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Genetic Information (genetic + information)
Selected AbstractsPRIVACY, THE INDIVIDUAL AND GENETIC INFORMATION: A BUDDHIST PERSPECTIVEBIOETHICS, Issue 7 2009SORAJ HONGLADAROM ABSTRACT Bioinformatics is a new field of study whose ethical implications involve a combination of bioethics, computer ethics and information ethics. This paper is an attempt to view some of these implications from the perspective of Buddhism. Privacy is a central concern in both computer/information ethics and bioethics, and with information technology being increasingly utilized to process biological and genetic data, the issue has become even more pronounced. Traditionally, privacy presupposes the individual self but as Buddhism does away with the ultimate conception of an individual self, it has to find a way to analyse and justify privacy that does not presuppose such a self. It does this through a pragmatic conception that does not depend on a positing of the substantial self, which is then found to be unnecessary for an effective protection of privacy. As it may be possible one day to link genetic data to individuals, the Buddhist conception perhaps offers a more flexible approach, as what is considered to be integral to an individual person is not fixed in objectivity but depends on convention. [source] What is Genetic Information, and why is it Significant?JOURNAL OF APPLIED PHILOSOPHY, Issue 1 2006A Contextual, Approach, Contrastive abstract Is genetic information of special ethical significance? Does it require special regulation? There is considerable contemporary debate about this question (the ,genetic exceptionalism' debate). ,Genetic information' is an ambiguous term and, as an aid to avoiding conflation in the genetic exceptionalism debate, a detailed account is given of just how and why ,genetic information' is ambiguous. Whilst ambiguity is a ubiquitous problem of communication, it is suggested that ,genetic information' is ambiguous in a particular way, one that gives rise to the problem of ,significance creep' (i.e., where claims about the significance of certain kinds of genetic information in one context influence our thinking about the significance of other kinds of genetic information in other contexts). A contextual and contrastive methodology is proposed: evaluating the significance of genetic information requires us to be sensitive to the polysemy of ,genetic information' across contexts and then examine the contrast in significance (if any) of genetic, as opposed to nongenetic, information within contexts. This, in turn, suggests that a proper solution to the regulatory question requires us to pay more attention to how and why information, and its acquisition, possession and use, come to be of ethical significance. [source] Genetic Testing, Genetic Information, and the Role of Maternal-Child Health Nurses in IsraelJOURNAL OF NURSING SCHOLARSHIP, Issue 3 2006Sivia Barnoy Purpose: To examine the rate of genetic testing, the characteristics of those who had these tests, and to examine the public's openness to the possibility of expanding nurses' roles in maternal-child health (MCH) clinics to include providing genetic information. Design: The study was conducted in nine MCH clinics in the central district of Israel. All women attending the clinics during 1 week were requested to complete the questionnaire. The sample consisted of 361 participants. Findings: A high rate of genetic testing (80.4%) was shown. Higher education, being secular, and native-born Israeli predicted testing performance. Half of the tested participants reported that they did not understand the test results and were interested in receiving explanations regarding these results. Forty-four percent of respondents were interested in receiving genetic information from an MCH nurse. Conclusions: A high rate of genetic testing performance was reported. The public reported lack of information regarding genetic tests and their results. An appropriate setting for providing this information is the maternal-child health clinics. [source] Protecting Medical Privacy: Challenges in the Age of Genetic InformationJOURNAL OF SOCIAL ISSUES, Issue 2 2003Sheri A. Alpert This article examines the privacy issues that arise from the convergence of two trends: the computerization of medical records, and the increasingly detailed level of personal genetic information that will potentially be placed within the electronic medical record. The article discusses the privacy and public policy implications for medical care, group identity, and familial relationships arising from the transition toward electronic medical records which will increasingly contain highly detailed genetic information. As such, the article focuses on the confidentiality of the electronic medical record, the increasing prevalence and sophistication of genetic testing and analysis, and the implications of electronic genetic information. [source] Managing Genetic Information in Families of Children with Sickle Cell DiseaseNURSING & HEALTH SCIENCES, Issue 3 2007Agatha Gallo [source] The Physician as Gatekeeper to the Use of Genetic Information in the Criminal Justice SystemTHE JOURNAL OF LAW, MEDICINE & ETHICS, Issue 1 2002Samuel C. Seiden First page of article [source] Balancing Population Size and Genetic Information in Parentage Analysis StudiesBIOMETRICS, Issue 3 2003Beatrix Jones Summary. In parentage analysis studies, the parameters of interest typically are not the parent assignments themselves, but population parameters such as variance in fertility, self-pollination rate, or average dispersal distances. The precision of parameter estimates is affected by two factors: the number of offspring under consideration, and the precision with which the offspring can be assigned to parents. When assignment of parents is based on genetic information, the confidence in assignments is affected by the number and polymorphism of the loci considered, and by the number of potential parents in the population. Studying larger populations may yield higher numbers of offspring, but since larger populations contain more potential parents, more (or more highly polymorphic) loci are necessary to attain a given level of confidence in the parent assignments. This article addresses how to relate the size of the population and the number of loci when designing a study. It is shown that the number of loci needed to assign all offspring unambiguously is proportional to the logarithm of the population size. In some cases, the constant of proportionality can be determined, eliminating the need for simulation-based projections. Population-wide measures of uncertainty in parent assignments are also introduced, and it is shown that holding uncertainty "steady" as the population size increases also requires increasing the number of loci proportional to the logarithm of the population size. Data from a study of self-pollination are used to illustrate the techniques suggested. [source] The Use of Genetic Information in the WorkplaceBUSINESS AND SOCIETY REVIEW, Issue 4 2002Kenneth A. Kovach [source] Genetic Data and the Listing of Species Under the U.S. Endangered Species ActCONSERVATION BIOLOGY, Issue 5 2007SYLVIA M. FALLON Acta de Especies en Peligro de E. U. A.; decisiones de enlistado; segmento poblacional distinto Abstract:,Genetic information is becoming an influential factor in determining whether species, subspecies, and distinct population segments qualify for protection under the U.S. Endangered Species Act. Nevertheless, there are currently no standards or guidelines that define how genetic information should be used by the federal agencies that administer the act. I examined listing decisions made over a 10-year period (February 1996,February 2006) that relied on genetic information. There was wide variation in the genetic data used to inform listing decisions in terms of which genomes (mitochondrial vs. nuclear) were sampled and the number of markers (or genetic techniques) and loci evaluated. In general, whether the federal agencies identified genetic distinctions between putative taxonomic units or populations depended on the type and amount of genetic data. Studies that relied on multiple genetic markers were more likely to detect distinctions, and those organisms were more likely to receive protection than studies that relied on a single genetic marker. Although the results may, in part, reflect the corresponding availability of genetic techniques over the given time frame, the variable use of genetic information for listing decisions has the potential to misguide conservation actions. Future management policy would benefit from guidelines for the critical evaluation of genetic information to list or delist organisms under the Endangered Species Act. Resumen:,La información genética se está convirtiendo en un factor influyente para determinar sí una especie, subespecie y segmentos poblacionales distintos califican para ser protegidos por el Acta de Especies en Peligro de E. U. A. Sin embargo, actualmente no hay estándares o lineamientos que definan como deben utilizar información genética las agencias federales que administran el acta. Examiné las decisiones de enlistado basadas en información genética tomadas en un período de 10 años (febrero 1996,febrero 2006). Hubo una amplia variación en los datos genéticos utilizados para informar las decisiones de enlistado en términos de cuáles genomas (mitocondrial vs. nuclear) fueron muestreados y el número de marcadores (o técnicas genéticas) y los loci evaluados. En general, las agencias federales identificaron diferencias genéticas entre unidades taxonómicas putativas o poblaciones dependiendo del tipo y cantidad de datos genéticos. Los estudios que se basaron en marcadores genéticos múltiples tuvieron mayor probabilidad de identificar distinciones, y esos organismos tuvieron mayor probabilidad de recibir protección, que los estudios basados en un solo marcador genético. Aunque los resultados pueden, en parte, reflejar la disponibilidad de técnicas genéticas para decisiones de enlistado en el período analizado, el uso variable de información genética para la toma de decisiones puede desinformar acciones de conservación. Las políticas de manejo futuras se beneficiarían de directrices para la evaluación crítica de información genética para enlistar o quitar de la lista a organismos bajo el Acta de Especies en Peligro. [source] Ethical, Legal, and Social Dimensions of Epilepsy GeneticsEPILEPSIA, Issue 10 2006Sara Shostak Summary:,Purpose: Emerging genetic information and the availability of genetic testing has the potential to increase understanding of the disease and improve clinical management of some types of epilepsy. However, genetic testing is also likely to raise significant ethical, legal, and social issues for people with epilepsy, their family members, and their health care providers. We review the genetic and social dimensions of epilepsy relevant to understanding the complex questions raised by epilepsy genetics. Methods: We reviewed two literatures: (a) research on the genetics of epilepsy, and (b) social science research on the social experience and social consequences of epilepsy. For each, we note key empiric findings and discuss their implications with regard to the consequences of emerging genetic information about epilepsy. We also briefly review available principles and guidelines from professional and advocacy groups that might help to direct efforts to ascertain and address the ethical, legal, and social dimensions of genetic testing for epilepsy. Results: Genetic information about epilepsy may pose significant challenges for people with epilepsy and their family members. Although some general resources are available for navigating this complex new terrain, no guidelines specific to epilepsy have yet been developed to assist people with epilepsy, their family members, or their health care providers. Conclusions: Research is needed on the ethical, legal, and social concerns raised by genetic research on epilepsy and the advent of genetic testing. This research should include the perspectives of people with epilepsy and their family members, as well as those of health care professionals, policymakers, and bioethicists. [source] Nurse or physician: whose recommendation influences the decision to take genetic tests more?JOURNAL OF ADVANCED NURSING, Issue 4 2010Sivia Barnoy barnoy s., levy o. & bar-tal y. (2010) Nurse or physician: whose recommendation influences the decision to take genetic tests more? Journal of Advanced Nursing66(4), 806,813. Abstract Title.,Nurse or physician: whose recommendation influences the decision to take genetic tests more? Aim., This paper is a report of a study conducted to explore factors influencing the decision to take genetic carrier testing. Background., Genetic testing has become a popular means of elucidating the risk of giving birth to a sick/disabled child but what influences prospective parents to take genetic tests or not is unclear. Methods., The study was based on a factorial 2 × 2 × 2 within-between subjects design. The questionnaire presented four scenarios, each illustrating a healthcare worker presenting information on a devastating genetic disease. The variables manipulated were: the health care worker's expertise (novice vs. expert), the recommender's role (nurse vs. physician) and type of recommendation (recommendation vs. no recommendation). After each scenario participants were asked their own intention to take the test and their intention to recommend a friend to take the test. Data were collected in 2007. Results., Altogether 156 questionnaires were collected. Expert nurses and expert physicians were accorded the same level of compliance. However, a novice physician's recommendation to take a genetic test was complied with as much as an expert physician's, whereas a novice nurse's recommendation was less accepted than that of an expert nurse. When no recommendation was made, more compliance with the nurse was found (i.e. less intention to take the test). Conclusion., Genetic information should be presented to the public with caution to avoid over-testing. For the public to accept a nurse's recommendation, the nurse has to be perceived as an expert; therefore, expert nurses' proficiency should be made clear. [source] Mitochondrial DNA sequence variation within and between tuna Thunnus species and its application to species identificationJOURNAL OF FISH BIOLOGY, Issue 6 2001H. Takeyama Restriction analysis detected two types of bigeye tuna (, and ,); the , type was in the majority in the Atlantic but nearly absent in the Indo-Pacific. The , type shared a larger number of restriction sites with other species than the conspecific , type, but bigeye-specific nucleotide substitutions with a novel diagnostic restriction profile were found. Although the nucleotide sequence difference between Atlantic and Pacific sub-species of the northern bluefin tuna was nearly the largest among species, individuals possessing the Atlantic type of mtDNA were found at very low frequency in the Pacific and vice versa. Previous RFLP markers were found to be diagnostic for the other five species (albacore, blackfin, longtail, southern bluefin and yellowfin tunas). Genetic information is provided to discriminate all Thunnus species regardless of their origin and to identify the ocean of capture in the northern bluefin and bigeye tunas. [source] What is Genetic Information, and why is it Significant?JOURNAL OF APPLIED PHILOSOPHY, Issue 1 2006A Contextual, Approach, Contrastive abstract Is genetic information of special ethical significance? Does it require special regulation? There is considerable contemporary debate about this question (the ,genetic exceptionalism' debate). ,Genetic information' is an ambiguous term and, as an aid to avoiding conflation in the genetic exceptionalism debate, a detailed account is given of just how and why ,genetic information' is ambiguous. Whilst ambiguity is a ubiquitous problem of communication, it is suggested that ,genetic information' is ambiguous in a particular way, one that gives rise to the problem of ,significance creep' (i.e., where claims about the significance of certain kinds of genetic information in one context influence our thinking about the significance of other kinds of genetic information in other contexts). A contextual and contrastive methodology is proposed: evaluating the significance of genetic information requires us to be sensitive to the polysemy of ,genetic information' across contexts and then examine the contrast in significance (if any) of genetic, as opposed to nongenetic, information within contexts. This, in turn, suggests that a proper solution to the regulatory question requires us to pay more attention to how and why information, and its acquisition, possession and use, come to be of ethical significance. [source] Genetic Data and the Listing of Species Under the U.S. Endangered Species ActCONSERVATION BIOLOGY, Issue 5 2007SYLVIA M. FALLON Acta de Especies en Peligro de E. U. A.; decisiones de enlistado; segmento poblacional distinto Abstract:,Genetic information is becoming an influential factor in determining whether species, subspecies, and distinct population segments qualify for protection under the U.S. Endangered Species Act. Nevertheless, there are currently no standards or guidelines that define how genetic information should be used by the federal agencies that administer the act. I examined listing decisions made over a 10-year period (February 1996,February 2006) that relied on genetic information. There was wide variation in the genetic data used to inform listing decisions in terms of which genomes (mitochondrial vs. nuclear) were sampled and the number of markers (or genetic techniques) and loci evaluated. In general, whether the federal agencies identified genetic distinctions between putative taxonomic units or populations depended on the type and amount of genetic data. Studies that relied on multiple genetic markers were more likely to detect distinctions, and those organisms were more likely to receive protection than studies that relied on a single genetic marker. Although the results may, in part, reflect the corresponding availability of genetic techniques over the given time frame, the variable use of genetic information for listing decisions has the potential to misguide conservation actions. Future management policy would benefit from guidelines for the critical evaluation of genetic information to list or delist organisms under the Endangered Species Act. Resumen:,La información genética se está convirtiendo en un factor influyente para determinar sí una especie, subespecie y segmentos poblacionales distintos califican para ser protegidos por el Acta de Especies en Peligro de E. U. A. Sin embargo, actualmente no hay estándares o lineamientos que definan como deben utilizar información genética las agencias federales que administran el acta. Examiné las decisiones de enlistado basadas en información genética tomadas en un período de 10 años (febrero 1996,febrero 2006). Hubo una amplia variación en los datos genéticos utilizados para informar las decisiones de enlistado en términos de cuáles genomas (mitocondrial vs. nuclear) fueron muestreados y el número de marcadores (o técnicas genéticas) y los loci evaluados. En general, las agencias federales identificaron diferencias genéticas entre unidades taxonómicas putativas o poblaciones dependiendo del tipo y cantidad de datos genéticos. Los estudios que se basaron en marcadores genéticos múltiples tuvieron mayor probabilidad de identificar distinciones, y esos organismos tuvieron mayor probabilidad de recibir protección, que los estudios basados en un solo marcador genético. Aunque los resultados pueden, en parte, reflejar la disponibilidad de técnicas genéticas para decisiones de enlistado en el período analizado, el uso variable de información genética para la toma de decisiones puede desinformar acciones de conservación. Las políticas de manejo futuras se beneficiarían de directrices para la evaluación crítica de información genética para enlistar o quitar de la lista a organismos bajo el Acta de Especies en Peligro. [source] THE MOLECULAR FUTURE IN CYTOLOGYCYTOPATHOLOGY, Issue 2006M. Salto-Tellez Molecular diagnosis is the application of molecular biology techniques and knowledge of the molecular mechanisms of disease to diagnosis, prognostication and treatment of diseases. Molecular Diagnosis is, arguably, the fastest growing area of diagnostic medicine. The US market for molecular testing generated $1.3 billion in 2000, which was predicted to increase to about $4.2 billion by 2007.1 We proposed the term Diagnostic Molecular Cytopathology to define the application of molecular diagnosis to cytopathology2. Diagnostic Molecular Cytopathology is essential for the following reasons: (i) Molecular testing is sometimes indispensable to establish an unequivocal diagnosis on cell preparations; (ii) Molecular testing provides extra information on the prognosis or therapy of diseases diagnosed by conventional cytology; (iii) Molecular testing provides genetic information on the inherited nature of diseases that can be directly investigated in cytology samples, by either exfoliation or by fine needle aspiration; (iv) Sometimes the cytopathology sample is the most convenient (or the only available) source of material for molecular testing; (v). Direct molecular interrogation of cells allows for a diagnostic correlation that would otherwise not be possible. Parallel to this direct diagnostic implication, cytopathology is increasing important in the validation of biomarkers for specific diseases, and in therefore of significant importance in the overall translational research strategies. We illustrate its application in some of the main areas of oncology molecular testing, such as molecular fingerprinting of neoplasms,3 lymphoreticular diseases,2 sarcomas4 and lung cancer,5 as well as translational research using diagnostic cytopathology techniques. The next years will see the consolidation of Diagnostic Molecular Cytopathology, a process that will lead to a change of many paradigms. In general, diagnostic pathology departments will have to reorganize molecular testing to pursue a cost-efficient operation. Sample preparation will have to take into account optimal preservation of nuclear acids. The training of technical staff and the level of laboratory quality control and quality assurance would have to follow strict clinical (not research) laboratory parameters. And, most importantly, those pathologists undertaking molecular diagnosis as a discipline would have to develop their professional expertise within the same framework of fellowships and professional credentials that is offered in other sub-specialties. The price to pay if this effort is not undertaken is too important for the future of diagnostic pathology in general. The increasing characterization of molecular biomarkers with diagnostic, prognostic or therapeutic value is making the analysis of tissue and cell samples prior to treatment a more complex exercise. If cytopathologists and histopathologists allow others to take charge of molecular diagnosis, our overall contribution to the diagnostic process will be diminished. We may not become less important, but we may become less relevant. However, those within the discipline of diagnostic pathology who can combine the clinical background of diseases with the morphological, immunocytochemical and molecular diagnostic interpretation will represent bona fide diagnostic specialists. Such ,molecular cytopathologists' would place themselves at the centre of clinical decision-making. Reference:, 1. Liz Fletcher. Roche leads molecular diagnostics charge. Nature Biotechnol 20, 6,7; 2002 2. Salto-Tellez M and Koay ESC. Molecular Diagnostic Cytopathology - Definitions, Scope and Clinical Utility. Cytopathology 2004; 15:252,255 3. Salto-Tellez M, Zhang D, Chiu LL, Wang SC, Nilsson B, and Koay ESC. Immunocytochemistry Versus Molecular Fingerprinting of Metastases. Cytopathology, 2003 Aug; 14(4):186,90. 4. Chiu LL, Koay SCE, Chan NL and Salto-Tellez M. Molecular Cytopathology: Sequencing of the EWS-WT1 Gene Fusion Transcript in the Peritoneal Effusion of a Patient with Desmoplastic Small Round Cell Tumour. Diagnostic Cytopathology, 2003 Dec; 29(6): 341,3. 5. TM Chin, D Anuar, R Soo, M Salto-Tellez, WQ Li, B Ahmad, SC Lee, BC Goh, K Kawakami, A Segal, B Iacopetta, R Soong. Sensitive and Cost-Effective deptection of epidermal growth factor Receptor Mutations in Small Biopsies by denaturing High Performance Liquid Chromatography. (In press). [source] Psychiatric epidemiology of old age: the H70 study , the NAPE Lecture 2003ACTA PSYCHIATRICA SCANDINAVICA, Issue 1 2004I. Skoog Objective: To describe methodological issues and possibilities in the epidemiology of old age psychiatry using data from the H70 study in Göteborg, Sweden. Method: A representative sample born during 1901,02 was examined at 70, 75, 79, 81, 83, 85, 87, 90, 92, 95, 97, 99 and 100 years of age, another during 1906,07 was examined at 70 and 79 years of age, and samples born between 1922 and 1930 were examined at 70 years of age. The study includes psychiatric examinations and key informant interviews performed by psychiatrists, physical examinations performed by geriatricians, psychometric testings, blood sampling, computerized tomographies of the brain, cerebrospinal fluid analyses, anthropometric measurements, and psychosocial background factors. Results: Mental disorders are found in approximately 30% of the elderly, but is seldom detected or properly treated. Incidence of depression and dementia increases with age. The relationship between blood pressure and Alzheimer's disease is an example of how cross-sectional and longitudinal studies yield completely different results. Brain imaging is an important tool in epidemiologic studies of the elderly to detect silent cerebrovascular disease and other structural brain changes. The high prevalence of psychotic symptoms is an example of the importance to use several sources of information to detect these symptoms. Dementia should be diagnosed in all types of studies in the elderly, as it influences several outcomes such as mortality, blood pressure, and rates of depression. Suicidal feelings are rare in the elderly and are strongly related to mental disorders. Conclusion: Modern epidemiologic studies in population samples should be longitudinal and include assessments of psychosocial risk factors as well as comprehensive sets of biologic markers, such as brain imaging, neurochemical analyses, and genetic information to maximize the contribution that epidemiology can provide to increase our knowledge about the etiology of mental disorders. [source] Ethical, Legal, and Social Dimensions of Epilepsy GeneticsEPILEPSIA, Issue 10 2006Sara Shostak Summary:,Purpose: Emerging genetic information and the availability of genetic testing has the potential to increase understanding of the disease and improve clinical management of some types of epilepsy. However, genetic testing is also likely to raise significant ethical, legal, and social issues for people with epilepsy, their family members, and their health care providers. We review the genetic and social dimensions of epilepsy relevant to understanding the complex questions raised by epilepsy genetics. Methods: We reviewed two literatures: (a) research on the genetics of epilepsy, and (b) social science research on the social experience and social consequences of epilepsy. For each, we note key empiric findings and discuss their implications with regard to the consequences of emerging genetic information about epilepsy. We also briefly review available principles and guidelines from professional and advocacy groups that might help to direct efforts to ascertain and address the ethical, legal, and social dimensions of genetic testing for epilepsy. Results: Genetic information about epilepsy may pose significant challenges for people with epilepsy and their family members. Although some general resources are available for navigating this complex new terrain, no guidelines specific to epilepsy have yet been developed to assist people with epilepsy, their family members, or their health care providers. Conclusions: Research is needed on the ethical, legal, and social concerns raised by genetic research on epilepsy and the advent of genetic testing. This research should include the perspectives of people with epilepsy and their family members, as well as those of health care professionals, policymakers, and bioethicists. [source] CLINICAL STUDY: Predicting the effect of naltrexone and acamprosate in alcohol-dependent patients using genetic indicatorsADDICTION BIOLOGY, Issue 3 2009Wendy Ooteman ABSTRACT Acamprosate and naltrexone are effective medications in the treatment of alcoholism. However, effect sizes are modest. Pharmacogenomics may improve patient-treatment-matching and effect sizes. It is hypothesized that naltrexone exerts its effect through genetic characteristics associated with the dopaminergic/opioidergic positive reinforcement system, whereas acamprosate works through the glutamatergic/GABAergic negative reinforcement system. Alcohol-dependent subjects were randomly assigned to either acamprosate or naltrexone. Subjects participated in a cue-exposure experiment at the day before and at the last day of medication. Reductions in cue-induced craving and physiological cue reactivity were measured. Differential effects of naltrexone and acamprosate on these outcomes were tested for different polymorphisms of the opioid, dopamine, glutamate and GABA-receptors. Significant matching effects were found for polymorphisms at the DRD2, GABRA6 and GABRB2 gene. In addition, a trend was found for the OPRM1 polymorphism. This provides evidence for the matching potential of genotypes. It is expected that more effective treatments can be offered when genetic information is used in patient-treatment-matching. [source] Heterologous expression and characterization of the exopolysaccharide from Streptococcus thermophilus Sfi39FEBS JOURNAL, Issue 19 2001Jacques-Edouard Germond The genes responsible for exopolysaccharide (EPS) synthesis in Streptococcus thermophilus Sfi39 were identified on a 20-kb genomic fragment. The two genes, epsE and epsG, were shown to be involved in EPS synthesis as their disruption lead to the loss of the ropy phenotype. Several naturally selected nonropy mutants were isolated, one acquired an insertion sequence (IS)-element (IS905) in the middle of the eps gene cluster. The eps gene cluster was cloned and transferred into a nonEPS-producing heterologous host, Lactococcus lactis MG1363. The EPS produced was shown by chemical analysis and NMR spectroscopy to be identical to the EPS produced by S. thermophilus Sfi39. This demonstrated first that all genes needed for EPS production and export were present in the S. thermophilus Sfi39 eps gene cluster, and second that the heterologous production of an EPS was possible by transfer of the complete eps gene cluster alone, provided that the heterologous host possessed all necessary genetic information for precursor synthesis. [source] Shuffling genes around in hot environments: the unique DNA transporter of Thermus thermophilusFEMS MICROBIOLOGY REVIEWS, Issue 3 2009Beate Averhoff Abstract Natural transformation permits the transport of DNA through bacterial membranes and represents a dominant mode for the transfer of genetic information between bacteria and between microorganisms of distant evolutionary lineages and even between members of different domains. This phenomenon, known as horizontal, or lateral, gene transfer, has been a major force for genome plasticity over evolutionary history, and is largely responsible for the spread of fitness-enhancing traits, including antibiotic resistance and virulence factors. In particular, for adaptation of prokaryotes to extreme environments, lateral gene transfer seems to have played a crucial role. Here, we present a survey of the natural transformation machinery of the thermophile Thermus thermophilus HB27. A tentative model of the transformation machinery comprising of components similar to proteins of type IV pili and type II secretion systems is presented. A comparative discussion of the subunits and the structure of the DNA translocator and the underlying mechanism of transfer of free DNA in T. thermophilus highlights conserved and unique features of the DNA translocator in T. thermophilus. We hypothesize that the extraordinary broad substrate specificity and the high efficiency of the T. thermophilus DNA uptake system is of major importance for thermoadaptation and interdomain DNA transfer in hot environments. [source] Histone modifications and chromatin dynamics: a focus on filamentous fungiFEMS MICROBIOLOGY REVIEWS, Issue 3 2008Gerald Brosch Abstract The readout of the genetic information of eukaryotic organisms is significantly regulated by modifications of DNA and chromatin proteins. Chromatin alterations induce genome-wide and local changes in gene expression and affect a variety of processes in response to internal and external signals during growth, differentiation, development, in metabolic processes, diseases, and abiotic and biotic stresses. This review aims at summarizing the roles of histone H1 and the acetylation and methylation of histones in filamentous fungi and links this knowledge to the huge body of data from other systems. Filamentous fungi show a wide range of morphologies and have developed a complex network of genes that enables them to use a great variety of substrates. This fact, together with the possibility of simple and quick genetic manipulation, highlights these organisms as model systems for the investigation of gene regulation. However, little is still known about regulation at the chromatin level in filamentous fungi. Understanding the role of chromatin in transcriptional regulation would be of utmost importance with respect to the impact of filamentous fungi in human diseases and agriculture. The synthesis of compounds (antibiotics, immunosuppressants, toxins, and compounds with adverse effects) is also likely to be regulated at the chromatin level. [source] Evidence for cyanophages active against bloom-forming freshwater cyanobacteriaFRESHWATER BIOLOGY, Issue 6 2008LI DENG Summary 1. A total of 35 putative cyanophages able to infect non-axenic cultures of bloom-forming freshwater cyanobacteria in the genera Microcystis, Anabaena and Planktothrix were isolated from Lake Zurich (Switzerland) and lakes in the Cotswold Water Park (U.K.). Eleven lytic cyanophage isolates were isolated on Microcystis and 12 each on Anabaena and Planktothrix. Cyanophage isolation protocols varied when using these different cyanobacterial hosts. 2. The collection of putative cyanophage isolates encompassed a variety of morphotypes, including the first filamentous cyanophage from any environment and the second siphocyanophage reported from fresh water. 3. PCR primer sets for gp20, gp23 and MCP genes, which have been previously found to be conserved in other cyanophages, were used in an attempt to determine genetic diversity among the phage isolates. The failure to obtain specific amplification products from most isolates suggests that the cyanophages isolated in this study were different from those previously characterized from both marine and freshwater environments. 4. Some putative cyanophages within the collection of isolates proved to have a very broad host range and were able to infect Anabaena, Microcystis and Planktothrix. The ability to infect a wide range of host taxa extends the potential reproductive period for lytic propagation, and also has implications for the transfer of genetic information between deeply separated cyanobacterial lineages. [source] VDE-initiated intein homing in Saccharomyces cerevisiae proceeds in a meiotic recombination-like mannerGENES TO CELLS, Issue 7 2003Tomoyuki Fukuda Background: Inteins and group I introns found in prokaryotic and eukaryotic organisms occasionally behave as mobile genetic elements. During meiosis of the yeast Saccharomyces cerevisiae, the site-specific endonuclease encoded by VMA1 intein, VDE, triggers a single double-strand break (DSB) at an inteinless allele, leading to VMA1 intein homing. Besides the accumulating information on the in vitro activity of VDE, very little has been known about the molecular mechanism of intein homing in yeast nucleus. Results: We developed an assay to detect the product of VMA1 intein homing in yeast genome. We analysed mutant phenotypes of RecA homologs, Rad51p and Dmc1p, and their interacting proteins, Rad54p and Tid1p, and found that they all play critical roles in intein inheritance. The absence of DSB end processing proteins, Sae2p and those in the Mre11-Rad50-Xrs2 complex, also causes partial reduction in homing efficiency. As with meiotic recombination, crossover events are frequently observed during intein homing. We also observed that the absence of premeiotic DNA replication caused by hydroxyurea (HU) or clb5, clb6, mutation reduces VDE-mediated DSBs. Conclusion: The repairing system working in intein homing shares molecular machinery with meiotic recombination induced by Spo11p. Moreover, like Spo11p-induced DNA cleavage, premeiotic DNA replication is a prerequisite for a VDE-induced DSB. VMA1 intein thus utilizes several host factors involved in meiotic and recombinational processes to spread its genetic information and guarantee its progeny through establishment of a parasitic relationship with the organism. [source] Improved association analyses of disease subtypes in case-parent triadsGENETIC EPIDEMIOLOGY, Issue 3 2006Michael P. Epstein Abstract The sampling of case-parent triads is an appealing strategy for conducting association analyses of complex diseases. In certain situations, one may have interest in using the triads to identify genetic variants that are associated with a specific subtype of disease, perhaps related to a characteristic cluster of symptoms. A straightforward strategy for conducting such a subtype analysis would be to analyze only those triads with the subtype of interest. While such a strategy is valid, we show that triads without the subtype of interest can provide additional genetic information that increases power to detect association with the subtype of interest. We incorporate this additional information using a likelihood-based framework that permits flexible modeling and estimation of allelic effects on disease subtypes and also allows for missing parental data. Using simulated data under a variety of genetic models, we show that our proposed association test consistently outperforms association tests that only analyze triads with the subtype of interest. We also apply our method to a triad study of attention-deficit hyperactivity disorder and identify a genetic variant in the dopamine transporter gene that is associated with a subtype characterized by extreme levels of both inattentive and hyperactive-impulsive symptoms. Genet. Epidemiol. 2006. © 2006 Wiley-Liss, Inc. [source] Limits of fine-mapping a quantitative traitGENETIC EPIDEMIOLOGY, Issue 2 2003Larry D. Atwood Abstract Once a significant linkage is found, an important goal is reducing the error in the estimated location of the linked locus. A common approach to reducing location error, called fine-mapping, is the genotyping of additional markers in the linked region to increase the genetic information. The utility of fine-mapping for quantitative trait linkage analysis is largely unknown. To explore this issue, we performed a fine-mapping simulation in which the region containing a significant linkage at a 10-centiMorgan (cM) resolution was fine-mapped at 2, 1, and 0.5 cM. We simulated six quantitative trait models in which the proportion of variation due to the quantitative trait locus (QTL) ranged from 0.20,0.90. We used four sampling designs that were all combinations of 100 and 200 families of sizes 5 and 7. Variance components linkage analysis (Genehunter) was performed until 1,000 replicates were found with a maximum lodscore greater than 3.0. For each of these 1,000 replications, we repeated the linkage analysis three times: once for each of the fine-map resolutions. For the most realistic model, reduction in the average location error ranged from 3,15% for 2-cM fine-mapping and from 3,18% for 1-cM fine-mapping, depending on the number of families and family size. Fine-mapping at 0.5 cM did not differ from the 1-cM results. Thus, if the QTL accounts for a small proportion of the variation, as is the case for realistic traits, fine-mapping has little value. Genet Epidemiol 24:99,106, 2003. © 2003 Wiley-Liss, Inc. [source] Combining fMRI and SNP data to investigate connections between brain function and genetics using parallel ICA,HUMAN BRAIN MAPPING, Issue 1 2009Jingyu Liu Abstract There is current interest in understanding genetic influences on both healthy and disordered brain function. We assessed brain function with functional magnetic resonance imaging (fMRI) data collected during an auditory oddball task,detecting an infrequent sound within a series of frequent sounds. Then, task-related imaging findings were utilized as potential intermediate phenotypes (endophenotypes) to investigate genomic factors derived from a single nucleotide polymorphism (SNP) array. Our target is the linkage of these genomic factors to normal/abnormal brain functionality. We explored parallel independent component analysis (paraICA) as a new method for analyzing multimodal data. The method was aimed to identify simultaneously independent components of each modality and the relationships between them. When 43 healthy controls and 20 schizophrenia patients, all Caucasian, were studied, we found a correlation of 0.38 between one fMRI component and one SNP component. This fMRI component consisted mainly of parietal lobe activations. The relevant SNP component was contributed to significantly by 10 SNPs located in genes, including those coding for the nicotinic ,-7cholinergic receptor, aromatic amino acid decarboxylase, disrupted in schizophrenia 1, among others. Both fMRI and SNP components showed significant differences in loading parameters between the schizophrenia and control groups (P = 0.0006 for the fMRI component; P = 0.001 for the SNP component). In summary, we constructed a framework to identify interactions between brain functional and genetic information; our findings provide a proof-of-concept that genomic SNP factors can be investigated by using endophenotypic imaging findings in a multivariate format. Hum Brain Mapp, 2009. © 2007 Wiley-Liss, Inc. [source] Detection of single nucleotide substitution by competitive allele-specific short oligonucleotide hybridization (CASSOH) with immunochromatographic strip,HUMAN MUTATION, Issue 2 2003Yoichi Matsubara Abstract Recent advances in human genome research have revealed that genetic polymorphisms, such as single nucleotide polymorphisms (SNPs), are closely associated with susceptibility to various common diseases and adverse drug reactions. Also, numerous mutations responsible for a number of genetic diseases have been identified. Clinical application of genetic information to individual health care requires simple and rapid identification of nucleotide changes in clinical settings. We have devised a novel low-tech method for the detection of a single nucleotide substitution using competitive allele-specific short oligonucleotide hybridization with immunochromatographic strip. The gene of interest is PCR-amplified, hybridized to an allele-specific short oligonucleotide probe in the presence of a competitive oligonucleotide, and subjected to chromatography using a DNA test strip at room temperature. The genotype is unambiguously determined by the presence or the absence of visible purple lines on a strip. Feasibility of the method was demonstrated by the detection of a prevalent disease-causing mutations in glycogen storage disease type Ia (G6PC), medium-chain acyl-CoA dehydrogenase deficiency (ACADM), non-ketotic hyperglycinemia (GLDC), and clinically important polymorphisms in the CYP2C19 gene and the aldehyde dehydrogenase 2 gene (ALDH2). The procedure does not demand either technical expertise or expensive instruments and is readily performed in local clinical laboratories. The result is obtained within 10 min after PCR. This rapid and simple method of SNP detection may be used for point-of-care genetic diagnosis with potentially diverse clinical applications. Hum Mutat 22:166,172, 2003. © 2003 Wiley-Liss, Inc. [source] Study on VNTR polymorphism of gene IL-1RA in 19 Chinese populationsINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 2 2010J. Jiang Summary Earlier studies suggested that a variable number tandem repeat (VNTR) polymorphism in intron 2 of the interleukin-1 receptor antagonist (IL-1RA) gene might be associated with some chronic inflammatory diseases, autoimmune diseases and solid tumours. To study the distribution of this polymorphism in China, 1352 samples were collected from 19 widely distributed Chinese populations. PCR was used to genotype the VNTR. The overall frequencies of allele 1 and allele 2 were 0.913 and 0.064 respectively. The frequency of the allele 2 was significantly different between the northeastern and the northwestern populations. Moreover, the allele frequencies at this locus in three Chinese Han populations were different from that in minority populations. When compared with other populations worldwide, the frequencies of the two alleles in China were not significantly different from those in the Asian and Pacific Islands. However, the prevalence of allele 1 in China was significantly higher, and the prevalence of allele 2 was significantly lower, than those in American and European Caucasians, and the pairwise Fst values reinforced this observation. The differences of the allele frequencies between different regions and within the same region showed that geography and race have important roles in the population differentiation for the IL-1RA gene. In summary, our results provide a valuable reference for population genetic information and future disease association studies in Chinese populations. [source] Reproductive stem cell research and its application to urologyINTERNATIONAL JOURNAL OF UROLOGY, Issue 2 2008Takehiko Ogawa Abstract: Germ cells are defined by their innate potential to transmit genetic information to the next generation through fertilization. Males produce numerous sperm for long periods to maximize chances of fertilization. Key to the continuous production of large numbers of sperm are germline stem cells and their immediate daughter cells, functioning as transit amplifying cells. Recently, it has become possible to expand germline stem cells of rodents in vitro. In addition, multipotent stem cells, which are functionally the same as embryonic stem cells, have been established from neonatal mouse testes. These stem cells derived from the testis should contribute to biological research and technologies. On the other hand, the nature of human spermatogenesis is largely unknown due to the lack of an appropriate experimental system. However, the prevailing testicular sperm extraction procedure unraveled hitherto unknown facets of human spermatogenesis. The establishment of a culturing method for human spermatogonial stem cells in hopefully the near future would be a great benefit for achieving further insight into human spermatogenesis and should lead to more sophisticated diagnostic and therapeutic clinical measures for male infertility. [source] A multimodal, multidimensional atlas of the C57BL/6J mouse brainJOURNAL OF ANATOMY, Issue 2 2004Allan MacKenzie-Graham Abstract Strains of mice, through breeding or the disruption of normal genetic pathways, are widely used to model human diseases. Atlases are an invaluable aid in understanding the impact of such manipulations by providing a standard for comparison. We have developed a digital atlas of the adult C57BL/6J mouse brain as a comprehensive framework for storing and accessing the myriad types of information about the mouse brain. Our implementation was constructed using several different imaging techniques: magnetic resonance microscopy, blockface imaging, classical histology and immunohistochemistry. Along with raw and annotated images, it contains database management systems and a set of tools for comparing information from different techniques. The framework allows facile correlation of results from different animals, investigators or laboratories by establishing a canonical representation of the mouse brain and providing the tools for the insertion of independent data into the same space as the atlas. This tool will aid in managing the increasingly complex and voluminous amounts of information about the mammalian brain. It provides a framework that encompasses genetic information in the context of anatomical imaging and holds tremendous promise for producing new insights into the relationship between genotype and phenotype. We describe a suite of tools that enables the independent entry of other types of data, facile retrieval of information and straightforward display of images. Thus, the atlas becomes a framework for managing complex genetic and epigenetic information about the mouse brain. The atlas and associated tools may be accessed at http://www.loni.ucla.edu/MAP. [source] | ||||||||||||||||||||||||||||||||||||||||||||||