in the neutral model. This condition for S1 to be favoured by weak selection is obtained from a strong migration limit of the genealogical process under neutrality for a sample of individuals, which is proven using a two-time scale argument. The condition is applied to games between individuals in colonies with linear or cyclic dominance and between individuals belonging to groups represented by subsets of a given set.

Molecular relationships of fungi within the Fusarium redolens - F. hostae clade

NARCIS (Netherlands)

Baayen, R.P.; O'Donnell, K.; Breeuwsma, S.; Geiser, D.M.; Waalwijk, C.

2001-01-01

The evolutionary relationships of fungi in the Fusarium redolens - F. hostae clade were investigated by constructing nuclear and mitochondrial gene genealogies for 37 isolates representing the known genetic and pathogenic diversity of this lineage, together with 15 isolates from putative sister

Population Structure Analysis of Bull Genomes of European and Western Ancestry

DEFF Research Database (Denmark)

Chung, Neo Christopher; Szyda, Joanna; Frąszczak, Magdalena

2017-01-01

Since domestication, population bottlenecks, breed formation, and selective breeding have radically shaped the genealogy and genetics of Bos taurus. In turn, characterization of population structure among diverse bull (males of Bos taurus) genomes enables detailed assessment of genetic resources...... and origins. By analyzing 432 unrelated bull genomes from 13 breeds and 16 countries, we demonstrate genetic diversity and structural complexity among the European/Western cattle population. Importantly, we relaxed a strong assumption of discrete or admixed population, by adapting latent variable models...... harboring largest genetic differentiation suggest positive selection underlying population structure. We carried out gene set analysis using SNP annotations to identify enriched functional categories such as energy-related processes and multiple development stages. Our population structure analysis of bull...

New microsatellites revealed strong gene flow among populations of a new outbreak pest, Athetis lepigone (Möschler).

Science.gov (United States)

Zhu, W-C; Sun, J-T; Dai, J; Huang, J-R; Chen, L; Hong, X-Y

2017-11-27

Athetis lepigone (Möschler) (Lepidoptera: Noctuidae) is a new outbreak pest in China. Consequently, it is unclear whether the emergence and spread of the outbreak of this pest are triggered by rapid in situ population size increases in each outbreak area, or by immigrants from a potential source area in China. In order to explore the outbreak process of this pest through a population genetics approach, we developed ten novel polymorphic expressed sequence tags (EST)-derived microsatellites. These new microsatellites had moderately high levels of polymorphism in the tested population. The number of alleles per locus ranged from 3 to 19, with an average of 8.6, and the expected heterozygosity ranged from 0.269 to 0.783. A preliminary population genetic analysis using these new microsatellites revealed a lack of population genetic structure in natural populations of A. lepigone. The estimates of recent migration rate revealed strong gene flow among populations. In conclusion, our study developed the first set of EST-microsatellite markers and shed a new light on the population genetic structure of this pest in China.

A genealogia em Foucault: uma trajetoria The genealogy in Foucault: a trajectory

Directory of Open Access Journals (Sweden)

Flavia Cristina Silveira Lemos

2009-12-01

Full Text Available Este artigo tem o objetivo de realizar uma trajetória da genealogia enquanto modo de escrever a história como pergunta/problema, de acordo com Michel Foucault, rompendo com uma história contínua, linear, teleológica, que buscava origens e semelhanças entre os objetos e as tentativas de estabelecer relações causais entre os acontecimentos. Uma história das práticas discursivas, de poder e subjetivação era a empreitada proposta por Foucault. A análise da proveniência e da emergência rompia com toda uma tradição historiográfica que fazia dos eventos memória e monumentos construídos e interpretados por categorias de semelhança. Foucault questiona este modelo de fazer história, trabalhando com novos temas e problemas e operando com a multiplicidade de acontecimentos dispersos, raros, heterogêneos, em recortes de séries de enunciados em arquivos, sem busca de origens primeiras e sem fins utilitaristas a alcançar.This article aims to achieve a path of genealogy as a way to write history as question / problem, according to Michel Foucault, breaking with a continuous, linear, teleological history, which sought origins and similarities between objects and attempts to establish causal relationships between the events. A history of discursive practices, power and subjectivity was the contract proposed by Foucault. The analysis of the source and emergency broke with a whole historiographical tradition which made the events memory and monuments constructed and interpreted by categories of similarity. Foucault questions this model to make history, working with new issues and problems and working with the multiplicity of scattered, rare, heterogeneous events, in clippings of series of statements in files, without searching for early origins and without utilitarian goals to be achieved.

IgV gene intraclonal diversification and clonal evolution in B-cell chronic lymphocytic leukaemia.

Science.gov (United States)

Bagnara, Davide; Callea, Vincenzo; Stelitano, Caterina; Morabito, Fortunato; Fabris, Sonia; Neri, Antonino; Zanardi, Sabrina; Ghiotto, Fabio; Ciccone, Ermanno; Grossi, Carlo Enrico; Fais, Franco

2006-04-01

Intraclonal diversification of immunoglobulin (Ig) variable (V) genes was evaluated in leukaemic cells from a B-cell chronic lymphocytic leukaemia (B-CLL) case over a 2-year period at four time points. Intraclonal heterogeneity was analysed by sequencing 305 molecular clones derived from polymerase chain reaction amplification of B-CLL cell IgV heavy (H) and light (C) chain gene rearrangements. Sequences were compared with evaluating intraclonal variation and the nature of somatic mutations. Although IgV intraclonal variation was detected at all time points, its level decreased with time and a parallel emergence of two more represented V(H)DJ(H) clones was observed. They differed by nine nucleotide substitutions one of which only caused a conservative replacement aminoacid change. In addition, one V(L)J(L) rearrangement became more represented over time. Analyses of somatic mutations suggest antigen selection and impairment of negative selection of neoplastic cells. In addition, a genealogical tree representing a model of clonal evolution of the neoplastic cells was created. It is of note that, during the period of study, the patient showed clinical progression of disease. We conclude that antigen stimulation and somatic hypermutation may participate in disease progression through the selection and expansion of neoplastic subclone(s).

Gene-gene, gene-environment, gene-nutrient interactions and single nucleotide polymorphisms of inflammatory cytokines.

Science.gov (United States)

Nadeem, Amina; Mumtaz, Sadaf; Naveed, Abdul Khaliq; Aslam, Muhammad; Siddiqui, Arif; Lodhi, Ghulam Mustafa; Ahmad, Tausif

2015-05-15

Inflammation plays a significant role in the etiology of type 2 diabetes mellitus (T2DM). The rise in the pro-inflammatory cytokines is the essential step in glucotoxicity and lipotoxicity induced mitochondrial injury, oxidative stress and beta cell apoptosis in T2DM. Among the recognized markers are interleukin (IL)-6, IL-1, IL-10, IL-18, tissue necrosis factor-alpha (TNF-α), C-reactive protein, resistin, adiponectin, tissue plasminogen activator, fibrinogen and heptoglobins. Diabetes mellitus has firm genetic and very strong environmental influence; exhibiting a polygenic mode of inheritance. Many single nucleotide polymorphisms (SNPs) in various genes including those of pro and anti-inflammatory cytokines have been reported as a risk for T2DM. Not all the SNPs have been confirmed by unifying results in different studies and wide variations have been reported in various ethnic groups. The inter-ethnic variations can be explained by the fact that gene expression may be regulated by gene-gene, gene-environment and gene-nutrient interactions. This review highlights the impact of these interactions on determining the role of single nucleotide polymorphism of IL-6, TNF-α, resistin and adiponectin in pathogenesis of T2DM.

Phylogeography of the barbel (Barbus barbus) assessed by mitochondrial DNA variation

Czech Academy of Sciences Publication Activity Database

Kotlík, Petr; Berrebi, P.

2001-01-01

Roč. 10, č. 8 (2001), s. 2177-2185 ISSN 0962-1083 R&D Projects: GA ČR GA206/00/0668; GA AV ČR KSK6005114 Keywords : Barbus * biogeography * gene genealogy Subject RIV: EG - Zoology Impact factor: 2.478, year: 2001

Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae)

Science.gov (United States)

Hybridization is currently considered to be a frequent and important force in plant evolution; NGS methods offer new possibilities for clade resolution and ambitious sampling of gene genealogies, yet difficulty remains in detecting deep reticulation events using currently available methods. We exami...

Processes of social flourishing and their liminal collapse: elements to a genealogy of globalization.

Science.gov (United States)

Szakolczai, Arpad

2016-09-01

This article aims at exploring a long-term historical perspective on which contemporary globalization can be more meaningfully situated. A central problem with established approaches to globalization is that they are even more presentist than the literature on modernization was. Presentism not only means the ignoring of history, but also the unreflective application to history of concepts taken from the study of the modern world. In contrast, it is argued that contemporary globalization is not a unique development, but rather is a concrete case of a historical type. Taking as its point of departure the spirit, rather than the word, of Max Weber, this article extends the scope of sociological investigation into archaeological evidence. Having a genealogical design and introducing the concept of 'liminality', the article approaches the modern process of globalization through reconstructing the internal dynamics of another type of historical change called 'social flourishing'. Taking up the Weberian approach continued by Eisenstadt in his writings on 'axial age', it moves away from situations of crisis as reference point, shifting attention to periods of revival by introducing the term 'epiphany'. Through the case of early Mesopotamia, it shows how social flourishing can be transmogrified into globalizing growth, gaining a new perspective concerning the kind of 'animating spirit' that might have driven the shift from Renaissance to Reformation, the rise of modern colonialism, or contemporary globalization. More generally, it will retrieve the long-term historical background of the axial age and demonstrate the usefulness and importance of archaeological evidence for sociology. © London School of Economics and Political Science 2016.

77 FR 9259 - Agency Information Collection Activities: Forms G-1041 and G-1041A, Extension of a Currently...

Science.gov (United States)

2012-02-16

..., Genealogy Index Search Request and Genealogy Records Request. The Department of Homeland Security, U.S... the Forms/Collections: Genealogy Index Search Request and Genealogy Records Request. (3) Agency form.... USCIS will use these forms will to facilitate an accurate and timely response to genealogy index search...

Philanthropy and Human Rights - The Genealogy of the Idea from Antiquity to Global Society

Directory of Open Access Journals (Sweden)

Øjvind Larsen

2013-06-01

Full Text Available In the last couple of decades, philanthropy has become a concern which is taken seriously in the Western world. Normal people give donations and volunteer on a large scale within the institutions of civil society. This is the case for business corporations as well, who now have to act with a form of personal responsibility. Such a responsibility is institutionalized in the big global CSR movement, which has now been integrated in the UN Global Compact. Philanthropy has many dimensions; these include ethical, juridical, political, economic and cultural dimensions. In the last years, a lot has been written about philanthropy from a political, sociological, anthropological and managerial perspective. However, an essential question remains: what does philanthropy mean? In a Greek context, philanthropy is connected to a friendly act towards one’s owns close connections such as family or fellow citizens, and normally utilized to promote one’s own prestige in the city-state. In Roman context, universal humanism, humanitas, was invented. This universal perspective was also supported by Christianity. It is this universal concept of philanthropy which is the foundation for the different philanthropic traditions in Germany, England, France and USA. In each tradition is developed special features of the concept of philanthropy. The four traditions are summarized in the UN universal human rights, which has become the common normative reference for global philanthropy. In this way philanthropy has become, in a modern sense, a charitable act with the aim to promote human happiness independent of gender, class, race, etc. This is the genealogy of the modern understanding of philanthropy, which will be developed in this paper.

Using extended genealogy to estimate components of heritability for 23 quantitative and dichotomous traits.

Science.gov (United States)

Zaitlen, Noah; Kraft, Peter; Patterson, Nick; Pasaniuc, Bogdan; Bhatia, Gaurav; Pollack, Samuela; Price, Alkes L

2013-05-01

Important knowledge about the determinants of complex human phenotypes can be obtained from the estimation of heritability, the fraction of phenotypic variation in a population that is determined by genetic factors. Here, we make use of extensive phenotype data in Iceland, long-range phased genotypes, and a population-wide genealogical database to examine the heritability of 11 quantitative and 12 dichotomous phenotypes in a sample of 38,167 individuals. Most previous estimates of heritability are derived from family-based approaches such as twin studies, which may be biased upwards by epistatic interactions or shared environment. Our estimates of heritability, based on both closely and distantly related pairs of individuals, are significantly lower than those from previous studies. We examine phenotypic correlations across a range of relationships, from siblings to first cousins, and find that the excess phenotypic correlation in these related individuals is predominantly due to shared environment as opposed to dominance or epistasis. We also develop a new method to jointly estimate narrow-sense heritability and the heritability explained by genotyped SNPs. Unlike existing methods, this approach permits the use of information from both closely and distantly related pairs of individuals, thereby reducing the variance of estimates of heritability explained by genotyped SNPs while preventing upward bias. Our results show that common SNPs explain a larger proportion of the heritability than previously thought, with SNPs present on Illumina 300K genotyping arrays explaining more than half of the heritability for the 23 phenotypes examined in this study. Much of the remaining heritability is likely to be due to rare alleles that are not captured by standard genotyping arrays.

Using extended genealogy to estimate components of heritability for 23 quantitative and dichotomous traits.

Directory of Open Access Journals (Sweden)

Noah Zaitlen

2013-05-01

Full Text Available Important knowledge about the determinants of complex human phenotypes can be obtained from the estimation of heritability, the fraction of phenotypic variation in a population that is determined by genetic factors. Here, we make use of extensive phenotype data in Iceland, long-range phased genotypes, and a population-wide genealogical database to examine the heritability of 11 quantitative and 12 dichotomous phenotypes in a sample of 38,167 individuals. Most previous estimates of heritability are derived from family-based approaches such as twin studies, which may be biased upwards by epistatic interactions or shared environment. Our estimates of heritability, based on both closely and distantly related pairs of individuals, are significantly lower than those from previous studies. We examine phenotypic correlations across a range of relationships, from siblings to first cousins, and find that the excess phenotypic correlation in these related individuals is predominantly due to shared environment as opposed to dominance or epistasis. We also develop a new method to jointly estimate narrow-sense heritability and the heritability explained by genotyped SNPs. Unlike existing methods, this approach permits the use of information from both closely and distantly related pairs of individuals, thereby reducing the variance of estimates of heritability explained by genotyped SNPs while preventing upward bias. Our results show that common SNPs explain a larger proportion of the heritability than previously thought, with SNPs present on Illumina 300K genotyping arrays explaining more than half of the heritability for the 23 phenotypes examined in this study. Much of the remaining heritability is likely to be due to rare alleles that are not captured by standard genotyping arrays.

Notas para uma genealogia da Psicologia Social Notes for a genealogy of Social Psychology

Directory of Open Access Journals (Sweden)

Rosane Neves da Silva

2004-08-01

Full Text Available A partir de uma "desnaturalização" do conceito de social, pretende-se situar as condições de possibilidade para a invenção da psicologia social. Utilizando uma estratégia genealógica, nosso objetivo é mostrar que, no lugar da psicologia explicar o social, é o próprio social que deve explicar o surgimento da psicologia moderna. Para tanto, é preciso deixar de considerar o social como sinônimo da noção de sociabilidade e passar a considerá-lo como algo essencialmente construído a partir de determinadas práticas humanas. Tal problematização permite entender como se produzem, no final do século XIX, as primeiras aproximações da psicologia moderna em direção ao social a partir das questões relacionadas ao fenômeno das multidões.The "denaturalization" of the concept "social" allow us to situate the conditions to the invention of social psychology. Using the genealogy strategy, our goal is to show that it is not psychology that explains the "social" but it is the "social" itself that explains the emergence of modern psychology. In order to attain our goal it is necessary to abandon the use of social as a synonym of sociability and to consider the "social" as a product essentially constructed by determinate human practices. This strategy allows us to understand how, at the end of the XIX century, modern psychology's firsts theoretical approaches towards the "social" were produced from matters related to the phenomena of the masses.

Circum Black sea phylogeography of Barbus freshwater fishes: divergence in the Pontic glacial refugium

Czech Academy of Sciences Publication Activity Database

Kotlík, Petr; Bogutskaya, N. G.; Ekmekci, F. G.

2004-01-01

Roč. 13, č. 1 (2004), s. 87-95 ISSN 0962-1083 R&D Projects: GA AV ČR IBS5045111 Institutional research plan: CEZ:AV0Z5045916 Keywords : Black Sea flood * coalescent simulation * gene genealogy Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.375, year: 2004

The middle-class nature of identity and its implications for education: a genealogical analysis and reevaluation of a culturally and historically bounded concept.

Science.gov (United States)

Matusov, Eugene; Smith, Mark Philip

2012-09-01

We consider identity as a historically emerging discourse that requires genealogical analysis - not to discover the roots of our identity but to commit [ourselves] to its dissipation (Foucault 1977, p. 162). We suggest analyzing identity through the history of socio-economic classes, their life struggles, ambitions, development, and reproduction. We see learning not as a project of transformation of identity, but rather as developing access to socially valuable practices and developing one's own voice within these practices (through addressing and responding to other voices). The access and voice projects free agents from unnecessary finalization and objectivization by oneself and others (Bakhtin 1999; Bakhtin 1990). In education, we should develop indigenous discourses of learning and develop a conceptual framework that makes analysis of diverse discourses possible. We argue that learning, as transformation of participation in a sociocultural practice to gain more access, is a better conceptual framework than learning as transformation of identity.

Clonal genotype of Geomyces destructans among bats with White Nose Syndrome, New York, USA.

Science.gov (United States)

Rajkumar, Sunanda S; Li, Xiaojiang; Rudd, Robert J; Okoniewski, Joseph C; Xu, Jianping; Chaturvedi, Sudha; Chaturvedi, Vishnu

2011-07-01

The dispersal mechanism of Geomyces destructans, which causes geomycosis (white nose syndrome) in hibernating bats, remains unknown. Multiple gene genealogic analyses were conducted on 16 fungal isolates from diverse sites in New York State during 2008-2010. The results are consistent with the clonal dispersal of a single G. destructans genotype.

Strong combined gene-environment effects in anti-cyclic citrullinated peptide-positive rheumatoid arthritis

DEFF Research Database (Denmark)

Pedersen, Line Merete Blak; Jacobsen, Søren; Garred, Peter

2007-01-01

To study the role of shared epitope (SE) susceptibility genes, alone and in combination with tobacco smoking and other environmental risk factors, for risk of subtypes of rheumatoid arthritis (RA) defined by the presence or absence of serum antibodies against cyclic citrullinated peptides (CCPs)....

Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties.

Science.gov (United States)

Upadhyay, Atul K; Chacko, Anita R; Gandhimathi, A; Ghosh, Pritha; Harini, K; Joseph, Agnel P; Joshi, Adwait G; Karpe, Snehal D; Kaushik, Swati; Kuravadi, Nagesh; Lingu, Chandana S; Mahita, J; Malarini, Ramya; Malhotra, Sony; Malini, Manoharan; Mathew, Oommen K; Mutt, Eshita; Naika, Mahantesha; Nitish, Sathyanarayanan; Pasha, Shaik Naseer; Raghavender, Upadhyayula S; Rajamani, Anantharamanan; Shilpa, S; Shingate, Prashant N; Singh, Heikham Russiachand; Sukhwal, Anshul; Sunitha, Margaret S; Sumathi, Manojkumar; Ramaswamy, S; Gowda, Malali; Sowdhamini, Ramanathan

2015-08-28

Krishna Tulsi, a member of Lamiaceae family, is a herb well known for its spiritual, religious and medicinal importance in India. The common name of this plant is 'Tulsi' (or 'Tulasi' or 'Thulasi') and is considered sacred by Hindus. We present the draft genome of Ocimum tenuiflurum L (subtype Krishna Tulsi) in this report. The paired-end and mate-pair sequence libraries were generated for the whole genome sequenced with the Illumina Hiseq 1000, resulting in an assembled genome of 374 Mb, with a genome coverage of 61 % (612 Mb estimated genome size). We have also studied transcriptomes (RNA-Seq) of two subtypes of O. tenuiflorum, Krishna and Rama Tulsi and report the relative expression of genes in both the varieties. The pathways leading to the production of medicinally-important specialized metabolites have been studied in detail, in relation to similar pathways in Arabidopsis thaliana and other plants. Expression levels of anthocyanin biosynthesis-related genes in leaf samples of Krishna Tulsi were observed to be relatively high, explaining the purple colouration of Krishna Tulsi leaves. The expression of six important genes identified from genome data were validated by performing q-RT-PCR in different tissues of five different species, which shows the high extent of urosolic acid-producing genes in young leaves of the Rama subtype. In addition, the presence of eugenol and ursolic acid, implied as potential drugs in the cure of many diseases including cancer was confirmed using mass spectrometry. The availability of the whole genome of O.tenuiflorum and our sequence analysis suggests that small amino acid changes at the functional sites of genes involved in metabolite synthesis pathways confer special medicinal properties to this herb.

Problematizando a reforma psiquiátrica brasileira: a genealogia da reabilitação psicossocial Problematizaciones de la reforma psiquiátrica brasileña: la genealogía de la rehabilitación psicosocial Problematizating the brazilian psychiatric reform: the genealogy of psychosocial rehabilitation

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Alessandra Teixeira Marques Pinto

2010-03-01

Full Text Available Este artigo tem por objetivo problematizar um dispositivo importante no processo de reforma psiquiátrica brasileira que é a reabilitação psicossocial. Os autores observam que novas modalidades de tratamento em saúde mental não determinam que os doentes mentais possam efetivamente assumir a condição de cidadão, pois princípios manicomiais podem estar presentes, embasando serviços e práticas. O que se observou é que a reabilitação psicossocial tem uma grande importância na vida dos ditos doentes mentais, mas apresenta o risco de promover a manutenção da condição de psiquiatrizado. Para se pensar sobre essa questão, recorre-se à genealogia de Michel Foucault que consiste na problematização das práticas de poder subjacentes aos discursos psiquiátricos contemporâneos no Brasil.Este artículo tiene por finalidad problematizar un dispositivo importante en el proceso de reforma psiquiátrica brasileña que es la rehabilitación psicosocial. Los autores observan que nuevas modalidades de tratamiento en salud mental no determinan que los enfermos mentales puedan efectivamente asumir la condición de ciudadano, pues principios de las prácticas manicomiales pueden estar presentes, dando soporte a los servicios y prácticas actuales. Lo observado es que la rehabilitación psicosocial tiene una enorme importancia en la vida de dichos enfermos mentales, pero presenta el riesgo de promover la manutención de la condición de psiquiatrizados. Para pensar sobre esta cuestión, se recurre a la genealogía de Michel Foucault a fin de poner en cuestión las prácticas de poder subyacentes en los discursos psiquiátricos contemporáneos en Brasil.The aim of this article is to question a very important device of the actual Brazilian psychiatric reform process: psycho-social rehabilitation. The authors formulated a hypothesis that the creation of new forms of treatment in mental health does not determine that the mentally-diseased can

147 between the holocaust museum in washington dc and ghana's

African Journals Online (AJOL)

HP-G61

opens up a whole debate surrounding race, “horrors of the middle passage, the brutality of ... interesting that African Americans make strong genealogical bonds with the site as a ... mentioned parties were involved in the conflicting perspectives that laid .... However, some white Americans have propagated a message not in.

Clonal Genotype of Geomyces destructans among Bats with White Nose Syndrome, New York, USA

OpenAIRE

Rajkumar, Sunanda S.; Li, Xiaojiang; Rudd, Robert J.; Okoniewski, Joseph C.; Xu, Jianping; Chaturvedi, Sudha; Chaturvedi, Vishnu

2011-01-01

The dispersal mechanism of Geomyces destructans, which causes geomycosis (white nose syndrome) in hibernating bats, remains unknown. Multiple gene genealogic analyses were conducted on 16 fungal isolates from diverse sites in New York State during 2008–2010. The results are consistent with the clonal dispersal of a single G. destructans genotype.

Codon adaptation and synonymous substitution rate in diatom plastid genes.

Science.gov (United States)

Morton, Brian R; Sorhannus, Ulf; Fox, Martin

2002-07-01

Diatom plastid genes are examined with respect to codon adaptation and rates of silent substitution (Ks). It is shown that diatom genes follow the same pattern of codon usage as other plastid genes studied previously. Highly expressed diatom genes display codon adaptation, or a bias toward specific major codons, and these major codons are the same as those in red algae, green algae, and land plants. It is also found that there is a strong correlation between Ks and variation in codon adaptation across diatom genes, providing the first evidence for such a relationship in the algae. It is argued that this finding supports the notion that the correlation arises from selective constraints, not from variation in mutation rate among genes. Finally, the diatom genes are examined with respect to variation in Ks among different synonymous groups. Diatom genes with strong codon adaptation do not show the same variation in synonymous substitution rate among codon groups as the flowering plant psbA gene which, previous studies have shown, has strong codon adaptation but unusually high rates of silent change in certain synonymous groups. The lack of a similar finding in diatoms supports the suggestion that the feature is unique to the flowering plant psbA due to recent relaxations in selective pressure in that lineage.

Functional characterisation of an Arabidopsis gene strongly induced by ionising radiation: the gene coding the poly(ADP-ribose)polymerase-1 (AthPARP-1)

International Nuclear Information System (INIS)

Doucet-Chabeaud, G.

2000-01-01

Arabidopsis thaliana, the model-system in plant genetics, has been used to study the responses to DNA damage, experimentally introduced by γ-irradiation. We have characterised a radiation-induced gene coding a 111 kDa protein, AthPARP-1, homologous to the human poly(ADP-ribose)polymerase-1 (hPARP-1). As hPARP-1 is composed by three functional domain with characteristic motifs, AthPARP-1 binds to DNA bearing single-strand breaks and shows DNA damage-dependent poly(ADP-ribosyl)ation. The preferential expression of AthPARP-1 in mitotically active tissues is in agreement with a potential role in the maintenance of genome integrity during DNA replication, as proposed for its human counterpart. Transcriptional gene activation by ionising radiation of AthPARP-1 and AthPARP-2 genes is to date plant specific activation. Our expression analyses after exposure to various stress indicate that 1) AthPARP-1 and AthPARP-2 play an important role in the response to DNA lesions, particularly they are activated by genotoxic agents implicating the BER DNA repair pathway 2) AthPARP-2 gene seems to play an additional role in the signal transduction induced by oxidative stress 3) the observed expression profile of AthPARP-1 is in favour of the regulation of AthPARP-1 gene expression at the level of transcription and translation. This mode of regulation of AthPARP-1 protein biosynthesis, clearly distinct from that observed in animals, needs the implication of a so far unidentified transcription factor that is activated by the presence of DNA lesions. The major outcome of this work resides in the isolation and characterisation of such new transcription factor, which will provide new insight on the regulation of plant gene expression by genotoxic stress. (author) [fr

Expression of AQP3 gene in chronic atrophic and chronic superficial gastritis patients

Directory of Open Access Journals (Sweden)

Shijun Zhang

2007-12-01

Full Text Available <strong>BACKGROUND>: Most studies about aquaporin 3 (AQP3 in the gastrointestinal tract were carried out on both in vivo and in vitro. The role of AQP3-mediated water transport in human gastrointestinal tract is still unclear. Our aim in this study was to explore the expression of AQP3 gene in chronic atrophic gastritis (CAG and chronic superficial gastritis (CSG atients and to determine its possible function in the development of gastritis.
<strong>METHODS>: Twenty-two outpatients diagnosed as CSG and 12 outpatients diagnosed as CAG were selected randomly. Ten cases of healthy individuals were selected as normal control group. In all cases, AQP3 gene expression of gastric mucosa was detected by fluorescence quantitative polymerase chain reaction (FQ-PCR.
<strong>RESULTS>: The AQP3 gene expression was significantly higher in gastric mucosa of CSG and healthy individuals than that in CAG (P<0.01. However, there was no significant difference in the AQP3 gene expression between helicobacter pylori positive patients and helicobacter pylori negative patients (P>0.05.
<strong>CONCLUSIONS>: AQP3 expression might play certain role in the occurrence and development of gastritis.
<strong>KEY WORDSstrong>: Aquaporin 3, chronic superficial gastritis, chronic atrophic gastritis.

The phylogenetic position of Lygodactylus angularis and the utility of using the 16S rDNA gene for delimiting species in Lygodactylus (Squamata, Gekkonidae

Directory of Open Access Journals (Sweden)

Riccardo Castiglia

2011-06-01

Full Text Available The African genus Lygodactylus Gray, is composed of roughly 60 species of diurnal geckos that inhabit tropical and temperate Africa, Madagascar, and South America. In this study, we assessed the phylogenetic position of L. angularis, for which molecular data were so far lacking, by means of sequence analysis of the mitochondrial 16S rDNA gene. We also compared intraspecific vs. interspecific genetic divergences using an extended data set (34 species, 153 sequences, to determine whether a fragment of this gene can be useful for species identification and to reveal the possible existence of new cryptic species in the genus. The analysis placed L. angularis in a monophyletic group together with members of “fischeri” and “picturatus” groups. Nevertheless, the independence of the “angularis” lineage is supported by the high genetic divergence. Comparison of intraspecific vs. interspecific genetic distances highlights that, assuming an equal molecular rate of evolution among the studied species for the used gene, the threshold value useful for recognising a candidate new species can be tentatively placed at 7%. We identified four species that showed an intraspecific divergence higher than, or close to, the 7% threshold: L. capensis (8.7%, L. gutturalis (9.3%, L. madagascariensis (6.5% and L. picturatus (8.1%. Moreover, two species, L. mombasicus and L. verticillatus, are paraphyletic in terms of gene genealogy. Thus, the study shows that a short fragment of the 16S rDNA gene can be an informative tool for species-level taxonomy in the genus Lygodactylus.

Reconstructing Harry: a genealogical study of a colonial family 'inside' and 'outside' the Grahamstown Asylum, 1888-1918.

Science.gov (United States)

Wilbraham, Lindy

2014-04-01

Recent scholarship has explored the dynamics between families and colonial lunatic asylums in the late nineteenth century, where families actively participated in the processes of custodial care, committal, treatment and release of their relatives. This paper works in this historical field, but with some methodological and theoretical differences. The Foucauldian study is anchored to a single case and family as an illness narrative that moves cross-referentially between bureaucratic state archival material, psychiatric case records, and intergenerational family-storytelling and family photographs. Following headaches and seizures, Harry Walter Wilbraham was medically boarded from his position as Postmaster in the Cape of Good Hope Colony of South Africa with a 'permanent disease of the brain', and was committed to the Grahamstown Asylum in 1910, where he died the following year, aged 40 years. In contrast to writings about colonial asylums that usually describe several patient cases and thematic patterns in archival material over time and place, this study's genealogical lens examines one white settler male patient's experiences within mental health care in South Africa between 1908 and 1911. The construction of Harry's 'case' interweaves archival sources and reminiscences inside and outside the asylum, and places it within psychiatric discourse of the time, and family dynamics in the years that followed. Thus, this case study maps the constitution of 'patient' and 'family' in colonial life, c.1888-1918, and considers the calamity, uncertainty, stigma and silences of mental illness.

Species delimitation and phylogeography of Aphonopelma hentzi (Araneae, Mygalomorphae, Theraphosidae: cryptic diversity in North American tarantulas.

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Chris A Hamilton

Full Text Available The primary objective of this study is to reconstruct the phylogeny of the hentzi species group and sister species in the North American tarantula genus, Aphonopelma, using a set of mitochondrial DNA markers that include the animal "barcoding gene". An mtDNA genealogy is used to consider questions regarding species boundary delimitation and to evaluate timing of divergence to infer historical biogeographic events that played a role in shaping the present-day diversity and distribution. We aimed to identify potential refugial locations, directionality of range expansion, and test whether A. hentzi post-glacial expansion fit a predicted time frame.A Bayesian phylogenetic approach was used to analyze a 2051 base pair (bp mtDNA data matrix comprising aligned fragments of the gene regions CO1 (1165 bp and ND1-16S (886 bp. Multiple species delimitation techniques (DNA tree-based methods, a "barcode gap" using percent of pairwise sequence divergence (uncorrected p-distances, and the GMYC method consistently recognized a number of divergent and genealogically exclusive groups.The use of numerous species delimitation methods, in concert, provide an effective approach to dissecting species boundaries in this spider group; as well they seem to provide strong evidence for a number of nominal, previously undiscovered, and cryptic species. Our data also indicate that Pleistocene habitat fragmentation and subsequent range expansion events may have shaped contemporary phylogeographic patterns of Aphonopelma diversity in the southwestern United States, particularly for the A. hentzi species group. These findings indicate that future species delimitation approaches need to be analyzed in context of a number of factors, such as the sampling distribution, loci used, biogeographic history, breadth of morphological variation, ecological factors, and behavioral data, to make truly integrative decisions about what constitutes an evolutionary lineage recognized as a

What's in a Name: Elective Genealogy in Schwarz-Bart's Early Novels

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Clarisse Zimra

1993-01-01

Full Text Available This essay considers the question of the textual inscription of history in Solitude, Plat de porc and Télumée , by focusing on a narrative feature present in all three: the naming scene, wherein characters claim elective descent from a real historical figure, the pregnant mulatto woman, Solitude, captured and executed after the battle of Matouba in 1802 on Guadeloupe. Every Schwarz-Bart novel to date contains at least one scene, often several, staging this retelling of specifically Guadeloupean origins: the resistance to the reinstatement of slavery, and the ensuing tragedy on Matouba. In Un Plat de porc aux bananes vertes (1967, the child Mariotte, refusing the white values of her household, claims Solitude as model and ancestor. Later in Plule et vent sur Télumée Miracle (1972, Télumée regains her rightful place, through the connecting links of the oral chain, within a whole genealogy that is both biological and elective. Schwarz-Bart's corpus should be read as a gradual expansion of storytelling as a naming moment that makes sense of history in the retelling of it. This dramatized primal scene serves as matrix for the fictional discourse: it is the moment of revelation that simultaneously structures the narrator's individual consciousness and the narrative unfolding of a once-repressed collective memory. In the text's matricial moment, the daughter refuses the name—and the law—of the patriarchal Father (upending Lacan's "nom/non du père," so to speak to reclaim the name, and, in Solitude's own pregnancy, the body of the Mother. It is a political act in that its coming into existence demands a radical shift in power relations as well as in consciousness. For a Schwarz-Bart heroine, this represents the first necessary step towards grounding herself in a tradition and an oral chain of her own choosing, with Negritude as its implied counter-text. What is remarkable is that Schwarz-Bart eventually rejects the binary, essentialist trap

Study of Deafness Associated with DFNB59 Gene (pejvakin Mutation in Fars Province

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S Raeisi

2012-05-01

Full Text Available

<strong>Background and Objectives:strong> Hearing loss is the most frequent sensory disorder affecting 1 in 500 neonates with more than 50% of inherited cases. This trait is a very heterogeneous disorder and happens due to genetic or environmental causes or both. More than 46 genes may be involved in non-syndromic hearing loss. Recently, DFNB59 gene has been shown to cause deafness in some Iranian populations. The aim of this study was to determine the role of DFNB59 gene mutations causing deafness in a group of 130 deaf pupils in Fars province. <strong>Methods:> This descriptive-laboratory based study investigated the frequency of DFNB59 gene mutations using PCR-SSCP/HA strategy. <strong>Results:> Two different DFNB59 polymorphism including 874G>A and 793C>G were found in 1 and 9 of 130 patients studied respectively. However, no DFNB59 mutation was identified. <strong>Conclusion:> The results of this study shows that the association of DFNB59 mutations with deafness in Fars province is very low.

The downside of strong emotional memories: how human memory-related genes influence the risk for posttraumatic stress disorder--a selective review.

Science.gov (United States)

Wilker, Sarah; Elbert, Thomas; Kolassa, Iris-Tatjana

2014-07-01

A good memory for emotionally arousing experiences may be intrinsically adaptive, as it helps the organisms to predict safety and danger and to choose appropriate responses to prevent potential harm. However, under conditions of repeated exposure to traumatic stressors, strong emotional memories of these experiences can lead to the development of trauma-related disorders such as posttraumatic stress disorder (PTSD). This syndrome is characterized by distressing intrusive memories that can be so intense that the survivor is unable to discriminate past from present experiences. This selective review on the role of memory-related genes in PTSD etiology is divided in three sections. First, we summarize studies indicating that the likelihood to develop PTSD depends on the cumulative exposure to traumatic stressors and on individual predisposing risk factors, including a substantial genetic contribution to PTSD risk. Second, we focus on memory processes supposed to be involved in PTSD etiology and present evidence for PTSD-associated alterations in both implicit (fear conditioning, fear extinction) and explicit memory for emotional material. This is supplemented by a brief description of structural and functional alterations in memory-relevant brain regions in PTSD. Finally, we summarize a selection of studies indicating that genetic variations found to be associated with enhanced fear conditioning, reduced fear extinction or better episodic memory in human experimental studies can have clinical implications in the case of trauma exposure and influence the risk of PTSD development. Here, we focus on genes involved in noradrenergic (ADRA2B), serotonergic (SLC6A4), and dopaminergic signaling (COMT) as well as in the molecular cascades of memory formation (PRKCA and WWC1). This is supplemented by initial evidence that such memory-related genes might also influence the response rates of exposure-based psychotherapy or pharmacological treatment of PTSD, which underscores the

Cloning of a postreplication repair gene in Drosophila

International Nuclear Information System (INIS)

Banga, S.S.; Yamamoto, A.H.; Mason, J.M.; Boyd, J.B.

1987-01-01

Mutants at the mei-41 locus in Drosophila are strongly hypersensitive to each of eight tested mutagens. Mutant flies exhibit reduced meiotic recombination and elevated levels of chromosomal aberrations. In analogy with the defect in xeroderma pigmentosum variant cells, mei-41 cells are strongly defective in postreplication repair following UV radiation. In preparation for cloning that gene they have performed complementation studies between chromosomal aberrations and mei-41 mutants. That study has localized the mei-41 gene to polytene chromosome bands 14C4-6. A chromosomal walk conducted in that region has recovered about 65 kb of contiguous DNA sequence. The position of the mei-41 gene within that region has been established with the aid of a mutation in that gene which was generated by the insertion of a transposable element. Transcription mapping is being employed to define the complete coding region of the gene in preparation for investigations of gene function

The Disciplinary Society and the Birth of Sociology: A Foucauldian Perspective

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Dušan Ristić

2016-12-01

Full Text Available This paper is genealogical research that aims to present one of the historical ways that led to the emergence of sociology as a modern science. We discuss how and why this kind of genealogical research is important for explaining the emergence, transformation and regionalisation of power/knowledge. By following the arguments developed by Michel Foucault, we argue that the disciplinary practices emerging in European societies during the 18th and 19th centuries strongly influenced the upsurge of power/knowledge that would be transformed in sociology. We conclude that the appearance of the institutions – elements of what Foucault called the disciplinary society – led to the rise of new discourses of their legitimisation and to the birth of sociology.

77 FR 23735 - Agency Information Collection Activities: Forms G-1041 and G-1041A, Extension of a Currently...

Science.gov (United States)

2012-04-20

..., Genealogy Index Search Request and Genealogy Records Request. The Department of Homeland Security, U.S... existing information collection. (2) Title of the Form/Collection: Genealogy Index Search Request and Genealogy Records Request. (3) Agency form number, if any, and the applicable component of the Department of...

Tocar a través del cuadro: una genealogía del interfaz como metáfora de control en el espacio del arte, el cine y los videojuegos

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Alfonso Cuadrado Alvarado

2014-07-01

Full Text Available ResumenEl objetivo del artículo es examinar las relaciones que el interfaz mantiene con el concepto de pantalla y cuadro en el arte, la realidad virtual,  el cine y los videojuegos.Para ello se establece una genealogía de la mediación a través de la pantalla desde el nacimiento de la perspectiva en el Renacimiento, como punto de inicio de la representación visual dominante, hasta el presente.El análisis muestra los cambios en la relación entre los tres elementos de la representación: el espectador, la pantalla y la escena, que se han producido por el surgimiento de las vanguardias artísticas y el arte interactivo como reacción al modelo de representación realista. Este recorrido lleva a concluir que el interfaz además de su papel mediador, se ha convertido en el paradigma de la comunicación actual, integrándose en el proceso de relevo que la representación realista ha dado al mito digital.AbstractThe aim of the paper is to examine the relationships maintained with the interface screen concept and box art, virtual reality, film and video games.To do a genealogy of mediation is established through the screen from the birth of perspective in the Renaissance, as the starting point of the dominant visual representation to present.The analysis shows the changes in the relationship between the three elements of the representation: the viewer, the screen and the scene, which were caused by the emergence of the avant-garde and interactive art in reaction to model realistic representation. This route leads to the conclusion that the interface in addition to its mediating role, has become the paradigm of modern communication, integrated into the process of relief that realistic digital representation has given myth.

Paulus i Aristoteles' hønsegård

DEFF Research Database (Denmark)

Buch-Hansen, Gitte

2014-01-01

of Abraham’s seed was too strong an identity marker to be dispensed with. The article demonstrates how Paul – as the apostle to the Gentiles – navigates between Jewish genealogy and Hellenistic ideas about generation. The solution to Paul’s predicament is found in 1 Cor 15:45: as spiritualized body, Christ...

Network Diffusion-Based Prioritization of Autism Risk Genes Identifies Significantly Connected Gene Modules

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Ettore Mosca

2017-09-01

Full Text Available Autism spectrum disorder (ASD is marked by a strong genetic heterogeneity, which is underlined by the low overlap between ASD risk gene lists proposed in different studies. In this context, molecular networks can be used to analyze the results of several genome-wide studies in order to underline those network regions harboring genetic variations associated with ASD, the so-called “disease modules.” In this work, we used a recent network diffusion-based approach to jointly analyze multiple ASD risk gene lists. We defined genome-scale prioritizations of human genes in relation to ASD genes from multiple studies, found significantly connected gene modules associated with ASD and predicted genes functionally related to ASD risk genes. Most of them play a role in synapsis and neuronal development and function; many are related to syndromes that can be in comorbidity with ASD and the remaining are involved in epigenetics, cell cycle, cell adhesion and cancer.

Synthetic promoter libraries- tuning of gene expression

DEFF Research Database (Denmark)

Hammer, Karin; Mijakovic, Ivan; Jensen, Peter Ruhdal

2006-01-01

knockout and strong overexpression. However, applications such as metabolic optimization and control analysis necessitate a continuous set of expression levels with only slight increments in strength to cover a specific window around the wildtype expression level of the studied gene; this requirement can......The study of gene function often requires changing the expression of a gene and evaluating the consequences. In principle, the expression of any given gene can be modulated in a quasi-continuum of discrete expression levels but the traditional approaches are usually limited to two extremes: gene...

Octodon Degus: A Strong Attractor for Alzheimer Research

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Rafael Castro-Fuentes

2013-01-01

Full Text Available   The most popular animal models of Alzheimer’s disease (AD are transgenic mice expressing human genes with known mutations which do not represent the most abundant sporadic form of the disease. An increasing number of genetic, vascular and psychosocial data strongly support that the Octodon degus, a moderate-sized and diurnal precocial rodent, provides a naturalistic model for the study of the early neurodegenerative process associated with sporadic AD. In this minireview we describe and analyze the risk factors that contribute to Alzheimer-like characteristics in the degus, following recent publications, and establish some guidelines for future studies in this model of natural aging associated with the disease. Given the heterogeneity of current data derived from the diverse transgenic animal models of AD, now may be the time for the degus to become a strong attractor for academic research labs and companies involved with AD. This may help to understand the mechanisms responsible for the early neurodegenerative process associated with this devastating disease.

Octodon Degus: A Strong Attractor for Alzheimer Research

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Rafael Castro-Fuentes

2013-02-01

Full Text Available The most popular animal models of Alzheimer’s disease (AD are transgenic mice expressing human genes with known mutations which do not represent the most abundant sporadic form of the disease. An increasing number of genetic, vascular and psychosocial data strongly support that the Octodon degus, a moderate-sized and diurnal precocial rodent, provides a naturalistic model for the study of the early neurodegenerative process associated with sporadic AD. In this minireview we describe and analyze the risk factors that contribute to Alzheimer-like characteristics in the degus, following recent publications, and establish some guidelines for future studies in this model of natural aging associated with the disease. Given the heterogeneity of current data derived from the diverse transgenic animal models of AD, now may be the time for the degus to become a strong attractor for academic research labs and companies involved with AD. This may help to understand the mechanisms responsible for the early neurodegenerative process associated with this devastating disease.

Strong FANCA/FANCG but weak FANCA/FANCC interaction in the yeast 2-hybrid system.

Science.gov (United States)

Reuter, T; Herterich, S; Bernhard, O; Hoehn, H; Gross, H J

2000-01-15

Three of at least 8 Fanconi anemia (FA) genes have been cloned (FANCA, FANCC, FANCG), but their functions remain unknown. Using the yeast 2-hybrid system and full-length cDNA, the authors found a strong interaction between FANCA and FANCG proteins. They also obtained evidence for a weak interaction between FANCA and FANCC. Neither FANCA nor FANCC was found to interact with itself. These results support the notion of a functional association between the FA gene products. (Blood. 2000;95:719-720)

Biochemical mechanisms determine the functional compatibility of heterologous genes

DEFF Research Database (Denmark)

Porse, Andreas; Schou, Thea S.; Munck, Christian

2018-01-01

-gene libraries have suggested that sequence composition is a strong barrier for the successful integration of heterologous genes. Here we sample 200 diverse genes, representing >80% of sequenced antibiotic resistance genes, to interrogate the factors governing genetic compatibility in new hosts. In contrast...... factors governing the functionality and fitness of antibiotic resistance genes. These findings emphasize the importance of biochemical mechanism for heterologous gene compatibility, and suggest physiological constraints as a pivotal feature orienting the evolution of antibiotic resistance....

Evolutionary dynamics of the Pgk1 gene in the polyploid genus Kengyilia (Triticeae: Poaceae and its diploid relatives.

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Xing Fan

Full Text Available The level and pattern of nucleotide variation in duplicate gene provide important information on the evolutionary history of polyploids and divergent process between homoeologous loci within lineages. Kengyilia is a group of allohexaploid species with the StYP genomic constitutions in the wheat tribe. To investigate the evolutionary dynamics of the Pgk1 gene in Kengyilia and its diploid relatives, three copies of Pgk1 homoeologues were isolated from all sampled hexaploid Kengyilia species and analyzed with the Pgk1 sequences from 47 diploid taxa representing 18 basic genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that (1 Kengyilia species from the Central Asia and the Qinghai-Tibetan plateau have independent origins with geographically differentiated P genome donors and diverged levels of nucleotide diversity at Pgk1 locus; (2 a relatively long-time sweep event has allowed the Pgk1 gene within Agropyron to adapt to cold climate triggered by the recent uplifts of the Qinghai-Tibetan Plateau; (3 sweep event and population expansion might result in the difference in the d(N/d(S value of the Pgk1 gene in allopatric Agropyron populations, and this difference may be genetically transmitted to Kengyilia lineages via independent polyploidization events; (4 an 83 bp MITE element insertion has shaped the Pgk1 loci in the P genome lineage with different geographical regions; (5 the St and P genomes in Kengyilia were donated by Pseudoroegneria and Agropyron, respectively, and the Y genome is closely related to the Xp genome of Peridictyon sanctum. The interplay of evolutionary forces involving diverged natural selection, population expansion, and transposable events in geographically differentiated P genome donors could attribute to geographical differentiation of Kengyilia species via independent origins.

The transmission of cytoplasmic genes in Aspergillus nidulans

NARCIS (Netherlands)

Coenen, A.

1997-01-01

<strong>Introduction>

This manuscript concerns the spread of selfish cytoplasmic genes in the fungus Aspergillus nidulans. A.nidulans is a common soil fungus that grows vegetatively by forming a network (mycelium) of hyphae and reproduces

The evaluation of angiotensin-converting enzyme (ACE) gene I/D and IL-4 gene intron 3 VNTR polymorphisms in coronary artery disease.

Science.gov (United States)

Basol, Nursah; Celik, Atac; Karakus, Nevin; Ozturk, Sibel Demir; Ozsoy, Sibel Demir; Yigit, Serbulent

2014-01-01

Genetic polymorphism is a strong risk factor for coronary artery disease (CAD). In the present study, our aim was to evaluate angiotensin-converting enzyme (ACE) gene I/D polymorphism and interleukin-4 (IL-4) gene Intron 3 variable number of tandem repeat (VNTR) polymorphism in CAD. One hundred and twenty-four CAD patients and one hundred and twenty-three controls were enrolled. Genomic DNA was isolated and genotyped using polymerase chain reaction (PCR) analyses. The risk associated with inheriting the combined genotypes for the two polymorphisms were evaluated and it was found that the individuals who were P2P2-homozygous at IL-4 gene intron 3 VNTR and DD-homozygous at ACE gene I/D have a higher risk of developing CAD. Although, there is no correlation between IL4 VNTR polymorphism and ACE gene polymorphism and CAD, there is a strong association between CAD and co-existence of IL-4 VNTR and ACE gene polymorphisms in the Turkish population. Copyright © 2014 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Reranking candidate gene models with cross-species comparison for improved gene prediction

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Pereira Fernando CN

2008-10-01

Full Text Available Abstract Background Most gene finders score candidate gene models with state-based methods, typically HMMs, by combining local properties (coding potential, splice donor and acceptor patterns, etc. Competing models with similar state-based scores may be distinguishable with additional information. In particular, functional and comparative genomics datasets may help to select among competing models of comparable probability by exploiting features likely to be associated with the correct gene models, such as conserved exon/intron structure or protein sequence features. Results We have investigated the utility of a simple post-processing step for selecting among a set of alternative gene models, using global scoring rules to rerank competing models for more accurate prediction. For each gene locus, we first generate the K best candidate gene models using the gene finder Evigan, and then rerank these models using comparisons with putative orthologous genes from closely-related species. Candidate gene models with lower scores in the original gene finder may be selected if they exhibit strong similarity to probable orthologs in coding sequence, splice site location, or signal peptide occurrence. Experiments on Drosophila melanogaster demonstrate that reranking based on cross-species comparison outperforms the best gene models identified by Evigan alone, and also outperforms the comparative gene finders GeneWise and Augustus+. Conclusion Reranking gene models with cross-species comparison improves gene prediction accuracy. This straightforward method can be readily adapted to incorporate additional lines of evidence, as it requires only a ranked source of candidate gene models.

Comparative genomic analysis of 45 type strains of the genus Bifidobacterium: a snapshot of its genetic diversity and evolution.

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Zhihong Sun

Full Text Available Bifidobacteria are well known for their human health-promoting effects and are therefore widely applied in the food industry. Members of the Bifidobacterium genus were first identified from the human gastrointestinal tract and were then found to be widely distributed across various ecological niches. Although the genetic diversity of Bifidobacterium has been determined based on several marker genes or a few genomes, the global diversity and evolution scenario for the entire genus remain unresolved. The present study comparatively analyzed the genomes of 45 type strains. We built a robust genealogy for Bifidobacterium based on 402 core genes and defined its root according to the phylogeny of the tree of bacteria. Our results support that all human isolates are of younger lineages, and although species isolated from bees dominate the more ancient lineages, the bee was not necessarily the original host for bifidobacteria. Moreover, the species isolated from different hosts are enriched with specific gene sets, suggesting host-specific adaptation. Notably, bee-specific genes are strongly associated with respiratory metabolism and are potential in helping those bacteria adapt to the oxygen-rich gut environment in bees. This study provides a snapshot of the genetic diversity and evolution of Bifidobacterium, paving the way for future studies on the taxonomy and functional genomics of the genus.

<strong>Mini-project>

DEFF Research Database (Denmark)

Katajainen, Jyrki

2008-01-01

In this project the goal is to develop the safe * family of containers for the CPH STL. The containers to be developed should be safer and more reliable than any of the existing implementations. A special focus should be put on strong exception safety since none of the existing prototypes available...

Phylogenomics provides strong evidence for relationships of butterflies and moths.

Science.gov (United States)

Kawahara, Akito Y; Breinholt, Jesse W

2014-08-07

Butterflies and moths constitute some of the most popular and charismatic insects. Lepidoptera include approximately 160 000 described species, many of which are important model organisms. Previous studies on the evolution of Lepidoptera did not confidently place butterflies, and many relationships among superfamilies in the megadiverse clade Ditrysia remain largely uncertain. We generated a molecular dataset with 46 taxa, combining 33 new transcriptomes with 13 available genomes, transcriptomes and expressed sequence tags (ESTs). Using HaMStR with a Lepidoptera-specific core-orthologue set of single copy loci, we identified 2696 genes for inclusion into the phylogenomic analysis. Nucleotides and amino acids of the all-gene, all-taxon dataset yielded nearly identical, well-supported trees. Monophyly of butterflies (Papilionoidea) was strongly supported, and the group included skippers (Hesperiidae) and the enigmatic butterfly-moths (Hedylidae). Butterflies were placed sister to the remaining obtectomeran Lepidoptera, and the latter was grouped with greater than or equal to 87% bootstrap support. Establishing confident relationships among the four most diverse macroheteroceran superfamilies was previously challenging, but we recovered 100% bootstrap support for the following relationships: ((Geometroidea, Noctuoidea), (Bombycoidea, Lasiocampoidea)). We present the first robust, transcriptome-based tree of Lepidoptera that strongly contradicts historical placement of butterflies, and provide an evolutionary framework for genomic, developmental and ecological studies on this diverse insect order. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Gene by Environment Interaction and Resilience: Effects of Child Maltreatment and Serotonin, Corticotropin Releasing Hormone, Dopamine, and Oxytocin Genes

Science.gov (United States)

Cicchetti, Dante; Rogosch, Fred A.

2013-01-01

In this investigation, gene-environment interaction effects in predicting resilience in adaptive functioning among maltreated and nonmaltreated low-income children (N = 595) were examined. A multi-component index of resilient functioning was derived and levels of resilient functioning were identified. Variants in four genes, 5-HTTLPR, CRHR1, DRD4 -521C/T, and OXTR, were investigated. In a series of ANCOVAs, child maltreatment demonstrated a strong negative main effect on children’s resilient functioning, whereas no main effects for any of the genotypes of the respective genes were found. However, gene-environment interactions involving genotypes of each of the respective genes and maltreatment status were obtained. For each respective gene, among children with a specific genotype, the relative advantage in resilient functioning of nonmaltreated compared to maltreated children was stronger than was the case for nonmaltreated and maltreated children with other genotypes of the respective gene. Across the four genes, a composite of the genotypes that more strongly differentiated resilient functioning between nonmaltreated and maltreated children provided further evidence of genetic variations influencing resilient functioning in nonmaltreated children, whereas genetic variation had a negligible effect on promoting resilience among maltreated children. Additional effects were observed for children based on the number of subtypes of maltreatment children experienced, as well as for abuse and neglect subgroups. Finally, maltreated and nonmaltreated children with high levels of resilience differed in their average number of differentiating genotypes. These results suggest that differential resilient outcomes are based on the interaction between genes and developmental experiences. PMID:22559122

Gene copy number variation throughout the Plasmodium falciparum genome

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Stewart Lindsay B

2009-08-01

Full Text Available Abstract Background Gene copy number variation (CNV is responsible for several important phenotypes of the malaria parasite Plasmodium falciparum, including drug resistance, loss of infected erythrocyte cytoadherence and alteration of receptor usage for erythrocyte invasion. Despite the known effects of CNV, little is known about its extent throughout the genome. Results We performed a whole-genome survey of CNV genes in P. falciparum using comparative genome hybridisation of a diverse set of 16 laboratory culture-adapted isolates to a custom designed high density Affymetrix GeneChip array. Overall, 186 genes showed hybridisation signals consistent with deletion or amplification in one or more isolate. There is a strong association of CNV with gene length, genomic location, and low orthology to genes in other Plasmodium species. Sub-telomeric regions of all chromosomes are strongly associated with CNV genes independent from members of previously described multigene families. However, ~40% of CNV genes were located in more central regions of the chromosomes. Among the previously undescribed CNV genes, several that are of potential phenotypic relevance are identified. Conclusion CNV represents a major form of genetic variation within the P. falciparum genome; the distribution of gene features indicates the involvement of highly non-random mutational and selective processes. Additional studies should be directed at examining CNV in natural parasite populations to extend conclusions to clinical settings.

Strong seasonality and interannual recurrence in marine myovirus communities.

Science.gov (United States)

Pagarete, A; Chow, C-E T; Johannessen, T; Fuhrman, J A; Thingstad, T F; Sandaa, R A

2013-10-01

The temporal community dynamics and persistence of different viral types in the marine environment are still mostly obscure. Polymorphism of the major capsid protein gene, g23, was used to investigate the community composition dynamics of T4-like myoviruses in a North Atlantic fjord for a period of 2 years. A total of 160 unique operational taxonomic units (OTUs) were identified by terminal restriction fragment length polymorphism (TRFLP) of the gene g23. Three major community profiles were identified (winter-spring, summer, and autumn), which resulted in a clear seasonal succession pattern. These seasonal transitions were recurrent over the 2 years and significantly correlated with progression of seawater temperature, Synechococcus abundance, and turbidity. The appearance of the autumn viral communities was concomitant with the occurrence of prominent Synechococcus blooms. As a whole, we found a highly dynamic T4-like viral community with strong seasonality and recurrence patterns. These communities were unexpectedly dominated by a group of persistently abundant viruses.

An exceptional horizontal gene transfer in plastids: gene replacement by a distant bacterial paralog and evidence that haptophyte and cryptophyte plastids are sisters

Directory of Open Access Journals (Sweden)

Palmer Jeffrey D

2006-09-01

Full Text Available Abstract Background Horizontal gene transfer (HGT to the plant mitochondrial genome has recently been shown to occur at a surprisingly high rate; however, little evidence has been found for HGT to the plastid genome, despite extensive sequencing. In this study, we analyzed all genes from sequenced plastid genomes to unearth any neglected cases of HGT and to obtain a measure of the overall extent of HGT to the plastid. Results Although several genes gave strongly supported conflicting trees under certain conditions, we are confident of HGT in only a single case beyond the rubisco HGT already reported. Most of the conflicts involved near neighbors connected by long branches (e.g. red algae and their secondary hosts, where phylogenetic methods are prone to mislead. However, three genes – clpP, ycf2, and rpl36 – provided strong support for taxa moving far from their organismal position. Further taxon sampling of clpP and ycf2 resulted in rejection of HGT due to long-branch attraction and a serious error in the published plastid genome sequence of Oenothera elata, respectively. A single new case, a bacterial rpl36 gene transferred into the ancestor of the cryptophyte and haptophyte plastids, appears to be a true HGT event. Interestingly, this rpl36 gene is a distantly related paralog of the rpl36 type found in other plastids and most eubacteria. Moreover, the transferred gene has physically replaced the native rpl36 gene, yet flanking genes and intergenic regions show no sign of HGT. This suggests that gene replacement somehow occurred by recombination at the very ends of rpl36, without the level and length of similarity normally expected to support recombination. Conclusion The rpl36 HGT discovered in this study is of considerable interest in terms of both molecular mechanism and phylogeny. The plastid acquisition of a bacterial rpl36 gene via HGT provides the first strong evidence for a sister-group relationship between haptophyte and

An exceptional horizontal gene transfer in plastids: gene replacement by a distant bacterial paralog and evidence that haptophyte and cryptophyte plastids are sisters

Science.gov (United States)

Rice, Danny W; Palmer, Jeffrey D

2006-01-01

Background Horizontal gene transfer (HGT) to the plant mitochondrial genome has recently been shown to occur at a surprisingly high rate; however, little evidence has been found for HGT to the plastid genome, despite extensive sequencing. In this study, we analyzed all genes from sequenced plastid genomes to unearth any neglected cases of HGT and to obtain a measure of the overall extent of HGT to the plastid. Results Although several genes gave strongly supported conflicting trees under certain conditions, we are confident of HGT in only a single case beyond the rubisco HGT already reported. Most of the conflicts involved near neighbors connected by long branches (e.g. red algae and their secondary hosts), where phylogenetic methods are prone to mislead. However, three genes – clpP, ycf2, and rpl36 – provided strong support for taxa moving far from their organismal position. Further taxon sampling of clpP and ycf2 resulted in rejection of HGT due to long-branch attraction and a serious error in the published plastid genome sequence of Oenothera elata, respectively. A single new case, a bacterial rpl36 gene transferred into the ancestor of the cryptophyte and haptophyte plastids, appears to be a true HGT event. Interestingly, this rpl36 gene is a distantly related paralog of the rpl36 type found in other plastids and most eubacteria. Moreover, the transferred gene has physically replaced the native rpl36 gene, yet flanking genes and intergenic regions show no sign of HGT. This suggests that gene replacement somehow occurred by recombination at the very ends of rpl36, without the level and length of similarity normally expected to support recombination. Conclusion The rpl36 HGT discovered in this study is of considerable interest in terms of both molecular mechanism and phylogeny. The plastid acquisition of a bacterial rpl36 gene via HGT provides the first strong evidence for a sister-group relationship between haptophyte and cryptophyte plastids to the

Molecular genetic studies of natives on Easter Island: evidence of an early European and Amerindian contribution to the Polynesian gene pool.

Science.gov (United States)

Lie, B A; Dupuy, B M; Spurkland, A; Fernández-Viña, M A; Hagelberg, E; Thorsby, E

2007-01-01

Most archaeological and linguistic evidence suggest a Polynesian origin of the population of Easter Island (Rapanui), and this view has been supported by the identification of Polynesian mitochondrial DNA (mtDNA) polymorphisms in prehistoric skeletal remains. However, some evidence of an early South American contact also exists (the sweet potato, bottle gourd etc.), but genetic studies have so far failed to show an early Amerindian contribution to the gene pool on Easter Island. To address this issue, we analyzed mtDNA and Y chromosome markers and performed high-resolution human leukocyte antigen (HLA) genotyping of DNA harvested from previously collected sera of 48 reputedly nonadmixed native Easter Islanders. All individuals carried mtDNA types and HLA alleles previously found in Polynesia, and most men carried Y chromosome markers of Polynesian origin, providing further evidence of a Polynesian origin of the population of Easter Island. A few individuals carried HLA alleles and/or Y chromosome markers of European origin. More interestingly, some individuals carried the HLA alleles A*0212 and B*3905, which are of typical Amerindian origin. The genealogy of some of the individuals carrying these non-Polynesian HLA alleles and their haplotypic backgrounds suggest an introduction into Easter Island in the early 1800s, or earlier. Thus, there may have been an early European and Amerindian contribution to the Polynesian gene pool of Easter Island.

Gene expression in periodontal tissues following treatment

Directory of Open Access Journals (Sweden)

Eisenacher Martin

2008-07-01

Full Text Available Abstract Background In periodontitis, treatment aimed at controlling the periodontal biofilm infection results in a resolution of the clinical and histological signs of inflammation. Although the cell types found in periodontal tissues following treatment have been well described, information on gene expression is limited to few candidate genes. Therefore, the aim of the study was to determine the expression profiles of immune and inflammatory genes in periodontal tissues from sites with severe chronic periodontitis following periodontal therapy in order to identify genes involved in tissue homeostasis. Gingival biopsies from 12 patients with severe chronic periodontitis were taken six to eight weeks following non-surgical periodontal therapy, and from 11 healthy controls. As internal standard, RNA of an immortalized human keratinocyte line (HaCaT was used. Total RNA was subjected to gene expression profiling using a commercially available microarray system focusing on inflammation-related genes. Post-hoc confirmation of selected genes was done by Realtime-PCR. Results Out of the 136 genes analyzed, the 5% most strongly expressed genes compared to healthy controls were Interleukin-12A (IL-12A, Versican (CSPG-2, Matrixmetalloproteinase-1 (MMP-1, Down syndrome critical region protein-1 (DSCR-1, Macrophage inflammatory protein-2β (Cxcl-3, Inhibitor of apoptosis protein-1 (BIRC-1, Cluster of differentiation antigen 38 (CD38, Regulator of G-protein signalling-1 (RGS-1, and Finkel-Biskis-Jinkins murine osteosarcoma virus oncogene (C-FOS; the 5% least strongly expressed genes were Receptor-interacting Serine/Threonine Kinase-2 (RIP-2, Complement component 3 (C3, Prostaglandin-endoperoxide synthase-2 (COX-2, Interleukin-8 (IL-8, Endothelin-1 (EDN-1, Plasminogen activator inhibitor type-2 (PAI-2, Matrix-metalloproteinase-14 (MMP-14, and Interferon regulating factor-7 (IRF-7. Conclusion Gene expression profiles found in periodontal tissues following

The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes.

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Marion Ouedraogo

Full Text Available BACKGROUND: There has been a surge in studies linking genome structure and gene expression, with special focus on duplicated genes. Although initially duplicated from the same sequence, duplicated genes can diverge strongly over evolution and take on different functions or regulated expression. However, information on the function and expression of duplicated genes remains sparse. Identifying groups of duplicated genes in different genomes and characterizing their expression and function would therefore be of great interest to the research community. The 'Duplicated Genes Database' (DGD was developed for this purpose. METHODOLOGY: Nine species were included in the DGD. For each species, BLAST analyses were conducted on peptide sequences corresponding to the genes mapped on a same chromosome. Groups of duplicated genes were defined based on these pairwise BLAST comparisons and the genomic location of the genes. For each group, Pearson correlations between gene expression data and semantic similarities between functional GO annotations were also computed when the relevant information was available. CONCLUSIONS: The Duplicated Gene Database provides a list of co-localised and duplicated genes for several species with the available gene co-expression level and semantic similarity value of functional annotation. Adding these data to the groups of duplicated genes provides biological information that can prove useful to gene expression analyses. The Duplicated Gene Database can be freely accessed through the DGD website at http://dgd.genouest.org.

Determinants of human adipose tissue gene expression

DEFF Research Database (Denmark)

Viguerie, Nathalie; Montastier, Emilie; Maoret, Jean-José

2012-01-01

weight maintenance diets. For 175 genes, opposite regulation was observed during calorie restriction and weight maintenance phases, independently of variations in body weight. Metabolism and immunity genes showed inverse profiles. During the dietary intervention, network-based analyses revealed strong...... interconnection between expression of genes involved in de novo lipogenesis and components of the metabolic syndrome. Sex had a marked influence on AT expression of 88 transcripts, which persisted during the entire dietary intervention and after control for fat mass. In women, the influence of body mass index...... on expression of a subset of genes persisted during the dietary intervention. Twenty-two genes revealed a metabolic syndrome signature common to men and women. Genetic control of AT gene expression by cis signals was observed for 46 genes. Dietary intervention, sex, and cis genetic variants independently...

Root parasitic plant Orobanche aegyptiaca and shoot parasitic plant Cuscuta australis obtained Brassicaceae-specific strictosidine synthase-like genes by horizontal gene transfer.

Science.gov (United States)

Zhang, Dale; Qi, Jinfeng; Yue, Jipei; Huang, Jinling; Sun, Ting; Li, Suoping; Wen, Jian-Fan; Hettenhausen, Christian; Wu, Jinsong; Wang, Lei; Zhuang, Huifu; Wu, Jianqiang; Sun, Guiling

2014-01-13

Besides gene duplication and de novo gene generation, horizontal gene transfer (HGT) is another important way of acquiring new genes. HGT may endow the recipients with novel phenotypic traits that are important for species evolution and adaption to new ecological niches. Parasitic systems expectedly allow the occurrence of HGT at relatively high frequencies due to their long-term physical contact. In plants, a number of HGT events have been reported between the organelles of parasites and the hosts, but HGT between host and parasite nuclear genomes has rarely been found. A thorough transcriptome screening revealed that a strictosidine synthase-like (SSL) gene in the root parasitic plant Orobanche aegyptiaca and the shoot parasitic plant Cuscuta australis showed much higher sequence similarities with those in Brassicaceae than with those in their close relatives, suggesting independent gene horizontal transfer events from Brassicaceae to these parasites. These findings were strongly supported by phylogenetic analysis and their identical unique amino acid residues and deletions. Intriguingly, the nucleus-located SSL genes in Brassicaceae belonged to a new member of SSL gene family, which were originated from gene duplication. The presence of introns indicated that the transfer occurred directly by DNA integration in both parasites. Furthermore, positive selection was detected in the foreign SSL gene in O. aegyptiaca but not in C. australis. The expression of the foreign SSL genes in these two parasitic plants was detected in multiple development stages and tissues, and the foreign SSL gene was induced after wounding treatment in C. australis stems. These data imply that the foreign genes may still retain certain functions in the recipient species. Our study strongly supports that parasitic plants can gain novel nuclear genes from distantly related host species by HGT and the foreign genes may execute certain functions in the new hosts.

What Trajectory for Energy Transition? The Genealogy of the Energy Transition Law and its Positioning with regard to Pre-existing Scenarios

International Nuclear Information System (INIS)

Criqui, Patrick

2014-01-01

The many lively debates that preceded -and still fuel- discussion of the 'Energy Transition and Green Growth' bill attest to the importance of that law for many French citizens and economic actors. Without going back over the debate on the feasibility or realism of the law's objectives, to which Futuribles contributed through its web site in late September, it is possible to put these matters into some perspective, as Patrick Criqui does here, by reminding us of the genealogy of the bill and the various future scenarios that were developed during the French National Debate on Energy Transition of 2013 before the bill passed into law. Criqui reminds us of the possible scenarios discussed, grouped as they were around four major energy trajectories: 'Energy-saving', 'Efficiency', 'Diversity' and 'Decarbonization'. Among these, the most important sources of divergence were over the level of reduction of energy consumption by 2050 and the relative parts to be played by nuclear power and renewable energies. Basing himself on the target figures included in the bill, Patrick Criqui identifies the image of the future towards which, on the face of it, the law points -namely, the 'Efficiency' trajectory- even if, as he very rightly emphasizes, its implementation will definitely be a dynamic affair, incorporating the various adaptations that might turn out to be necessary between now and 2050. (author)

gPGA: GPU Accelerated Population Genetics Analyses.

Directory of Open Access Journals (Sweden)

Chunbao Zhou

Full Text Available The isolation with migration (IM model is important for studies in population genetics and phylogeography. IM program applies the IM model to genetic data drawn from a pair of closely related populations or species based on Markov chain Monte Carlo (MCMC simulations of gene genealogies. But computational burden of IM program has placed limits on its application.With strong computational power, Graphics Processing Unit (GPU has been widely used in many fields. In this article, we present an effective implementation of IM program on one GPU based on Compute Unified Device Architecture (CUDA, which we call gPGA.Compared with IM program, gPGA can achieve up to 52.30X speedup on one GPU. The evaluation results demonstrate that it allows datasets to be analyzed effectively and rapidly for research on divergence population genetics. The software is freely available with source code at https://github.com/chunbaozhou/gPGA.

Gene duplication, tissue-specific gene expression and sexual conflict in stalk-eyed flies (Diopsidae).

Science.gov (United States)

Baker, Richard H; Narechania, Apurva; Johns, Philip M; Wilkinson, Gerald S

2012-08-19

Gene duplication provides an essential source of novel genetic material to facilitate rapid morphological evolution. Traits involved in reproduction and sexual dimorphism represent some of the fastest evolving traits in nature, and gene duplication is intricately involved in the origin and evolution of these traits. Here, we review genomic research on stalk-eyed flies (Diopsidae) that has been used to examine the extent of gene duplication and its role in the genetic architecture of sexual dimorphism. Stalk-eyed flies are remarkable because of the elongation of the head into long stalks, with the eyes and antenna laterally displaced at the ends of these stalks. Many species are strongly sexually dimorphic for eyespan, and these flies have become a model system for studying sexual selection. Using both expressed sequence tag and next-generation sequencing, we have established an extensive database of gene expression in the developing eye-antennal imaginal disc, the adult head and testes. Duplicated genes exhibit narrower expression patterns than non-duplicated genes, and the testes, in particular, provide an abundant source of gene duplication. Within somatic tissue, duplicated genes are more likely to be differentially expressed between the sexes, suggesting gene duplication may provide a mechanism for resolving sexual conflict.

Biological chemistry as a foundation of DNA genealogy: the emergence of "molecular history".

Science.gov (United States)

Klyosov, A A

2011-05-01

This paper presents the basis of DNA genealogy, a new field of science, which is currently emerging as an unusual blend of biochemistry, history, linguistics, and chemical kinetics. The methodology of the new approach is comprised of chemical (biological) kinetics applied to a pattern of mutations in non-recombinant fragments of DNA (Y chromosome and mtDNA, the latter not being considered in this overview). The goal of the analysis is to translate DNA mutation patterns into time spans to the most recent common ancestors of a given population or tribe and to the dating of ancient migration routes. To illustrate this approach, time spans to the common ancestors are calculated for ethnic Russians, that is Eastern Slavs (R1a1 tribe), Western Slavs (I1 and I2 tribes), and Northern (or Uralic) Slavs (N1c tribe), which were found to live around 4600 years before present (R1a1), 3650 ybp (I1), 3000 and 10,500 ybp (I2, two principal DNA lineages), and 3525 ybp (N1c) (confidence intervals are given in the main text). The data were compared with the respective dates for the nearest common ancestor of the R1a1 "Indo-European" population in India, who lived 4050 years before present, whose descendants represent the majority of the upper castes in India today (up to 72%). Furthermore, it was found that the haplotypes of ethnic Russians of the R1a1 haplogroup (up to 62% of the population in the Russian Federation) and those of the R1a1 Indians (more than 100 million today) are practically identical to each other, up to 67-marker haplotypes. This essentially solves a 200-year-old mystery of who were the Aryans who arrived in India around 3500 years before the present. Haplotypes and time spans to the ancient common ancestors were also compared for the ethnic Russians of haplogroups I1 and I2, on one hand, and the respective I1 and I2 populations in Eastern and Western Europe and Scandinavia, on the other. It is suggested that the approach described in this overview lays the

Strong selective sweeps associated with ampliconic regions in great ape X chromosomes

DEFF Research Database (Denmark)

Nam, Kiwoong; Munch, Kasper; Hobolth, Asger

2014-01-01

The unique inheritance pattern of X chromosomes makes them preferential targets of adaptive evolution. We here investigate natural selection on the X chromosome in all species of great apes. We find that diversity is more strongly reduced around genes on the X compared with autosomes...... with ampliconic sequences we propose that intra-genomic conflict between the X and the Y chromosomes is a major driver of X chromosome evolution....

Detection of the Helicobacter pylori dupA gene is strongly affected by the PCR design

NARCIS (Netherlands)

Abadi, Amin Talebi Bezmin; Loffeld, Ruud J L F; Constancia, Ashandra C; Wagenaar, Jaap A; Kusters, Johannes G

2014-01-01

The Helicobacter pylori virulence gene dupA is usually detected by PCR, but the primer binding sites used are highly variable. Our newly designed qPCR against a conserved region of dupA was positive in 64.2% of 394 clinical isolates while the positivity rate of the commonly used PCRs ranged from

Susceptibility Genes in Thyroid Autoimmunity

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Yoshiyuki Ban

2005-01-01

Full Text Available The autoimmune thyroid diseases (AITD are complex diseases which are caused by an interaction between susceptibility genes and environmental triggers. Genetic susceptibility in combination with external factors (e.g. dietary iodine is believed to initiate the autoimmune response to thyroid antigens. Abundant epidemiological data, including family and twin studies, point to a strong genetic influence on the development of AITD. Various techniques have been employed to identify the genes contributing to the etiology of AITD, including candidate gene analysis and whole genome screening. These studies have enabled the identification of several loci (genetic regions that are linked with AITD, and in some of these loci, putative AITD susceptibility genes have been identified. Some of these genes/loci are unique to Graves' disease (GD and Hashimoto's thyroiditis (HT and some are common to both the diseases, indicating that there is a shared genetic susceptibility to GD and HT. The putative GD and HT susceptibility genes include both immune modifying genes (e.g. HLA, CTLA-4 and thyroid specific genes (e.g. TSHR, Tg. Most likely, these loci interact and their interactions may influence disease phenotype and severity.

Reconstructing Harry: A Genealogical Study of a Colonial Family ‘Inside’ and ‘Outside’ the Grahamstown Asylum, 1888–1918

Science.gov (United States)

Wilbraham, Lindy

2014-01-01

Recent scholarship has explored the dynamics between families and colonial lunatic asylums in the late nineteenth century, where families actively participated in the processes of custodial care, committal, treatment and release of their relatives. This paper works in this historical field, but with some methodological and theoretical differences. The Foucauldian study is anchored to a single case and family as an illness narrative that moves cross-referentially between bureaucratic state archival material, psychiatric case records, and intergenerational family-storytelling and family photographs. Following headaches and seizures, Harry Walter Wilbraham was medically boarded from his position as Postmaster in the Cape of Good Hope Colony of South Africa with a ‘permanent disease of the brain’, and was committed to the Grahamstown Asylum in 1910, where he died the following year, aged 40 years. In contrast to writings about colonial asylums that usually describe several patient cases and thematic patterns in archival material over time and place, this study’s genealogical lens examines one white settler male patient’s experiences within mental health care in South Africa between 1908 and 1911. The construction of Harry’s ‘case’ interweaves archival sources and reminiscences inside and outside the asylum, and places it within psychiatric discourse of the time, and family dynamics in the years that followed. Thus, this case study maps the constitution of ‘patient’ and ‘family’ in colonial life, c.1888–1918, and considers the calamity, uncertainty, stigma and silences of mental illness. PMID:24775428

Multiclass gene selection using Pareto-fronts.

Science.gov (United States)

Rajapakse, Jagath C; Mundra, Piyushkumar A

2013-01-01

Filter methods are often used for selection of genes in multiclass sample classification by using microarray data. Such techniques usually tend to bias toward a few classes that are easily distinguishable from other classes due to imbalances of strong features and sample sizes of different classes. It could therefore lead to selection of redundant genes while missing the relevant genes, leading to poor classification of tissue samples. In this manuscript, we propose to decompose multiclass ranking statistics into class-specific statistics and then use Pareto-front analysis for selection of genes. This alleviates the bias induced by class intrinsic characteristics of dominating classes. The use of Pareto-front analysis is demonstrated on two filter criteria commonly used for gene selection: F-score and KW-score. A significant improvement in classification performance and reduction in redundancy among top-ranked genes were achieved in experiments with both synthetic and real-benchmark data sets.

Genealogies and ages of cultural traits: An application of the theory of duality to the research on cultural evolution.

Science.gov (United States)

Kobayashi, Yutaka; Wakano, Joe Yuichiro; Ohtsuki, Hisashi

2018-05-09

A finite-population, discrete-generation model of cultural evolution is described, in which multiple discrete traits are transmitted independently. In this model, each newborn may inherit a trait from multiple cultural parents. Transmission fails with a positive probability unlike in population genetics. An ancestral process simulating the cultural genealogy of a sample of individuals is derived for this model. This ancestral process, denoted by M - , is shown to be dual to a process M + describing the change in the frequency of a trait. The age-frequency spectrum is defined as a two-dimensional array whose (i,k) element is the expected number of distinct cultural traits introduced k generations ago and now carried by i individuals in a sample of a particular size n. Numerical calculations reveal that the age-frequency spectrum and related metrics undergo a critical transition from a phase with a moderate number of young, rare traits to a phase with numerous very old, common traits when the expected number of cultural parents per individual exceeds one. It is shown that M + and M - converge to branching or deterministic processes, depending on the way population size tends to infinity, and these limiting processes bear some duality relationships. The critical behavior of the original processes M + and M - is explained in terms of a phase transition of the branching processes. Using the results of the limiting processes in combination, we derive analytical formulae that well approximate the age-frequency spectrum and also other metrics. Copyright © 2018 Elsevier Inc. All rights reserved.

Polymorphism of the VEGF gene and its association with growth ...

African Journals Online (AJOL)

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Keywords: VEGF gene, caprine, single nucleotide polymorphism (SNP), genetic variation, PCR-SSCP ... This field is strongly focusing on gene loci and polymorphisms that have ..... Enhance the efficiency of single-strand conformation polymorphism analysis by short polyacrylamide gel and modified silver staining. Anal.

El linaje de Cristo a la luz del “giro genealógico” del siglo XV. La respuesta de Juana de la Cruz (1481-1534

Directory of Open Access Journals (Sweden)

Muñoz Fernández, Ángela

2014-06-01

Full Text Available This research revolves around the sermon on Saint Anne in El Conhorte by Juana de la Cruz, focusing on imagery in the text about life and generation that supports the importance of maternal genealogies. Using this evidence as point of departure, this sermon is used as an example of shifting currents of opinion in female convents related to the Querelle des Femmes, currents of opinion that interacted with the main social and cultural debates of the period. These debates were closely related to the socalled “genealogical turn” which Iberian societies underwent in the 15th century.Este trabajo se articula en torno al sermón de Santa Ana de El Conhorte de Juana de la Cruz. Su temática incide en imágenes de vida y generación y defiende el peso de las genealogías maternas. A partir de esta evidencia, se plantea su estudio como exponente del desarrollo en el mundo de los conventos femeninos de corrientes de opinión relacionadas con la Querella de las Mujeres que interactuaron con los principales focos del debate social y cultural de su época, debates que guardaron relación con el llamado “giro genealógico” que experimentaron las sociedades ibéricas en el siglo XV.

Méthodes avancées pour la résolution du problème de maximum parcimonie

OpenAIRE

Vazquez Ortiz , Karla Esmeralda

2016-01-01

Phylogenetic reconstruction is considered a central underpinning of diverse fields like ecology, molecular biology and physiology where genealogical relationships of species or gene sequences represented as trees can provide the most meaningful insights into biology. Maximum Parsimony (MP) is an important approach to solve the phylogenetic reconstruction based on an optimality criterion under which the tree that minimizes the total number of genetic transformations is preferred. In this thesi...

[In process.

Science.gov (United States)

Jackson, Myles W

The story, which unfolds here, is a cultural history of science, one that closely analyzes the content of science. My story deals with an object, a gene. I use the CCR5 gene as a heuristic tool in order to probe the boundaries between science and society. Three important themes are discussed in this essay: genes as commodities (intellectual property and gene patents); alleles, natural selection, and the resistance to disease; and race and genomics. This is in part a story about neoliberalism, laissez-faire goverenments, free and open markets, the increase of privatization, and biotechnology. Many claim that the United States Patent and Trademake Office's (henceforth, USPTO) leniency in granting gene patenting led to the growth of biotechnology. I maintain the opposite: the growth of biotechnology led to decision to patent genes. My story is one of the present, a genealogy to borrow FOUCAULT'S and NIETZsCHE's terminology. How has it come about that genes are patentable entities, and that human classificatory schemes are usually based on race, although there are an infinite number of possibilities to characterize human variation? There are always alternatives, and historians are obliged to present those alternatives and explain why they were never chosen. I also use the concept of genealogy in the classical biological sense, i.e. to trace the passing of alleles from one generation to another. While this essay is similar to earlier studies dealing with the biography of objects, particularly scientific objects, the history told here is not a biography of the CCR5 gene, as that story is still ongoing. Rather, this essay concentrates upon a twenty-year period of the gene's life from the mid-1990s to the present. I am interested in understanding how it is we have reached the point we have today with respect to the relationship between science and society, and I use the CCR5 gene as a vehicle for that analysis.

Detecting lineage-specific adaptive evolution of brain-expressed genes in human using rhesus macaque as outgroup

DEFF Research Database (Denmark)

Yu, Xiao-Jing; Zheng, Hong-Kun; Wang, Jun

2006-01-01

related species as outgroup, it is difficult to identify human-lineage-specific changes, which is critical in delineating the biological uniqueness of humans. In this study, we conducted phylogeny-based analyses of 2633 human brain-expressed genes using rhesus macaque as the outgroup. We identified 47...... candidate genes showing strong evidence of positive selection in the human lineage. Genes with maximal expression in the brain showed a higher evolutionary rate in human than in chimpanzee. We observed that many immune-defense-related genes were under strong positive selection, and this trend was more...

Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding proteins

Directory of Open Access Journals (Sweden)

Bradley Michael E

2006-02-01

Full Text Available Abstract Background When accurate models for the divergent evolution of protein sequences are integrated with complementary biological information, such as folded protein structures, analyses of the combined data often lead to new hypotheses about molecular physiology. This represents an excellent example of how bioinformatics can be used to guide experimental research. However, progress in this direction has been slowed by the lack of a publicly available resource suitable for general use. Results The precomputed Magnum database offers a solution to this problem for ca. 1,800 full-length protein families with at least one crystal structure. The Magnum deliverables include 1 multiple sequence alignments, 2 mapping of alignment sites to crystal structure sites, 3 phylogenetic trees, 4 inferred ancestral sequences at internal tree nodes, and 5 amino acid replacements along tree branches. Comprehensive evaluations revealed that the automated procedures used to construct Magnum produced accurate models of how proteins divergently evolve, or genealogies, and correctly integrated these with the structural data. To demonstrate Magnum's capabilities, we asked for amino acid replacements requiring three nucleotide substitutions, located at internal protein structure sites, and occurring on short phylogenetic tree branches. In the cellular retinoid binding protein family a site that potentially modulates ligand binding affinity was discovered. Recruitment of cellular retinol binding protein to function as a lens crystallin in the diurnal gecko afforded another opportunity to showcase the predictive value of a browsable database containing branch replacement patterns integrated with protein structures. Conclusion We integrated two areas of protein science, evolution and structure, on a large scale and created a precomputed database, known as Magnum, which is the first freely available resource of its kind. Magnum provides evolutionary and structural

No Evidence That Schizophrenia Candidate Genes Are More Associated With Schizophrenia Than Noncandidate Genes.

Science.gov (United States)

Johnson, Emma C; Border, Richard; Melroy-Greif, Whitney E; de Leeuw, Christiaan A; Ehringer, Marissa A; Keller, Matthew C

2017-11-15

A recent analysis of 25 historical candidate gene polymorphisms for schizophrenia in the largest genome-wide association study conducted to date suggested that these commonly studied variants were no more associated with the disorder than would be expected by chance. However, the same study identified other variants within those candidate genes that demonstrated genome-wide significant associations with schizophrenia. As such, it is possible that variants within historic schizophrenia candidate genes are associated with schizophrenia at levels above those expected by chance, even if the most-studied specific polymorphisms are not. The present study used association statistics from the largest schizophrenia genome-wide association study conducted to date as input to a gene set analysis to investigate whether variants within schizophrenia candidate genes are enriched for association with schizophrenia. As a group, variants in the most-studied candidate genes were no more associated with schizophrenia than were variants in control sets of noncandidate genes. While a small subset of candidate genes did appear to be significantly associated with schizophrenia, these genes were not particularly noteworthy given the large number of more strongly associated noncandidate genes. The history of schizophrenia research should serve as a cautionary tale to candidate gene investigators examining other phenotypes: our findings indicate that the most investigated candidate gene hypotheses of schizophrenia are not well supported by genome-wide association studies, and it is likely that this will be the case for other complex traits as well. Copyright © 2017 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Detection of the Helicobacter pylori dupA gene is strongly affected by the PCR design.

Science.gov (United States)

Abadi, Amin Talebi Bezmin; Loffeld, Ruud J L F; Constancia, Ashandra C; Wagenaar, Jaap A; Kusters, Johannes G

2014-11-01

The Helicobacter pylori virulence gene dupA is usually detected by PCR, but the primer binding sites used are highly variable. Our newly designed qPCR against a conserved region of dupA was positive in 64.2% of 394 clinical isolates while the positivity rate of the commonly used PCRs ranged from 29.9% to 37.8%. Copyright © 2014. Published by Elsevier B.V.

Homeobox Genes in the Rodent Pineal Gland

DEFF Research Database (Denmark)

Rath, Martin Fredensborg; Rohde, Kristian; Klein, David C

2013-01-01

The pineal gland is a neuroendocrine gland responsible for nocturnal synthesis of melatonin. During early development of the rodent pineal gland from the roof of the diencephalon, homeobox genes of the orthodenticle homeobox (Otx)- and paired box (Pax)-families are expressed and are essential...... for normal pineal development consistent with the well-established role that homeobox genes play in developmental processes. However, the pineal gland appears to be unusual because strong homeobox gene expression persists in the pineal gland of the adult brain. Accordingly, in addition to developmental...... functions, homeobox genes appear to be key regulators in postnatal phenotype maintenance in this tissue. In this paper, we review ontogenetic and phylogenetic aspects of pineal development and recent progress in understanding the involvement of homebox genes in rodent pineal development and adult function...

In vivo Ebola virus infection leads to a strong innate response in circulating immune cells.

Science.gov (United States)

Caballero, Ignacio S; Honko, Anna N; Gire, Stephen K; Winnicki, Sarah M; Melé, Marta; Gerhardinger, Chiara; Lin, Aaron E; Rinn, John L; Sabeti, Pardis C; Hensley, Lisa E; Connor, John H

2016-09-05

Ebola virus is the causative agent of a severe syndrome in humans with a fatality rate that can approach 90 %. During infection, the host immune response is thought to become dysregulated, but the mechanisms through which this happens are not entirely understood. In this study, we analyze RNA sequencing data to determine the host response to Ebola virus infection in circulating immune cells. Approximately half of the 100 genes with the strongest early increases in expression were interferon-stimulated genes, such as ISG15, OAS1, IFIT2, HERC5, MX1 and DHX58. Other highly upregulated genes included cytokines CXCL11, CCL7, IL2RA, IL2R1, IL15RA, and CSF2RB, which have not been previously reported to change during Ebola virus infection. Comparing this response in two different models of exposure (intramuscular and aerosol) revealed a similar signature of infection. The strong innate response in the aerosol model was seen not only in circulating cells, but also in primary and secondary target tissues. Conversely, the innate immune response of vaccinated macaques was almost non-existent. This suggests that the innate response is a major aspect of the cellular response to Ebola virus infection in multiple tissues. Ebola virus causes a severe infection in humans that is associated with high mortality. The host immune response to virus infection is thought to be an important aspect leading to severe pathology, but the components of this overactive response are not well characterized. Here, we analyzed how circulating immune cells respond to the virus and found that there is a strong innate response dependent on active virus replication. This finding is in stark contrast to in vitro evidence showing a suppression of innate immune signaling, and it suggests that the strong innate response we observe in infected animals may be an important contributor to pathogenesis.

The tumor suppressor homolog in fission yeast, myh1+, displays a strong interaction with the checkpoint gene rad1+

International Nuclear Information System (INIS)

Jansson, Kristina; Warringer, Jonas; Farewell, Anne; Park, Han-Oh; Hoe, Kwang-Lae; Kim, Dong-Uk; Hayles, Jacqueline; Sunnerhagen, Per

2008-01-01

The DNA glycosylase MutY is strongly conserved in evolution, and homologs are found in most eukaryotes and prokaryotes examined. This protein is implicated in repair of oxidative DNA damage, in particular adenine mispaired opposite 7,8-dihydro-8-oxoguanine. Previous investigations in Escherichia coli, fission yeast, and mammalian cells show an association of mutations in MutY homologs with a mutator phenotype and carcinogenesis. Eukaryotic MutY homologs physically associate with several proteins with a role in replication, DNA repair, and checkpoint signaling, specifically the trimeric 9-1-1 complex. In a genetic investigation of the fission yeast MutY homolog, myh1 + , we show that the myh1 mutation confers a moderately increased UV sensitivity alone and in combination with mutations in several DNA repair genes. The myh1 rad1, and to a lesser degree myh1 rad9, double mutants display a synthetic interaction resulting in enhanced sensitivity to DNA damaging agents and hydroxyurea. UV irradiation of myh1 rad1 double mutants results in severe chromosome segregation defects and visible DNA fragmentation, and a failure to activate the checkpoint. Additionally, myh1 rad1 double mutants exhibit morphological defects in the absence of DNA damaging agents. We also found a moderate suppression of the slow growth and UV sensitivity of rhp51 mutants by the myh1 mutation. Our results implicate fission yeast Myh1 in repair of a wider range of DNA damage than previously thought, and functionally link it to the checkpoint pathway

Ocatilla : del paisaje monumental al monumento

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Fernando Quesada

2012-12-01

Full Text Available

<strong>Resumen>

Este artículo aborda el campamento Ocatilla, construido en el  desierto de Arizona por Frank Lloyd Wright como una estación  experimental de arquitectura en 1929. Se propone este campamento como un prototipo que tendría dos vectores  temporales por lo que se refiere a una posible genealogía y a un posible desarrollo futuro. Hacía el pasado habría que  rastrearlo en la Casa para la Familia Cristiana propuesta por  Catherine Beecher en 1869, mientras que hacia el futuro podría establecerse un posible epígono en la Burbuja Ambiental de  Reyner Banham y François Dallegret de 1965. El texto explora  las posibilidades de un ideal de arquitectura para el paisaje monumental, perfectamente ejemplarizado en los tres casos, frente a la arquitectura como monumento ante el paisaje, que ejemplificaría Taliesin West, su monumental contrafigura.<strong>

>Palabras clavestrong>

campamento, prototipo, paisaje, ambiental, monumental

<strong>Abstract>

This article discusses the Ocatilla camp, built in the Arizona  desert by Frank Lloyd Wright as an experimental architecture in  1929. This camp is proposed as a prototype with two temporary vectors, one would be to a possible genealogy and the other a  possible future development. Going to the past should be traced in the House for the Christian Family by Catherine Beecher proposed in 1869, while that to the future could be made a epigone in the Environmental Bubble of Reyner Banham and of François Dallegret in 1965. The text explores the possibilities of an ideal architecture for the monumental landscape, perfectly  exemplified in the three cases, compared to architecture as a monument to the landscape, which exemplify Taliesin West, his monumental counterpart.<strong>

>Key wordsstrong>

camp, prototype, landscape, environment, monumental

Burden analysis of rare microdeletions suggests a strong impact of neurodevelopmental genes in genetic generalised epilepsies

DEFF Research Database (Denmark)

Lal, Dennis; Ruppert, Ann-Kathrin; Trucks, Holger

2015-01-01

contribution of recurrent microdeletions at genomic rearrangement hotspots and non-recurrent microdeletions, and 3) identify potential candidate genes for GGE. We found a significant excess of microdeletions in 7.3% of GGE patients compared to 4.0% in controls (P = 1.8 x 10-7; OR = 1.9). Recurrent...

Isolation and characterization of CXC receptor genes in a range of elasmobranchs.

Science.gov (United States)

Goostrey, Anna; Jones, Gareth; Secombes, Christopher J

2005-01-01

The CXC group of chemokines exert their cellular effects via the CXCR group of G-protein coupled receptors. Six CXCR genes have been identified in humans (CXCR1-6), and homologues to some of these have been isolated from a range of vertebrate species. Here we isolate and characterize CXCR genes from a range of elasmobranch species. One CXCR1/2 gene fragment isolated from Scyliorhinus caniculus (lesser spotted catshark), and two CXCR1/2 copies from each of the elasmobranchs, Cetorhinus maximus (basking shark), Carcharodon carcharias (great white shark), and Raja naevus (cuckoo ray), exhibit high similarity to both CXCR1 and CXCR2. The two copies evident in the cuckoo ray and lamniform sharks provide strong evidence of CXCR1/2 lineage specific duplication in rays and sharks. A CXCR fragment isolated from Lamna ditropis (salmon shark) shows high similarity to a range of CXCR4 genes and strong clustering with CXCR4 gene homologues was apparent during phylogenetic reconstruction.

Prospective identification of malaria parasite genes under balancing selection.

Directory of Open Access Journals (Sweden)

Kevin K A Tetteh

Full Text Available Endemic human pathogens are subject to strong immune selection, and interrogation of pathogen genome variation for signatures of balancing selection can identify important target antigens. Several major antigen genes in the malaria parasite Plasmodium falciparum have shown such signatures in polymorphism-versus-divergence indices (comparing with the chimpanzee parasite P. reichenowi, and in allele frequency based indices.To compare methods for prospective identification of genes under balancing selection, 26 additional genes known or predicted to encode surface-exposed proteins of the invasive blood stage merozoite were first sequenced from a panel of 14 independent P. falciparum cultured lines and P. reichenowi. Six genes at the positive extremes of one or both of the Hudson-Kreitman-Aguade (HKA and McDonald-Kreitman (MK indices were identified. Allele frequency based analysis was then performed on a Gambian P. falciparum population sample for these six genes and three others as controls. Tajima's D (TjD index was most highly positive for the msp3/6-like PF10_0348 (TjD = 1.96 as well as the positive control ama1 antigen gene (TjD = 1.22. Across the genes there was a strong correlation between population TjD values and the relative HKA indices (whether derived from the population or the panel of cultured laboratory isolates, but no correlation with the MK indices.Although few individual parasite genes show significant evidence of balancing selection, analysis of population genomic and comparative sequence data with the HKA and TjD indices should discriminate those that do, and thereby identify likely targets of immunity.

Anterior-posterior regionalized gene expression in the Ciona notochord.

Science.gov (United States)

Reeves, Wendy; Thayer, Rachel; Veeman, Michael

2014-04-01

In the simple ascidian chordate Ciona, the signaling pathways and gene regulatory networks giving rise to initial notochord induction are largely understood and the mechanisms of notochord morphogenesis are being systematically elucidated. The notochord has generally been thought of as a non-compartmentalized or regionalized organ that is not finely patterned at the level of gene expression. Quantitative imaging methods have recently shown, however, that notochord cell size, shape, and behavior vary consistently along the anterior-posterior (AP) axis. Here we screen candidate genes by whole mount in situ hybridization for potential AP asymmetry. We identify 4 genes that show non-uniform expression in the notochord. Ezrin/radixin/moesin (ERM) is expressed more strongly in the secondary notochord lineage than the primary. CTGF is expressed stochastically in a subset of notochord cells. A novel calmodulin-like gene (BCamL) is expressed more strongly at both the anterior and posterior tips of the notochord. A TGF-β ortholog is expressed in a gradient from posterior to anterior. The asymmetries in ERM, BCamL, and TGF-β expression are evident even before the notochord cells have intercalated into a single-file column. We conclude that the Ciona notochord is not a homogeneous tissue but instead shows distinct patterns of regionalized gene expression. Copyright © 2013 Wiley Periodicals, Inc.

Isolating Barley ( Hordeum vulgare L.) B1 Hordein Gene Promoter ...

African Journals Online (AJOL)

Promoters play the most important role in determining the temporal and spatial expression pattern and transcript level of a gene. Some strong constitutive promoters, such as cauliflower mosaic virus 35s promoter, are widely used in plant genetic engineering research. However, the expression levels of the foreign genes in ...

Natural Selection in Virulence Genes of Francisella tularensis.

Science.gov (United States)

Gunnell, Mark K; Robison, Richard A; Adams, Byron J

2016-06-01

A fundamental tenet of evolution is that alleles that are under negative selection are often deleterious and confer no evolutionary advantage. Negatively selected alleles are removed from the gene pool and are eventually extinguished from the population. Conversely, alleles under positive selection do confer an evolutionary advantage and lead to an increase in the overall fitness of the organism. These alleles increase in frequency until they eventually become fixed in the population. Francisella tularensis is a zoonotic pathogen and a potential biothreat agent. The most virulent type of F. tularensis, Type A, is distributed across North America with Type A.I occurring mainly in the east and Type A.II appearing mainly in the west. F. tularensis is thought to be a genome in decay (losing genes) because of the relatively large number of pseudogenes present in its genome. We hypothesized that the observed frequency of gene loss/pseudogenes may be an artifact of evolution in response to a changing environment, and that genes involved in virulence should be under strong positive selection. To test this hypothesis, we sequenced and compared whole genomes of Type A.I and A.II isolates. We analyzed a subset of virulence and housekeeping genes from several F. tularensis subspecies genomes to ascertain the presence and extent of positive selection. Eleven previously identified virulence genes were screened for positive selection along with 10 housekeeping genes. Analyses of selection yielded one housekeeping gene and 7 virulence genes which showed significant evidence of positive selection at loci implicated in cell surface structures and membrane proteins, metabolism and biosynthesis, transcription, translation and cell separation, and substrate binding and transport. Our results suggest that while the loss of functional genes through disuse could be accelerated by negative selection, the genome decay in Francisella could also be the byproduct of adaptive evolution

Genealogy of the body and genealogical body

Directory of Open Access Journals (Sweden)

Paola Cecchetti

2011-06-01

Full Text Available A partire da un quadro di Frida Kahlo intitolato I miei nonni, i miei genitori e io le due autrici indagano quel testo-immagine che sta all'origine dello stile di lettura del soggetto. Posto dinanzi alla stessa immagine, ciascuno ne fa una rappresentazione estremamente personale, un quadro delle proprie vicissitudini interne e dei legami transgenerazionali che lo hanno segnato. I momenti nei quali si articola la ricerca sono tre: la scrittura dell’occhio, il ricalco e il percorso della mano, il negativo e l’assenza.A essi segue poi lo psicodramma. Tale successione temporale abitua a vedere nell'immagine disegnata l'immagine negata, assente. L'esperienza sembra aver creato un nuovo metodo di indagine della psiche rispetto al transgenerazionale, metodo che intreccia il genogramma (di origini sistemico-relazionale e lo psicodramma analitico, e che viene chiamato “genodramma psicoanalitico”. Partendo da un dato clinico – l'esilità del legame che le nuove generazioni intrattengono con quelle che le precedono, sembra vogliano rinegoziare il contratto narcisistico che assegna al passato il posto dell'assenza. Il contributo si chiude con un interrogativo: “Alla ricerca di che cosa? Della presenza o, meglio, delle tracce lasciate nel soggetto dall'Altro che precede l'insediamento dell'Io”.

Fine mapping of the genic male-sterile ms 1 gene in Capsicum annuum L.

Science.gov (United States)

Jeong, Kyumi; Choi, Doil; Lee, Jundae

2018-01-01

The genomic region cosegregating with the genic male-sterile ms 1 gene of Capsicum annuum L. was delimited to a region of 869.9 kb on chromosome 5 through fine mapping analysis. A strong candidate gene, CA05g06780, a homolog of the Arabidopsis MALE STERILITY 1 gene that controls pollen development, was identified in this region. Genic male sterility caused by the ms 1 gene has been used for the economically efficient production of massive hybrid seeds in paprika (Capsicum annuum L.), a colored bell-type sweet pepper. Previously, a CAPS marker, PmsM1-CAPS, located about 2-3 cM from the ms 1 locus, was reported. In this study, we constructed a fine map near the ms 1 locus using high-resolution melting (HRM) markers in an F 2 population consisting of 1118 individual plants, which segregated into 867 male-fertile and 251 male-sterile plants. A total of 12 HRM markers linked to the ms 1 locus were developed from 53 primer sets targeting intraspecific SNPs derived by comparing genome-wide sequences obtained by next-generation resequencing analysis. Using this approach, we narrowed down the region cosegregating with the ms 1 gene to 869.9 kb of sequence. Gene prediction analysis revealed 11 open reading frames in this region. A strong candidate gene, CA05g06780, was identified; this gene is a homolog of the Arabidopsis MALE STERILITY 1 (MS1) gene, which encodes a PHD-type transcription factor that regulates pollen and tapetum development. Sequence comparison analysis suggested that the CA05g06780 gene is the strongest candidate for the ms 1 gene of paprika. To summarize, we developed a cosegregated marker, 32187928-HRM, for marker-assisted selection and identified a strong candidate for the ms 1 gene.

Deregulation of an imprinted gene network in prostate cancer.

Science.gov (United States)

Ribarska, Teodora; Goering, Wolfgang; Droop, Johanna; Bastian, Klaus-Marius; Ingenwerth, Marc; Schulz, Wolfgang A

2014-05-01

Multiple epigenetic alterations contribute to prostate cancer progression by deregulating gene expression. Epigenetic mechanisms, especially differential DNA methylation at imprinting control regions (termed DMRs), normally ensure the exclusive expression of imprinted genes from one specific parental allele. We therefore wondered to which extent imprinted genes become deregulated in prostate cancer and, if so, whether deregulation is due to altered DNA methylation at DMRs. Therefore, we selected presumptive deregulated imprinted genes from a previously conducted in silico analysis and from the literature and analyzed their expression in prostate cancer tissues by qRT-PCR. We found significantly diminished expression of PLAGL1/ZAC1, MEG3, NDN, CDKN1C, IGF2, and H19, while LIT1 was significantly overexpressed. The PPP1R9A gene, which is imprinted in selected tissues only, was strongly overexpressed, but was expressed biallelically in benign and cancerous prostatic tissues. Expression of many of these genes was strongly correlated, suggesting co-regulation, as in an imprinted gene network (IGN) reported in mice. Deregulation of the network genes also correlated with EZH2 and HOXC6 overexpression. Pyrosequencing analysis of all relevant DMRs revealed generally stable DNA methylation between benign and cancerous prostatic tissues, but frequent hypo- and hyper-methylation was observed at the H19 DMR in both benign and cancerous tissues. Re-expression of the ZAC1 transcription factor induced H19, CDKN1C and IGF2, supporting its function as a nodal regulator of the IGN. Our results indicate that a group of imprinted genes are coordinately deregulated in prostate cancers, independently of DNA methylation changes.

Functional characterization of a Penicillium chrysogenum mutanase gene induced upon co-cultivation with Bacillus subtilis

NARCIS (Netherlands)

Bajaj, I.; Veiga, T.; Van Dissel, D.; Pronk, J.T.; Daran, J.M.

2014-01-01

Background Microbial gene expression is strongly influenced by environmental growth conditions. Comparison of gene expression under different conditions is frequently used for functional analysis and to unravel regulatory networks, however, gene expression responses to co-cultivation with other

Strong association of 677 C>T substitution in the MTHFR gene with male infertility--a study on an indian population and a meta-analysis.

Directory of Open Access Journals (Sweden)

Nishi Gupta

Full Text Available Methylenetetrahydrofolate reductase (MTHFR is an important enzyme of folate and methionine metabolism, making it crucial for DNA synthesis and methylation. The objective of this study was to analyze MTHFR gene 677C>T polymorphism in infertile male individuals from North India, followed by a meta-analysis on our data and published studies.We undertook genotyping on a total of 837 individuals including well characterized infertile (N = 522 and confirmed fertile (N = 315 individuals. The SNP was typed by direct DNA sequencing. Chi square test was done for statistical analysis. Published studies were searched using appropriate keywords. Source of data collection for meta-analysis included 'Pubmed', 'Ovid' and 'Google Scholar'. Those studies analyzing 677C>T polymorphism in male infertility and presenting all relevant data were included in meta-analysis. The genotype data for infertile subjects and fertile controls was extracted from each study. Chi square test was done to obtain odds ratio (OR and p-value. Meta-analysis was performed using Comprehensive Meta-analysis software (Version 2. The frequency of mutant (T allele (p = 0.0025 and genotypes (CT+TT (p = 0.0187 was significantly higher in infertile individuals in comparison to fertile controls in our case-control study. The overall summary estimate (OR for allele and genotype meta-analysis were 1.304 (p = 0.000, 1.310 (p = 0.000, respectively, establishing significant association of 677C>T polymorphism with male infertility.677C>T substitution associated strongly with male infertility in Indian population. Allele and genotype meta-analysis also supported its strong correlation with male infertility, thus establishing it as a risk factor.

Genealogical electronic coupling procedure incorporating the Hartree--Fock interacting space and suitable for degenerate point groups. Application to excited states of BH3

International Nuclear Information System (INIS)

Swope, W.C.; Schaefer, H.F. III; Yarkony, D.R.

1980-01-01

The use of Clebsch--Gordan-type coupling coefficients for finite point groups is applied to the problem of constructing symmetrized N-electron wave functions (configurations) for use by the Hartree--Fock SCF and CI methods of determining electronic wave functions for molecular systems. The configurations are eigenfunctions of electronic spin operators, and transform according to a particular irreducible representation of the relevant group of spatial operations which leave the Born--Oppenheimer Hamiltonian invariant. The method proposed for constructing the configurations involves a genealogical coupling procedure. It is particularly useful for studies of molecules which belong to a group which has multiply degenerate irreducible representations. The advantage of the method is that it results in configurations which are real linear combinations of determinants of real symmetry orbitals. This procedure for constructing configurations also allows for the identification of configurations which have no matrix element of the Hamiltonian with a reference configuration. It is therefore possible to construct a Hartree--Fock interacting space of configurations which can speed the convergence of a CI wave function. The coupling method is applied to a study of the ground and two excited electronic states of BH 3 in its D/sub 3h/ geometry. The theoretical approach involved Hartree--Fock SCF calculations followed by single and double substitution CI calculations, both of which employed double-zeta plus polarization quality basis sets

Individual genetic variations related to satiety and appetite control increase risk of obesity in preschool-age children in the STRONG kids program.

Science.gov (United States)

Wang, Yingying; Wang, Anthony; Donovan, Sharon M; Teran-Garcia, Margarita

2013-01-01

The burden of the childhood obesity epidemic is well recognized; nevertheless, the genetic markers and gene-environment interactions associated with the development of common obesity are still unknown. In this study, candidate genes associated to satiety and appetite control pathways with obesity-related traits were tested in Caucasian preschoolers from the STRONG Kids project. Eight genetic variants in genes related to obesity (BDNF, LEPR, FTO, PCSK1, POMC, TUB, LEP, and MC4R) were genotyped in 128 children from the STRONG Kids project (mean age 39.7 months). Data were analyzed for individual associations and to test for genetic predisposition scores (GPSs) with body mass index (BMI) and anthropometric traits (Z-scores, e.g. height-for-age Z-score, HAZ). Covariates included age, sex, and breastfeeding (BF) duration. Obesity and overweight prevalence was 6.3 and 19.5%, respectively, according to age- and sex-specific BMI percentiles. Individual genetic associations of MC4R and LEPR markers with HAZ were strengthened when BF duration was included as a covariate. Our GPSs show that, as the number of risk alleles increased, the risk of higher BMI and HAZ also increased. Overall, the GPSs assembled were able to explain 2-3% of the variability in BMI and HAZ phenotypes. Genetic associations with common obesity-related phenotypes were found in the STRONG Kids project. GPSs assembled for specific candidate genes were associated with BMI and HAZ phenotypes. © 2013 S. Karger AG, Basel.

Natural selection on protein-coding genes in the human genome

DEFF Research Database (Denmark)

Bustamente, Carlos D.; Fledel-Alon, Adi; Williamson, Scott

2005-01-01

, showing an excess of deleterious variation within local populations 9, 10 . Here we contrast patterns of coding sequence polymorphism identified by direct sequencing of 39 humans for over 11,000 genes to divergence between humans and chimpanzees, and find strong evidence that natural selection has shaped......Comparisons of DNA polymorphism within species to divergence between species enables the discovery of molecular adaptation in evolutionarily constrained genes as well as the differentiation of weak from strong purifying selection 1, 2, 3, 4 . The extent to which weak negative and positive darwinian...... selection have driven the molecular evolution of different species varies greatly 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 , with some species, such as Drosophila melanogaster, showing strong evidence of pervasive positive selection 6, 7, 8, 9 , and others, such as the selfing weed Arabidopsis thaliana...

Polymorphisms of the dopamine D4 receptor gene (DRD4 VNTR) and cannabinoid CB1 receptor gene (CNR1) are not strongly related to cue-reactivity after alcohol exposure

NARCIS (Netherlands)

Wildenberg, E. van den; Janssen, R.G.J.H.; Hutchison, K.E.; Breukelen, G.J.P. van; Wiers, R.W.H.J.

2007-01-01

Polymorphisms in the D4 dopamine receptor gene (DRD4) and the CB1 cannabinoid receptor gene (CNR1) have been associated with a differential response to alcohol after consumption. The goal of the present study was to investigate whether heavy drinkers with these polymorphisms would respond with

Genome-Wide Analysis in Three Fusarium Pathogens Identifies Rapidly Evolving Chromosomes and Genes Associated with Pathogenicity

Science.gov (United States)

Sperschneider, Jana; Gardiner, Donald M.; Thatcher, Louise F.; Lyons, Rebecca; Singh, Karam B.; Manners, John M.; Taylor, Jennifer M.

2015-01-01

Pathogens and hosts are in an ongoing arms race and genes involved in host–pathogen interactions are likely to undergo diversifying selection. Fusarium plant pathogens have evolved diverse infection strategies, but how they interact with their hosts in the biotrophic infection stage remains puzzling. To address this, we analyzed the genomes of three Fusarium plant pathogens for genes that are under diversifying selection. We found a two-speed genome structure both on the chromosome and gene group level. Diversifying selection acts strongly on the dispensable chromosomes in Fusarium oxysporum f. sp. lycopersici and on distinct core chromosome regions in Fusarium graminearum, all of which have associations with virulence. Members of two gene groups evolve rapidly, namely those that encode proteins with an N-terminal [SG]-P-C-[KR]-P sequence motif and proteins that are conserved predominantly in pathogens. Specifically, 29 F. graminearum genes are rapidly evolving, in planta induced and encode secreted proteins, strongly pointing toward effector function. In summary, diversifying selection in Fusarium is strongly reflected as genomic footprints and can be used to predict a small gene set likely to be involved in host–pathogen interactions for experimental verification. PMID:25994930

Strong-back safety latch

International Nuclear Information System (INIS)

DeSantis, G.N.

1995-01-01

The calculation decides the integrity of the safety latch that will hold the strong-back to the pump during lifting. The safety latch will be welded to the strong-back and will latch to a 1.5-in. dia cantilever rod welded to the pump baseplate. The static and dynamic analysis shows that the safety latch will hold the strong-back to the pump if the friction clamps fail and the pump become free from the strong-back. Thus, the safety latch will meet the requirements of the Lifting and Rigging Manual for under the hook lifting for static loading; it can withstand shock loads from the strong-back falling 0.25 inch

Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser

LENUS (Irish Health Repository)

Fitzpatrick, David A

2010-05-10

Abstract Background Candida species are the most common cause of opportunistic fungal infection worldwide. Recent sequencing efforts have provided a wealth of Candida genomic data. We have developed the Candida Gene Order Browser (CGOB), an online tool that aids comparative syntenic analyses of Candida species. CGOB incorporates all available Candida clade genome sequences including two Candida albicans isolates (SC5314 and WO-1) and 8 closely related species (Candida dubliniensis, Candida tropicalis, Candida parapsilosis, Lodderomyces elongisporus, Debaryomyces hansenii, Pichia stipitis, Candida guilliermondii and Candida lusitaniae). Saccharomyces cerevisiae is also included as a reference genome. Results CGOB assignments of homology were manually curated based on sequence similarity and synteny. In total CGOB includes 65617 genes arranged into 13625 homology columns. We have also generated improved Candida gene sets by merging\\/removing partial genes in each genome. Interrogation of CGOB revealed that the majority of tandemly duplicated genes are under strong purifying selection in all Candida species. We identified clusters of adjacent genes involved in the same metabolic pathways (such as catabolism of biotin, galactose and N-acetyl glucosamine) and we showed that some clusters are species or lineage-specific. We also identified one example of intron gain in C. albicans. Conclusions Our analysis provides an important resource that is now available for the Candida community. CGOB is available at http:\\/\\/cgob.ucd.ie.

An extensive analysis of the hereditary hemochromatosis gene HFE and neighboring histone genes: associations with childhood leukemia.

Science.gov (United States)

Davis, Charronne F; Dorak, M Tevfik

2010-04-01

The most common mutation of the HFE gene C282Y has shown a risk association with childhood acute lymphoblastic leukemia (ALL) in Welsh and Scottish case-control studies. This finding has not been replicated outside Britain. Here, we present a thorough analysis of the HFE gene in a panel of HLA homozygous reference cell lines and in the original population sample from South Wales (117 childhood ALL cases and 414 newborn controls). The 21 of 24 variants analyzed were from the HFE gene region extending 52 kb from the histone gene HIST1H1C to HIST1H1T. We identified the single-nucleotide polymorphism (SNP) rs807212 as a tagging SNP for the most common HFE region haplotype, which contains wild-type alleles of all HFE variants examined. This intergenic SNP rs807212 yielded a strong male-specific protective association (per allele OR = 0.38, 95% CI = 0.22-0.64, P (trend) = 0.0002; P = 0.48 in females), which accounted for the original C282Y risk association. In the HapMap project data, rs807212 was in strong linkage disequilibrium with 25 other SNPs spanning 151 kb around HFE. Minor alleles of these 26 SNPs characterized the most common haplotype for the HFE region, which lacked all disease-associated HFE variants. The HapMap data suggested positive selection in this region even in populations where the HFE C282Y mutation is absent. These results have implications for the sex-specific associations observed in this region and suggest the inclusion of rs807212 in future studies of the HFE gene and the extended HLA class I region.

Transcriptome of Dickeya dadantii infecting Acyrthosiphon pisum reveals a strong defense against antimicrobial peptides.

Science.gov (United States)

Costechareyre, Denis; Chich, Jean-François; Strub, Jean-Marc; Rahbé, Yvan; Condemine, Guy

2013-01-01

The plant pathogenic bacterium Dickeya dadantii has recently been shown to be able to kill the aphid Acyrthosiphon pisum. While the factors required to cause plant disease are now well characterized, those required for insect pathogeny remain mostly unknown. To identify these factors, we analyzed the transcriptome of the bacteria isolated from infected aphids. More than 150 genes were upregulated and 300 downregulated more than 5-fold at 3 days post infection. No homologue to known toxin genes could be identified in the upregulated genes. The upregulated genes reflect the response of the bacteria to the conditions encountered inside aphids. While only a few genes involved in the response to oxidative stress were induced, a strong defense against antimicrobial peptides (AMP) was induced. Expression of a great number of efflux proteins and transporters was increased. Besides the genes involved in LPS modification by addition of 4-aminoarabinose (the arnBCADTEF operon) and phosphoethanolamine (pmrC, eptB) usually induced in Gram negative bacteria in response to AMPs, dltBAC and pbpG genes, which confer Gram positive bacteria resistance to AMPs by adding alanine to teichoic acids, were also induced. Both types of modification confer D. dadantii resistance to the AMP polymyxin. A. pisum harbors symbiotic bacteria and it is thought that it has a very limited immune system to maintain these populations and do not synthesize AMPs. The arnB mutant was less pathogenic to A. pisum, which suggests that, in contrast to what has been supposed, aphids do synthesize AMP.

Transcriptome of Dickeya dadantii infecting Acyrthosiphon pisum reveals a strong defense against antimicrobial peptides.

Directory of Open Access Journals (Sweden)

Denis Costechareyre

Full Text Available The plant pathogenic bacterium Dickeya dadantii has recently been shown to be able to kill the aphid Acyrthosiphon pisum. While the factors required to cause plant disease are now well characterized, those required for insect pathogeny remain mostly unknown. To identify these factors, we analyzed the transcriptome of the bacteria isolated from infected aphids. More than 150 genes were upregulated and 300 downregulated more than 5-fold at 3 days post infection. No homologue to known toxin genes could be identified in the upregulated genes. The upregulated genes reflect the response of the bacteria to the conditions encountered inside aphids. While only a few genes involved in the response to oxidative stress were induced, a strong defense against antimicrobial peptides (AMP was induced. Expression of a great number of efflux proteins and transporters was increased. Besides the genes involved in LPS modification by addition of 4-aminoarabinose (the arnBCADTEF operon and phosphoethanolamine (pmrC, eptB usually induced in Gram negative bacteria in response to AMPs, dltBAC and pbpG genes, which confer Gram positive bacteria resistance to AMPs by adding alanine to teichoic acids, were also induced. Both types of modification confer D. dadantii resistance to the AMP polymyxin. A. pisum harbors symbiotic bacteria and it is thought that it has a very limited immune system to maintain these populations and do not synthesize AMPs. The arnB mutant was less pathogenic to A. pisum, which suggests that, in contrast to what has been supposed, aphids do synthesize AMP.

Interleukin 18 receptor 1 gene polymorphisms are associated with asthma

DEFF Research Database (Denmark)

Zhu, Guohua; Whyte, Moira K B; Vestbo, Jørgen

2008-01-01

The interleukin 18 receptor (IL18R1) gene is a strong candidate gene for asthma. It has been implicated in the pathophysiology of asthma and maps to an asthma susceptibility locus on chromosome 2q12. The possibility of association between polymorphisms in IL18R1 and asthma was examined by genotyp...

Homocysteine and coronary heart disease : the role of polymorphic genes and hemostasis

NARCIS (Netherlands)

Klerk, M.

2002-01-01

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Background> Homocysteine is a sulfur-containing amino acid formed during catabolism of the essential amino acid methionine. Defects in genes encoding enzymes or sub-optimal intake of B-vitamins (e.g. folate) involved in homocysteine