EMERGY METHODS: VALUABLE INTEGRATED ASSESSMENT TOOLS

EPA Science Inventory

NHEERL's Atlantic Ecology Division is investigating emergy methods as tools for integrated assessment in several projects evaluating environmental impacts, policies, and alternatives for remediation and intervention. Emergy accounting is a methodology that provides a quantitative...

CRISPR: a Versatile Tool for Both Forward and Reverse Genetics Research

PubMed Central

Gurumurthy, Channabasavaiah B.; Grati, M'hamed; Ohtsuka, Masato; Schilit, Samantha L.P.; Quadros, Rolen M.; Liu, Xue Zhong

2016-01-01

Human genetics research employs the two opposing approaches of forward and reverse genetics. While forward genetics identifies and links a mutation to an observed disease etiology, reverse genetics induces mutations in model organisms to study their role in disease. In most cases, causality for mutations identified by forward genetics is confirmed by reverse genetics through the development of genetically engineered animal models and an assessment of whether the model can recapitulate the disease. While many technological advances have helped improve these approaches, some gaps still remain. CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated) system, which has emerged as a revolutionary genetic engineering tool, holds great promise for closing such gaps. By combining the benefits of forward and reverse genetics, it has dramatically expedited human genetics research. We provide a perspective on the power of CRISPR-based forward and reverse genetics tools in human genetics and discuss its applications using some disease examples. PMID:27384229

The GMOseek matrix: a decision support tool for optimizing the detection of genetically modified plants

PubMed Central

2013-01-01

Background Since their first commercialization, the diversity of taxa and the genetic composition of transgene sequences in genetically modified plants (GMOs) are constantly increasing. To date, the detection of GMOs and derived products is commonly performed by PCR-based methods targeting specific DNA sequences introduced into the host genome. Information available regarding the GMOs’ molecular characterization is dispersed and not appropriately organized. For this reason, GMO testing is very challenging and requires more complex screening strategies and decision making schemes, demanding in return the use of efficient bioinformatics tools relying on reliable information. Description The GMOseek matrix was built as a comprehensive, online open-access tabulated database which provides a reliable, comprehensive and user-friendly overview of 328 GMO events and 247 different genetic elements (status: 18/07/2013). The GMOseek matrix is aiming to facilitate GMO detection from plant origin at different phases of the analysis. It assists in selecting the targets for a screening analysis, interpreting the screening results, checking the occurrence of a screening element in a group of selected GMOs, identifying gaps in the available pool of GMO detection methods, and designing a decision tree. The GMOseek matrix is an independent database with effective functionalities in a format facilitating transferability to other platforms. Data were collected from all available sources and experimentally tested where detection methods and certified reference materials (CRMs) were available. Conclusions The GMOseek matrix is currently a unique and very valuable tool with reliable information on GMOs from plant origin and their present genetic elements that enables further development of appropriate strategies for GMO detection. It is flexible enough to be further updated with new information and integrated in different applications and platforms. PMID:23965170

3D-Printed specimens as a valuable tool in anatomy education: A pilot study.

PubMed

Garas, Monique; Vaccarezza, Mauro; Newland, George; McVay-Doornbusch, Kylie; Hasani, Jamila

2018-06-06

Three-dimensional (3D) printing is a modern technique of creating 3D-printed models that allows reproduction of human structures from MRI and CT scans via fusion of multiple layers of resin materials. To assess feasibility of this innovative resource as anatomy educational tool, we conducted a preliminary study on Curtin University undergraduate students to investigate the use of 3D models for anatomy learning as a main goal, to assess the effectiveness of different specimen types during the sessions and personally preferred anatomy learning tools among students as secondary aim. The study consisted of a pre-test, exposure to test (anatomical test) and post-test survey. During pre-test, all participants (both without prior experience and experienced groups) were given a brief introduction on laboratory safety and study procedure thus participants were exposed to 3D, wet and plastinated specimens of the heart, shoulder and thigh to identify the pinned structures (anatomical test). Then, participants were provided a post-test survey containing five questions. In total, 23 participants completed the anatomical test and post-test survey. A larger number of participants (85%) achieved right answers for 3D models compared to wet and plastinated materials, 74% of population selected 3D models as the most usable tool for identification of pinned structures and 45% chose 3D models as their preferred method of anatomy learning. This preliminary small-size study affirms the feasibility of 3D-printed models as a valuable asset in anatomy learning and shows their capability to be used adjacent to cadaveric materials and other widely used tools in anatomy education. Copyright © 2018 Elsevier GmbH. All rights reserved.

Professional regulation: a potentially valuable tool in responding to "stem cell tourism".

PubMed

Zarzeczny, Amy; Caulfield, Timothy; Ogbogu, Ubaka; Bell, Peter; Crooks, Valorie A; Kamenova, Kalina; Master, Zubin; Rachul, Christen; Snyder, Jeremy; Toews, Maeghan; Zoeller, Sonja

2014-09-09

The growing international market for unproven stem cell-based interventions advertised on a direct-to-consumer basis over the internet ("stem cell tourism") is a source of concern because of the risks it presents to patients as well as their supporters, domestic health care systems, and the stem cell research field. Emerging responses such as public and health provider-focused education and national regulatory efforts are encouraging, but the market continues to grow. Physicians play a number of roles in the stem cell tourism market and, in many jurisdictions, are members of a regulated profession. In this article, we consider the use of professional regulation to address physician involvement in stem cell tourism. Although it is not without its limitations, professional regulation is a potentially valuable tool that can be employed in response to problematic types of physician involvement in the stem cell tourism market. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Professional Regulation: A Potentially Valuable Tool in Responding to “Stem Cell Tourism”

PubMed Central

Zarzeczny, Amy; Caulfield, Timothy; Ogbogu, Ubaka; Bell, Peter; Crooks, Valorie A.; Kamenova, Kalina; Master, Zubin; Rachul, Christen; Snyder, Jeremy; Toews, Maeghan; Zoeller, Sonja

2014-01-01

The growing international market for unproven stem cell-based interventions advertised on a direct-to-consumer basis over the internet (“stem cell tourism”) is a source of concern because of the risks it presents to patients as well as their supporters, domestic health care systems, and the stem cell research field. Emerging responses such as public and health provider-focused education and national regulatory efforts are encouraging, but the market continues to grow. Physicians play a number of roles in the stem cell tourism market and, in many jurisdictions, are members of a regulated profession. In this article, we consider the use of professional regulation to address physician involvement in stem cell tourism. Although it is not without its limitations, professional regulation is a potentially valuable tool that can be employed in response to problematic types of physician involvement in the stem cell tourism market. PMID:25241736

Genetic Simulation Tools for Post-Genome Wide Association Studies of Complex Diseases

PubMed Central

Amos, Christopher I.; Bafna, Vineet; Hauser, Elizabeth R.; Hernandez, Ryan D.; Li, Chun; Liberles, David A.; McAllister, Kimberly; Moore, Jason H.; Paltoo, Dina N.; Papanicolaou, George J.; Peng, Bo; Ritchie, Marylyn D.; Rosenfeld, Gabriel; Witte, John S.

2014-01-01

Genetic simulation programs are used to model data under specified assumptions to facilitate the understanding and study of complex genetic systems. Standardized data sets generated using genetic simulation are essential for the development and application of novel analytical tools in genetic epidemiology studies. With continuing advances in high-throughput genomic technologies and generation and analysis of larger, more complex data sets, there is a need for updating current approaches in genetic simulation modeling. To provide a forum to address current and emerging challenges in this area, the National Cancer Institute (NCI) sponsored a workshop, entitled “Genetic Simulation Tools for Post-Genome Wide Association Studies of Complex Diseases” at the National Institutes of Health (NIH) in Bethesda, Maryland on March 11-12, 2014. The goals of the workshop were to: (i) identify opportunities, challenges and resource needs for the development and application of genetic simulation models; (ii) improve the integration of tools for modeling and analysis of simulated data; and (iii) foster collaborations to facilitate development and applications of genetic simulation. During the course of the meeting the group identified challenges and opportunities for the science of simulation, software and methods development, and collaboration. This paper summarizes key discussions at the meeting, and highlights important challenges and opportunities to advance the field of genetic simulation. PMID:25371374

Genetic Tools for the Industrially Promising Methanotroph Methylomicrobium buryatense

DOE Office of Scientific and Technical Information (OSTI.GOV)

Puri, AW; Owen, S; Chu, F

2015-02-10

Aerobic methanotrophs oxidize methane at ambient temperatures and pressures and are therefore attractive systems for methane-based bioconversions. In this work, we developed and validated genetic tools for Methylomicrobium buryatense, a haloalkaliphilic gammaproteobacterial (type I) methanotroph. M. buryatense was isolated directly on natural gas and grows robustly in pure culture with a 3-h doubling time, enabling rapid genetic manipulation compared to many other methanotrophic species. As a proof of concept, we used a sucrose counterselection system to eliminate glycogen production in M. buryatense by constructing unmarked deletions in two redundant glycogen synthase genes. We also selected for a more genetically tractablemore » variant strain that can be conjugated with small incompatibility group P (IncP)-based broad-host-range vectors and determined that this capability is due to loss of the native plasmid. These tools make M. buryatense a promising model system for studying aerobic methanotroph physiology and enable metabolic engineering in this bacterium for industrial biocatalysis of methane.« less

Genetic basis in motor skill and hand preference for tool use in chimpanzees (Pan troglodytes).

PubMed

Hopkins, William D; Reamer, Lisa; Mareno, Mary Catherine; Schapiro, Steven J

2015-02-07

Chimpanzees are well known for their tool using abilities. Numerous studies have documented variability in tool use among chimpanzees and the role that social learning and other factors play in their development. There are also findings on hand use in both captive and wild chimpanzees; however, less understood are the potential roles of genetic and non-genetic mechanisms in determining individual differences in tool use skill and laterality. Here, we examined heritability in tool use skill and handedness for a probing task in a sample of 243 captive chimpanzees. Quantitative genetic analysis, based on the extant pedigrees, showed that overall both tool use skill and handedness were significantly heritable. Significant heritability in motor skill was evident in two genetically distinct populations of apes, and between two cohorts that received different early social rearing experiences. We further found that motor skill decreased with age and that males were more commonly left-handed than females. Collectively, these data suggest that though non-genetic factors do influence tool use performance and handedness in chimpanzees, genetic factors also play a significant role, as has been reported in humans. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Personalized genetic testing as a tool for integrating ethics instruction into biology courses.

PubMed

Zhang, Tenny R; Anderson, Misti Ault

2014-12-01

Personalized genetic testing (PGT) has been used by some educational institutions as a pedagogical tool for teaching human genetics. While work has been done that examines the potential for PGT to improve students' interest and understanding of the science involved in genetic testing, there has been less dialogue about how this method might be useful for integrating ethical and societal issues surrounding genetic testing into classroom discussions. Citing the importance of integrating ethics into the biology classroom, we argue that PGT can be an effective educational tool for integrating ethics and science education, and discuss relevant ethical considerations for instructors using this approach.

Introduction to metabolic genetic engineering for the production of valuable secondary metabolites in in vivo and in vitro plant systems.

PubMed

Benedito, Vagner A; Modolo, Luzia V

2014-01-01

Plants are capable of producing a myriad of chemical compounds. While these compounds serve specific functions in the plant, many have surprising effects on the human body, often with positive action against diseases. These compounds are often difficult to synthesize ex vivo and require the coordinated and compartmentalized action of enzymes in living organisms. However, the amounts produced in whole plants are often small and restricted to single tissues of the plant or even cellular organelles, making their extraction an expensive process. Since most natural products used in therapeutics are specialized, secondary plant metabolites, we provide here an overview of the classification of the main classes of these compounds, with its biochemical pathways and how this information can be used to create efficient in and ex planta production pipelines to generate highly valuable compounds. Metabolic genetic engineering is introduced in light of physiological and genetic methods to enhance production of high-value plant secondary metabolites.

Mutation extraction tools can be combined for robust recognition of genetic variants in the literature

PubMed Central

Jimeno Yepes, Antonio; Verspoor, Karin

2014-01-01

As the cost of genomic sequencing continues to fall, the amount of data being collected and studied for the purpose of understanding the genetic basis of disease is increasing dramatically. Much of the source information relevant to such efforts is available only from unstructured sources such as the scientific literature, and significant resources are expended in manually curating and structuring the information in the literature. As such, there have been a number of systems developed to target automatic extraction of mutations and other genetic variation from the literature using text mining tools. We have performed a broad survey of the existing publicly available tools for extraction of genetic variants from the scientific literature. We consider not just one tool but a number of different tools, individually and in combination, and apply the tools in two scenarios. First, they are compared in an intrinsic evaluation context, where the tools are tested for their ability to identify specific mentions of genetic variants in a corpus of manually annotated papers, the Variome corpus. Second, they are compared in an extrinsic evaluation context based on our previous study of text mining support for curation of the COSMIC and InSiGHT databases. Our results demonstrate that no single tool covers the full range of genetic variants mentioned in the literature. Rather, several tools have complementary coverage and can be used together effectively. In the intrinsic evaluation on the Variome corpus, the combined performance is above 0.95 in F-measure, while in the extrinsic evaluation the combined recall performance is above 0.71 for COSMIC and above 0.62 for InSiGHT, a substantial improvement over the performance of any individual tool. Based on the analysis of these results, we suggest several directions for the improvement of text mining tools for genetic variant extraction from the literature. PMID:25285203

Personalized Genetic Testing as a Tool for Integrating Ethics Instruction into Biology Courses

PubMed Central

Zhang, Tenny R.; Anderson, Misti Ault

2014-01-01

Personalized genetic testing (PGT) has been used by some educational institutions as a pedagogical tool for teaching human genetics. While work has been done that examines the potential for PGT to improve students’ interest and understanding of the science involved in genetic testing, there has been less dialogue about how this method might be useful for integrating ethical and societal issues surrounding genetic testing into classroom discussions. Citing the importance of integrating ethics into the biology classroom, we argue that PGT can be an effective educational tool for integrating ethics and science education, and discuss relevant ethical considerations for instructors using this approach. PMID:25574278

MALDI TOF imaging mass spectrometry in clinical pathology: a valuable tool for cancer diagnostics (review).

PubMed

Kriegsmann, Jörg; Kriegsmann, Mark; Casadonte, Rita

2015-03-01

Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) imaging mass spectrometry (IMS) is an evolving technique in cancer diagnostics and combines the advantages of mass spectrometry (proteomics), detection of numerous molecules, and spatial resolution in histological tissue sections and cytological preparations. This method allows the detection of proteins, peptides, lipids, carbohydrates or glycoconjugates and small molecules.Formalin-fixed paraffin-embedded tissue can also be investigated by IMS, thus, this method seems to be an ideal tool for cancer diagnostics and biomarker discovery. It may add information to the identification of tumor margins and tumor heterogeneity. The technique allows tumor typing, especially identification of the tumor of origin in metastatic tissue, as well as grading and may provide prognostic information. IMS is a valuable method for the identification of biomarkers and can complement histology, immunohistology and molecular pathology in various fields of histopathological diagnostics, especially with regard to identification and grading of tumors.

Genetic Engineering: A Promising Tool to Engender Physiological, Biochemical, and Molecular Stress Resilience in Green Microalgae

PubMed Central

Guihéneuf, Freddy; Khan, Asif; Tran, Lam-Son P.

2016-01-01

As we march into the 21st century, the prevailing scenario of depleting energy resources, global warming and ever increasing issues of human health and food security will quadruple. In this context, genetic and metabolic engineering of green microalgae complete the quest toward a continuum of environmentally clean fuel and food production. Evolutionarily related, but unlike land plants, microalgae need nominal land or water, and are best described as unicellular autotrophs using light energy to fix atmospheric carbon dioxide (CO2) into algal biomass, mitigating fossil CO2 pollution in the process. Remarkably, a feature innate to most microalgae is synthesis and accumulation of lipids (60–65% of dry weight), carbohydrates and secondary metabolites like pigments and vitamins, especially when grown under abiotic stress conditions. Particularly fruitful, such an application of abiotic stress factors such as nitrogen starvation, salinity, heat shock, etc., can be used in a biorefinery concept for production of multiple valuable products. The focus of this mini-review underlies metabolic reorientation practices and tolerance mechanisms as applied to green microalgae under specific stress stimuli for a sustainable pollution-free future. Moreover, we entail current progress on genetic engineering as a promising tool to grasp adaptive processes for improving strains with potential biotechnological interests. PMID:27066043

Applying Genomic and Genetic Tools to Understand and Mitigate Damage from Exposure to Toxins

DTIC Science & Technology

2013-10-01

sequences to the human genome . Genome Biol 10, R25 (2009). 26 Award number: W81XWH-09-1-0715 Title: Applying Genomic and Genetic Tools to Understand...utilizing the high-throughput technology of mRNA-seq. BODY The goal of our research program (W81XWH-09-1-0715) was to utilize genetic and genomic ...also acquired the achetf222a * * * * * 5 Award number: W81XWH-09-1-0715 Title: Applying Genomic and Genetic Tools to Understand and Mitigate

Moving Genetic Biomonitoring from a Concept to a Tool

EPA Science Inventory

Molecular genetic techniques like DNA barcoding and environmental DNA have been proposed as tools for aquatic biomonitoring for nearly a decade, but have yet to break through into widespread acceptance. The potential benefits of these methods, such as quicker, cheaper, more detai...

MetaGenyo: a web tool for meta-analysis of genetic association studies.

PubMed

Martorell-Marugan, Jordi; Toro-Dominguez, Daniel; Alarcon-Riquelme, Marta E; Carmona-Saez, Pedro

2017-12-16

Genetic association studies (GAS) aims to evaluate the association between genetic variants and phenotypes. In the last few years, the number of this type of study has increased exponentially, but the results are not always reproducible due to experimental designs, low sample sizes and other methodological errors. In this field, meta-analysis techniques are becoming very popular tools to combine results across studies to increase statistical power and to resolve discrepancies in genetic association studies. A meta-analysis summarizes research findings, increases statistical power and enables the identification of genuine associations between genotypes and phenotypes. Meta-analysis techniques are increasingly used in GAS, but it is also increasing the amount of published meta-analysis containing different errors. Although there are several software packages that implement meta-analysis, none of them are specifically designed for genetic association studies and in most cases their use requires advanced programming or scripting expertise. We have developed MetaGenyo, a web tool for meta-analysis in GAS. MetaGenyo implements a complete and comprehensive workflow that can be executed in an easy-to-use environment without programming knowledge. MetaGenyo has been developed to guide users through the main steps of a GAS meta-analysis, covering Hardy-Weinberg test, statistical association for different genetic models, analysis of heterogeneity, testing for publication bias, subgroup analysis and robustness testing of the results. MetaGenyo is a useful tool to conduct comprehensive genetic association meta-analysis. The application is freely available at http://bioinfo.genyo.es/metagenyo/ .

Genetic tool development and systemic regulation in biosynthetic technology.

PubMed

Dai, Zhongxue; Zhang, Shangjie; Yang, Qiao; Zhang, Wenming; Qian, Xiujuan; Dong, Weiliang; Jiang, Min; Xin, Fengxue

2018-01-01

With the increased development in research, innovation, and policy interest in recent years, biosynthetic technology has developed rapidly, which combines engineering, electronics, computer science, mathematics, and other disciplines based on classical genetic engineering and metabolic engineering. It gives a wider perspective and a deeper level to perceive the nature of life via cell mechanism, regulatory networks, or biological evolution. Currently, synthetic biology has made great breakthrough in energy, chemical industry, and medicine industries, particularly in the programmable genetic control at multiple levels of regulation to perform designed goals. In this review, the most advanced and comprehensive developments achieved in biosynthetic technology were represented, including genetic engineering as well as synthetic genomics. In addition, the superiority together with the limitations of the current genome-editing tools were summarized.

Malus sieversii, a valuable genetic resource for disease resistance in apple

USDA-ARS?s Scientific Manuscript database

Domesticated crop cultivars inevitably represent a subset of the genetic variation found in their wild ancestors (progenitors) due to genetic bottlenecks that result during the process of crop domestication. Malus sieversii, a wild apple species native to Central Asia, is one of the ancestral proge...

Microbial population Diversity of indigenous acidophilic bacteria for recovering the valuable resources

NASA Astrophysics Data System (ADS)

Kim, B.; Cho, K.; Lee, D.; Choi, N.; Park, C.

2011-12-01

A taxon- or group-specific PCR primer serves as a valuable tool for studying the bioleaching mechanisms of a particular group of microorganisms. Especially for an uncultured (or very difficult to isolate from their environments) group of microorganisms, the group-specific PCR primer is essential for the investigation of distribution patterns and the estimation of genetic diversity of the target microorganisms. This study investigated the Biodiversity through molecular biology method using the three different indigenous acidophilic bacteria collected from acid mine drainage in Go-seong and Yeon-hwa, Korea and acidic hot spring in Hatchnobaru, Japan. We performed the optical analysis (phase-contrast microscope and SEM), base sequencing. In the phase-contrast microscope(X 4,000) and SEM analysis, the rod-shaped bacteria with 1μm in length were observed. The results of base sequencing using EzTaxon server data revealed Acidithiobacillus ferrooxidans (Go-seong - 97.79%, Yeon-hwa - 97.90% and Hatchnobaru - 97.97%)

Sustainable production of valuable compound 3-succinoyl-pyridine by genetically engineering Pseudomonas putida using the tobacco waste.

PubMed

Wang, Weiwei; Xu, Ping; Tang, Hongzhi

2015-11-17

Treatment of solid and liquid tobacco wastes with high nicotine content remains a longstanding challenge. Here, we explored an environmentally friendly approach to replace tobacco waste disposal with resource recovery by genetically engineering Pseudomonas putida. The biosynthesis of 3-succinoyl-pyridine (SP), a precursor in the production of hypotensive agents, from the tobacco waste was developed using whole cells of the engineered Pseudomonas strain, S16dspm. Under optimal conditions in fed-batch biotransformation, the final concentrations of product SP reached 9.8 g/L and 8.9 g/L from aqueous nicotine solution and crude suspension of the tobacco waste, respectively. In addition, the crystal compound SP produced from aqueous nicotine of the tobacco waste in batch biotransformation was of high purity and its isolation yield on nicotine was 54.2%. This study shows a promising route for processing environmental wastes as raw materials in order to produce valuable compounds.

Population Genetic Structure and Colonisation History of the Tool-Using New Caledonian Crow

PubMed Central

Abdelkrim, Jawad; Hunt, Gavin R.; Gray, Russell D.; Gemmell, Neil J.

2012-01-01

New Caledonian crows exhibit considerable variation in tool making between populations. Here, we present the first study of the species’ genetic structure over its geographical distribution. We collected feathers from crows on mainland Grande Terre, the inshore island of Toupéti, and the nearby island of Maré where it is believed birds were introduced after European colonisation. We used nine microsatellite markers to establish the genotypes of 136 crows from these islands and classical population genetic tools as well as Approximate Bayesian Computations to explore the distribution of genetic diversity. We found that New Caledonian crows most likely separate into three main distinct clusters: Grande Terre, Toupéti and Maré. Furthermore, Toupéti and Maré crows represent a subset of the genetic diversity observed on Grande Terre, confirming their mainland origin. The genetic data are compatible with a colonisation of Maré taking place after European colonisation around 1900. Importantly, we observed (1) moderate, but significant, genetic differentiation across Grande Terre, and (2) that the degree of differentiation between populations on the mainland increases with geographic distance. These data indicate that despite individual crows’ potential ability to disperse over large distances, most gene flow occurs over short distances. The temporal and spatial patterns described provide a basis for further hypothesis testing and investigation of the geographical variation observed in the tool skills of these crows. PMID:22590576

MutAIT: an online genetic toxicology data portal and analysis tools.

PubMed

Avancini, Daniele; Menzies, Georgina E; Morgan, Claire; Wills, John; Johnson, George E; White, Paul A; Lewis, Paul D

2016-05-01

Assessment of genetic toxicity and/or carcinogenic activity is an essential element of chemical screening programs employed to protect human health. Dose-response and gene mutation data are frequently analysed by industry, academia and governmental agencies for regulatory evaluations and decision making. Over the years, a number of efforts at different institutions have led to the creation and curation of databases to house genetic toxicology data, largely, with the aim of providing public access to facilitate research and regulatory assessments. This article provides a brief introduction to a new genetic toxicology portal called Mutation Analysis Informatics Tools (MutAIT) (www.mutait.org) that provides easy access to two of the largest genetic toxicology databases, the Mammalian Gene Mutation Database (MGMD) and TransgenicDB. TransgenicDB is a comprehensive collection of transgenic rodent mutation data initially compiled and collated by Health Canada. The updated MGMD contains approximately 50 000 individual mutation spectral records from the published literature. The portal not only gives access to an enormous quantity of genetic toxicology data, but also provides statistical tools for dose-response analysis and calculation of benchmark dose. Two important R packages for dose-response analysis are provided as web-distributed applications with user-friendly graphical interfaces. The 'drsmooth' package performs dose-response shape analysis and determines various points of departure (PoD) metrics and the 'PROAST' package provides algorithms for dose-response modelling. The MutAIT statistical tools, which are currently being enhanced, provide users with an efficient and comprehensive platform to conduct quantitative dose-response analyses and determine PoD values that can then be used to calculate human exposure limits or margins of exposure. © The Author 2015. Published by Oxford University Press on behalf of the UK Environmental Mutagen Society. All rights

Arabidopsis research requires a critical re-evaluation of genetic tools.

PubMed

Nikonorova, Natalia; Yue, Kun; Beeckman, Tom; De Smet, Ive

2018-06-27

An increasing number of reports question conclusions based on loss-of-function lines that have unexpected genetic backgrounds. In this opinion paper, we urge researchers to meticulously (re)investigate phenotypes retrieved from various genetic backgrounds and be critical regarding some previously drawn conclusions. As an example, we provide new evidence that acr4-2 mutant phenotypes with respect to columella stem cells are due to the lack of ACR4 and not - at least not as a major contributor - to a mutation in QRT1. In addition, we take the opportunity to alert the scientific community about the qrt1-2 background of a large number of Syngenta Arabidopsis Insertion Library (SAIL) T-DNA lines, a feature that is not commonly recognized by Arabidopsis researchers. This qrt1-2 background might have an important impact on the interpretation of the results obtained using these research tools, now and in the past. In conclusion, as a community, we should continuously assess and - if necessary - correct our conclusions based on the large number of (genetic) tools our work is built on. In addition, the positive or negative results of this self-criticism should be made available to the scientific community.

Genotator: a disease-agnostic tool for genetic annotation of disease.

PubMed

Wall, Dennis P; Pivovarov, Rimma; Tong, Mark; Jung, Jae-Yoon; Fusaro, Vincent A; DeLuca, Todd F; Tonellato, Peter J

2010-10-29

Disease-specific genetic information has been increasing at rapid rates as a consequence of recent improvements and massive cost reductions in sequencing technologies. Numerous systems designed to capture and organize this mounting sea of genetic data have emerged, but these resources differ dramatically in their disease coverage and genetic depth. With few exceptions, researchers must manually search a variety of sites to assemble a complete set of genetic evidence for a particular disease of interest, a process that is both time-consuming and error-prone. We designed a real-time aggregation tool that provides both comprehensive coverage and reliable gene-to-disease rankings for any disease. Our tool, called Genotator, automatically integrates data from 11 externally accessible clinical genetics resources and uses these data in a straightforward formula to rank genes in order of disease relevance. We tested the accuracy of coverage of Genotator in three separate diseases for which there exist specialty curated databases, Autism Spectrum Disorder, Parkinson's Disease, and Alzheimer Disease. Genotator is freely available at http://genotator.hms.harvard.edu. Genotator demonstrated that most of the 11 selected databases contain unique information about the genetic composition of disease, with 2514 genes found in only one of the 11 databases. These findings confirm that the integration of these databases provides a more complete picture than would be possible from any one database alone. Genotator successfully identified at least 75% of the top ranked genes for all three of our use cases, including a 90% concordance with the top 40 ranked candidates for Alzheimer Disease. As a meta-query engine, Genotator provides high coverage of both historical genetic research as well as recent advances in the genetic understanding of specific diseases. As such, Genotator provides a real-time aggregation of ranked data that remains current with the pace of research in the disease

Tellurium as a valuable tool for studying the prokaryotic origins of mitochondria.

PubMed

Pontieri, Paola; De Stefano, Mario; Massardo, Domenica Rita; Gunge, Norio; Miyakawa, Isamu; Sando, Nobundo; Pignone, Domenico; Pizzolante, Graziano; Romano, Roberta; Alifano, Pietro; Del Giudice, Luigi

2015-04-01

Mitochondria are eukaryotic organelles which contain the own genetic material and evolved from free-living Eubacteria, namely hydrogen-producing Alphaproteobacteria. Since 1965, biologists provided, by research at molecular level, evidence for the prokaryotic origins of mitochondria. However, determining the precise origins of mitochondria is challenging due to inherent difficulties in phylogenetically reconstructing ancient evolutionary events. The use of new tools to evidence the prokaryotic origin of mitochondria could be useful to gain an insight into the bacterial endosymbiotic event that resulted in the permanent acquisition of bacteria, from the ancestral cell, that through time were transformed into mitochondria. Electron microscopy has shown that both proteobacterial and yeast cells during their growth in the presence of increasing amount of tellurite resulted in dose-dependent blackening of the culture due to elemental tellurium (Te(0)) that formed large deposits either along the proteobacterial membrane or along the yeast cell wall and mitochondria. Since the mitochondrial inner membrane composition is similar to that of proteobacterial membrane, in the present work we evidenced the black tellurium deposits on both, cell wall and mitochondria of ρ(+) and respiratory deficient ρ(-) mutants of yeast. A possible role of tellurite in studying the evolutionary origins of mitochondria will be discussed. Copyright © 2015. Published by Elsevier B.V.

Application of molecular genetic tools to studies of forest pathosystems [Chapter 2

Treesearch

Mee-Sook Kim; Ned B. Klopfenstein; Richard C. Hamelin

2005-01-01

The use of molecular genetics in forest pathology has greatly increased over the past 10 years. For the most part, molecular genetic tools were initially developed to focus on individual components (e.g., pathogen, host) of forest pathosystems. As part of broader forest ecosystem complexes, forest pathosystems involve dynamic interactions among living components (e.g...

A review of the key genetic tools to assist imperiled species conservation: analyzing West Indian manatee populations

USGS Publications Warehouse

Bonde, Robert K.; McGuire, Peter M.; Hunter, Margaret E.

2012-01-01

Managers faced with decisions on threatened and endangered wildlife populations often are lacking detailed information about the species of concern. Integration of genetic applications will provide management teams with a better ability to assess and monitor recovery efforts on imperiled species. The field of molecular biology continues to progress rapidly and many tools are currently available. Presently, little guidance is available to assist researchers and managers with the appropriate selection of genetic tools to study the status of wild manatee populations. We discuss several genetic tools currently employed in the application of conservation genetics, and address the utility of using these tools to determine population status to aid in conservation efforts. As an example, special emphasis is focused on the endangered West Indian manatee (Order Sirenia). All four extant species of sirenians are imperiled throughout their range, predominately due to anthropogenic sources; therefore, the need for genetic information on their population status is direly needed.

CRISPR/Cas9 System as a Valuable Genome Editing Tool for Wine Yeasts with Application to Decrease Urea Production

PubMed Central

Vigentini, Ileana; Gebbia, Marinella; Belotti, Alessandra; Foschino, Roberto; Roth, Frederick P.

2017-01-01

An extensive repertoire of molecular tools is available for genetic analysis in laboratory strains of S. cerevisiae. Although this has widely contributed to the interpretation of gene functionality within haploid laboratory isolates, the genetics of metabolism in commercially-relevant polyploid yeast strains is still poorly understood. Genetic engineering in industrial yeasts is undergoing major changes due to Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein (Cas) engineering approaches. Here we apply the CRISPR/Cas9 system to two commercial “starter” strains of S. cerevisiae (EC1118, AWRI796), eliminating the CAN1 arginine permease pathway to generate strains with reduced urea production (18.5 and 35.5% for EC1118 and AWRI796, respectively). In a wine-model environment based on two grape musts obtained from Chardonnay and Cabernet Sauvignon cultivars, both S. cerevisiae starter strains and CAN1 mutants completed the must fermentation in 8–12 days. However, recombinant strains carrying the can1 mutation failed to produce urea, suggesting that the genetic modification successfully impaired the arginine metabolism. In conclusion, the reduction of urea production in a wine-model environment confirms that the CRISPR/Cas9 system has been successfully established in S. cerevisiae wine yeasts. PMID:29163459

Tales from the front lines: the creative essay as a tool for teaching genetics.

PubMed

Koehler, K E; Hawley, R S

1999-07-01

In contrast to the more typical mock grant proposals or literature reviews, we describe the use of the creative essay as a novel tool for teaching human genetics at the college level. This method has worked well for both nonmajor and advanced courses for biology majors. The 10- to 15-page essay is written in storylike form and represents a student's response to the choice of 6-8 scenarios describing human beings coping with various genetic dilemmas. We have found this tool to be invaluable both in developing students' ability to express genetic concepts in lay terms and in promoting student awareness of genetic issues outside of the classroom. Examples from student essays are presented to illustrate these points, and guidelines are suggested regarding instructor expectations of student creativity and scientific accuracy. Methods of grading this assignment are also discussed.

Tales from the front lines: the creative essay as a tool for teaching genetics.

PubMed Central

Koehler, K E; Hawley, R S

1999-01-01

In contrast to the more typical mock grant proposals or literature reviews, we describe the use of the creative essay as a novel tool for teaching human genetics at the college level. This method has worked well for both nonmajor and advanced courses for biology majors. The 10- to 15-page essay is written in storylike form and represents a student's response to the choice of 6-8 scenarios describing human beings coping with various genetic dilemmas. We have found this tool to be invaluable both in developing students' ability to express genetic concepts in lay terms and in promoting student awareness of genetic issues outside of the classroom. Examples from student essays are presented to illustrate these points, and guidelines are suggested regarding instructor expectations of student creativity and scientific accuracy. Methods of grading this assignment are also discussed. PMID:10388836

The application of computer-based tools in obtaining the genetic family history.

PubMed

Giovanni, Monica A; Murray, Michael F

2010-07-01

Family health history is both an adjunct to and a focus of current genetic research, having long been known to be a powerful predictor of individual disease risk. As such, it has been primarily used as a proxy for genetic information. Over the past decade, new roles for family history have emerged, perhaps most importantly as a primary tool for guiding decision-making on the use of expensive genetic testing. The collection of family history information is an important but time-consuming process. Efforts to engage the patient or research subject in preliminary data collection have the potential to improve data accuracy and allow clinicians and researchers more time for analytic tasks. The U.S. Surgeon General, the Centers for Disease Control and Prevention (CDC), and others have developed tools for electronic family history collection. This unit describes the utility of the Web-based My Family Health Portrait (https://familyhistory.hhs.gov) as the prototype for patient-entered family history.

Assessing Website Quality in Context: Retrieving Information about Genetically Modified Food on the Web

ERIC Educational Resources Information Center

McInerney, Claire R.; Bird, Nora J.

2005-01-01

Introduction: Knowing the credibility of information about genetically modified food on the Internet is critical to the everyday life information seeking of consumers as they form opinions about this nascent agricultural technology. The Website Quality Evaluation Tool (WQET) is a valuable instrument that can be used to determine the credibility of…

Molecular tools for carotenogenesis analysis in the zygomycete Mucor circinelloides.

PubMed

Torres-Martínez, Santiago; Ruiz-Vázquez, Rosa M; Garre, Victoriano; López-García, Sergio; Navarro, Eusebio; Vila, Ana

2012-01-01

The carotene producer fungus Mucor circinelloides is the zygomycete more amenable to genetic manipulations by using molecular tools. Since the initial development of an effective procedure of genetic transformation, more than two decades ago, the availability of new molecular approaches such as gene replacement techniques and gene expression inactivation by RNA silencing, in addition to the sequencing of its genome, has made Mucor a valuable organism for the study of a number of processes. Here we describe in detail the main techniques and methods currently used to manipulate M. circinelloides, including transformation, gene replacement, gene silencing, RNAi, and immunoprecipitation.

Agrobacterium rhizogenes-mediated transformation of Superroot-derived Lotus corniculatus plants: a valuable tool for functional genomics.

PubMed

Jian, Bo; Hou, Wensheng; Wu, Cunxiang; Liu, Bin; Liu, Wei; Song, Shikui; Bi, Yurong; Han, Tianfu

2009-06-25

of the highly efficient transformation and the regeneration system of Superroot provides a valuable tool for functional genomics studies in L. corniculatus.

Genetic tools for the investigation of Roseobacter clade bacteria

PubMed Central

2009-01-01

Background The Roseobacter clade represents one of the most abundant, metabolically versatile and ecologically important bacterial groups found in marine habitats. A detailed molecular investigation of the regulatory and metabolic networks of these organisms is currently limited for many strains by missing suitable genetic tools. Results Conjugation and electroporation methods for the efficient and stable genetic transformation of selected Roseobacter clade bacteria including Dinoroseobacter shibae, Oceanibulbus indolifex, Phaeobacter gallaeciensis, Phaeobacter inhibens, Roseobacter denitrificans and Roseobacter litoralis were tested. For this purpose an antibiotic resistance screening was performed and suitable genetic markers were selected. Based on these transformation protocols stably maintained plasmids were identified. A plasmid encoded oxygen-independent fluorescent system was established using the flavin mononucleotide-based fluorescent protein FbFP. Finally, a chromosomal gene knockout strategy was successfully employed for the inactivation of the anaerobic metabolism regulatory gene dnr from D. shibae DFL12T. Conclusion A genetic toolbox for members of the Roseobacter clade was established. This provides a solid methodical basis for the detailed elucidation of gene regulatory and metabolic networks underlying the ecological success of this group of marine bacteria. PMID:20021642

EINVis: a visualization tool for analyzing and exploring genetic interactions in large-scale association studies.

PubMed

Wu, Yubao; Zhu, Xiaofeng; Chen, Jian; Zhang, Xiang

2013-11-01

Epistasis (gene-gene interaction) detection in large-scale genetic association studies has recently drawn extensive research interests as many complex traits are likely caused by the joint effect of multiple genetic factors. The large number of possible interactions poses both statistical and computational challenges. A variety of approaches have been developed to address the analytical challenges in epistatic interaction detection. These methods usually output the identified genetic interactions and store them in flat file formats. It is highly desirable to develop an effective visualization tool to further investigate the detected interactions and unravel hidden interaction patterns. We have developed EINVis, a novel visualization tool that is specifically designed to analyze and explore genetic interactions. EINVis displays interactions among genetic markers as a network. It utilizes a circular layout (specially, a tree ring view) to simultaneously visualize the hierarchical interactions between single nucleotide polymorphisms (SNPs), genes, and chromosomes, and the network structure formed by these interactions. Using EINVis, the user can distinguish marginal effects from interactions, track interactions involving more than two markers, visualize interactions at different levels, and detect proxy SNPs based on linkage disequilibrium. EINVis is an effective and user-friendly free visualization tool for analyzing and exploring genetic interactions. It is publicly available with detailed documentation and online tutorial on the web at http://filer.case.edu/yxw407/einvis/. © 2013 WILEY PERIODICALS, INC.

Genetic testing in congenital heart disease: A clinical approach

PubMed Central

Chaix, Marie A; Andelfinger, Gregor; Khairy, Paul

2016-01-01

Congenital heart disease (CHD) is the most common type of birth defect. Traditionally, a polygenic model defined by the interaction of multiple genes and environmental factors was hypothesized to account for different forms of CHD. It is now understood that the contribution of genetics to CHD extends beyond a single unified paradigm. For example, monogenic models and chromosomal abnormalities have been associated with various syndromic and non-syndromic forms of CHD. In such instances, genetic investigation and testing may potentially play an important role in clinical care. A family tree with a detailed phenotypic description serves as the initial screening tool to identify potentially inherited defects and to guide further genetic investigation. The selection of a genetic test is contingent upon the particular diagnostic hypothesis generated by clinical examination. Genetic investigation in CHD may carry the potential to improve prognosis by yielding valuable information with regards to personalized medical care, confidence in the clinical diagnosis, and/or targeted patient follow-up. Moreover, genetic assessment may serve as a tool to predict recurrence risk, define the pattern of inheritance within a family, and evaluate the need for further family screening. In some circumstances, prenatal or preimplantation genetic screening could identify fetuses or embryos at high risk for CHD. Although genetics may appear to constitute a highly specialized sector of cardiology, basic knowledge regarding inheritance patterns, recurrence risks, and available screening and diagnostic tools, including their strengths and limitations, could assist the treating physician in providing sound counsel. PMID:26981213

Genetics of Combined Pituitary Hormone Deficiency: Roadmap into the Genome Era

PubMed Central

Fang, Qing; George, Akima S.; Brinkmeier, Michelle L.; Mortensen, Amanda H.; Gergics, Peter; Cheung, Leonard Y. M.; Daly, Alexandre Z.; Ajmal, Adnan; Pérez Millán, María Ines; Ozel, A. Bilge; Kitzman, Jacob O.; Mills, Ryan E.; Li, Jun Z.

2016-01-01

The genetic basis for combined pituitary hormone deficiency (CPHD) is complex, involving 30 genes in a variety of syndromic and nonsyndromic presentations. Molecular diagnosis of this disorder is valuable for predicting disease progression, avoiding unnecessary surgery, and family planning. We expect that the application of high throughput sequencing will uncover additional contributing genes and eventually become a valuable tool for molecular diagnosis. For example, in the last 3 years, six new genes have been implicated in CPHD using whole-exome sequencing. In this review, we present a historical perspective on gene discovery for CPHD and predict approaches that may facilitate future gene identification projects conducted by clinicians and basic scientists. Guidelines for systematic reporting of genetic variants and assigning causality are emerging. We apply these guidelines retrospectively to reports of the genetic basis of CPHD and summarize modes of inheritance and penetrance for each of the known genes. In recent years, there have been great improvements in databases of genetic information for diverse populations. Some issues remain that make molecular diagnosis challenging in some cases. These include the inherent genetic complexity of this disorder, technical challenges like uneven coverage, differing results from variant calling and interpretation pipelines, the number of tolerated genetic alterations, and imperfect methods for predicting pathogenicity. We discuss approaches for future research in the genetics of CPHD. PMID:27828722

Genetics of Combined Pituitary Hormone Deficiency: Roadmap into the Genome Era.

PubMed

Fang, Qing; George, Akima S; Brinkmeier, Michelle L; Mortensen, Amanda H; Gergics, Peter; Cheung, Leonard Y M; Daly, Alexandre Z; Ajmal, Adnan; Pérez Millán, María Ines; Ozel, A Bilge; Kitzman, Jacob O; Mills, Ryan E; Li, Jun Z; Camper, Sally A

2016-12-01

The genetic basis for combined pituitary hormone deficiency (CPHD) is complex, involving 30 genes in a variety of syndromic and nonsyndromic presentations. Molecular diagnosis of this disorder is valuable for predicting disease progression, avoiding unnecessary surgery, and family planning. We expect that the application of high throughput sequencing will uncover additional contributing genes and eventually become a valuable tool for molecular diagnosis. For example, in the last 3 years, six new genes have been implicated in CPHD using whole-exome sequencing. In this review, we present a historical perspective on gene discovery for CPHD and predict approaches that may facilitate future gene identification projects conducted by clinicians and basic scientists. Guidelines for systematic reporting of genetic variants and assigning causality are emerging. We apply these guidelines retrospectively to reports of the genetic basis of CPHD and summarize modes of inheritance and penetrance for each of the known genes. In recent years, there have been great improvements in databases of genetic information for diverse populations. Some issues remain that make molecular diagnosis challenging in some cases. These include the inherent genetic complexity of this disorder, technical challenges like uneven coverage, differing results from variant calling and interpretation pipelines, the number of tolerated genetic alterations, and imperfect methods for predicting pathogenicity. We discuss approaches for future research in the genetics of CPHD.

Reprogenetics, Genetic Tools and Reproductive Risk: Attitudes and Understanding Among Ethnic Groups in Israel.

PubMed

Simonstein, Frida; Mashiach-Eizenberg, Michal

2016-02-01

The present study investigated a possible relationship between the attitudes toward genetic technologies and the understanding of genetics, reproduction, and reproductive risk among Israeli Arabs and Israeli Jews. The study included 203 respondents, who answered a structured self-report questionnaire. They were recruited using a snowball method, which increased the participation of Israeli Arabs in the sample, although the sample was not representative of the Israeli population as a whole (there were more Arabs and fewer men). The respondents in this study expressed a positive attitude toward genetic technologies, but were less in favor of using genetic tools for non-medical purposes. Respondents of both groups were not knowledgeable of genetics; however, they scored higher on the items related to reproductive risk, which suggests that some awareness about genetic risk exists in both sectors of the Israeli population. Nevertheless, Israeli Arabs were less positive than Israeli Jews regarding the application of genetic tools. Moreover, although an understanding of genetics correlated positively with the attitude among Arabs, it did not affect the attitude of Jews, who remained very positive, regardless of their level of understanding. This result suggests that other social and cultural factors, besides understanding, might be at work among these two major ethnic sectors. Further studies that integrate educational, social, and cultural aspects among ethnic sectors of the population are required to improve health services and genetic counselling in Israel and in other countries.

Genetic Tools and Techniques for Recombinant Expression in Thermophilic Bacillaceae.

PubMed

Drejer, Eivind B; Hakvåg, Sigrid; Irla, Marta; Brautaset, Trygve

2018-05-10

Although Escherichia coli and Bacillus subtilis are the most prominent bacterial hosts for recombinant protein production by far, additional species are being explored as alternatives for production of difficult-to-express proteins. In particular, for thermostable proteins, there is a need for hosts able to properly synthesize, fold, and excrete these in high yields, and thermophilic Bacillaceae represent one potentially interesting group of microorganisms for such purposes. A number of thermophilic Bacillaceae including B. methanolicus , B. coagulans , B. smithii , B. licheniformis , Geobacillus thermoglucosidasius , G. kaustophilus , and G. stearothermophilus are investigated concerning physiology, genomics, genetic tools, and technologies, altogether paving the way for their utilization as hosts for recombinant production of thermostable and other difficult-to-express proteins. Moreover, recent successful deployments of CRISPR/Cas9 in several of these species have accelerated the progress in their metabolic engineering, which should increase their attractiveness for future industrial-scale production of proteins. This review describes the biology of thermophilic Bacillaceae and in particular focuses on genetic tools and methods enabling use of these organisms as hosts for recombinant protein production.

Versatile Genetic Tool Box for the Crenarchaeote Sulfolobus acidocaldarius

PubMed Central

Wagner, Michaela; van Wolferen, Marleen; Wagner, Alexander; Lassak, Kerstin; Meyer, Benjamin H.; Reimann, Julia; Albers, Sonja-Verena

2012-01-01

For reverse genetic approaches inactivation or selective modification of genes are required to elucidate their putative function. Sulfolobus acidocaldarius is a thermoacidophilic Crenarchaeon which grows optimally at 76°C and pH 3. As many antibiotics do not withstand these conditions the development of a genetic system in this organism is dependent on auxotrophies. Therefore we constructed a pyrE deletion mutant of S. acidocaldarius wild type strain DSM639 missing 322 bp called MW001. Using this strain as the starting point, we describe here different methods using single as well as double crossover events to obtain markerless deletion mutants, tag genes genomically and ectopically integrate foreign DNA into MW001. These methods enable us to construct single, double, and triple deletions strains that can still be complemented with the pRN1 based expression vector. Taken together we have developed a versatile and robust genetic tool box for the crenarchaeote S. acidocaldarius that will promote the study of unknown gene functions in this organism and makes it a suitable host for synthetic biology approaches. PMID:22707949

The GenoChip: A New Tool for Genetic Anthropology

PubMed Central

Elhaik, Eran; Greenspan, Elliott; Staats, Sean; Krahn, Thomas; Tyler-Smith, Chris; Xue, Yali; Tofanelli, Sergio; Francalacci, Paolo; Cucca, Francesco; Pagani, Luca; Jin, Li; Li, Hui; Schurr, Theodore G.; Greenspan, Bennett; Spencer Wells, R.

2013-01-01

relevance, the GenoChip is a useful tool for genetic anthropology and population genetics. PMID:23666864

The GenoChip: a new tool for genetic anthropology.

PubMed

Elhaik, Eran; Greenspan, Elliott; Staats, Sean; Krahn, Thomas; Tyler-Smith, Chris; Xue, Yali; Tofanelli, Sergio; Francalacci, Paolo; Cucca, Francesco; Pagani, Luca; Jin, Li; Li, Hui; Schurr, Theodore G; Greenspan, Bennett; Spencer Wells, R

2013-01-01

relevance, the GenoChip is a useful tool for genetic anthropology and population genetics.

CRISPR/Cas9-loxP-Mediated Gene Editing as a Novel Site-Specific Genetic Manipulation Tool.

PubMed

Yang, Fayu; Liu, Changbao; Chen, Ding; Tu, Mengjun; Xie, Haihua; Sun, Huihui; Ge, Xianglian; Tang, Lianchao; Li, Jin; Zheng, Jiayong; Song, Zongming; Qu, Jia; Gu, Feng

2017-06-16

Cre-loxP, as one of the site-specific genetic manipulation tools, offers a method to study the spatial and temporal regulation of gene expression/inactivation in order to decipher gene function. CRISPR/Cas9-mediated targeted genome engineering technologies are sparking a new revolution in biological research. Whether the traditional site-specific genetic manipulation tool and CRISPR/Cas9 could be combined to create a novel genetic tool for highly specific gene editing is not clear. Here, we successfully generated a CRISPR/Cas9-loxP system to perform gene editing in human cells, providing the proof of principle that these two technologies can be used together for the first time. We also showed that distinct non-homologous end-joining (NHEJ) patterns from CRISPR/Cas9-mediated gene editing of the targeting sequence locates at the level of plasmids (episomal) and chromosomes. Specially, the CRISPR/Cas9-mediated NHEJ pattern in the nuclear genome favors deletions (64%-68% at the human AAVS1 locus versus 4%-28% plasmid DNA). CRISPR/Cas9-loxP, a novel site-specific genetic manipulation tool, offers a platform for the dissection of gene function and molecular insights into DNA-repair pathways. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Synthetic biology and molecular genetics in non-conventional yeasts: Current tools and future advances.

PubMed

Wagner, James M; Alper, Hal S

2016-04-01

Coupling the tools of synthetic biology with traditional molecular genetic techniques can enable the rapid prototyping and optimization of yeast strains. While the era of yeast synthetic biology began in the well-characterized model organism Saccharomyces cerevisiae, it is swiftly expanding to include non-conventional yeast production systems such as Hansenula polymorpha, Kluyveromyces lactis, Pichia pastoris, and Yarrowia lipolytica. These yeasts already have roles in the manufacture of vaccines, therapeutic proteins, food additives, and biorenewable chemicals, but recent synthetic biology advances have the potential to greatly expand and diversify their impact on biotechnology. In this review, we summarize the development of synthetic biological tools (including promoters and terminators) and enabling molecular genetics approaches that have been applied in these four promising alternative biomanufacturing platforms. An emphasis is placed on synthetic parts and genome editing tools. Finally, we discuss examples of synthetic tools developed in other organisms that can be adapted or optimized for these hosts in the near future. Copyright © 2015 Elsevier Inc. All rights reserved.

Genetically Engineered Mouse Models of Pituitary Tumors

PubMed Central

Cano, David A.; Soto-Moreno, Alfonso; Leal-Cerro, Alfonso

2014-01-01

Animal models constitute valuable tools for investigating the pathogenesis of cancer as well as for preclinical testing of novel therapeutics approaches. However, the pathogenic mechanisms of pituitary-tumor formation remain poorly understood, particularly in sporadic adenomas, thus, making it a challenge to model pituitary tumors in mice. Nevertheless, genetically engineered mouse models (GEMMs) of pituitary tumors have provided important insight into pituitary tumor biology. In this paper, we review various GEMMs of pituitary tumors, highlighting their contributions and limitations, and discuss opportunities for research in the field. PMID:25136513

Guidelines for collecting and maintaining archives for genetic monitoring

USGS Publications Warehouse

Jackson, Jennifer A.; Laikre, Linda; Baker, C. Scott; Kendall, Katherine C.; ,

2012-01-01

Rapid advances in molecular genetic techniques and the statistical analysis of genetic data have revolutionized the way that populations of animals, plants and microorganisms can be monitored. Genetic monitoring is the practice of using molecular genetic markers to track changes in the abundance, diversity or distribution of populations, species or ecosystems over time, and to follow adaptive and non-adaptive genetic responses to changing external conditions. In recent years, genetic monitoring has become a valuable tool in conservation management of biological diversity and ecological analysis, helping to illuminate and define cryptic and poorly understood species and populations. Many of the detected biodiversity declines, changes in distribution and hybridization events have helped to drive changes in policy and management. Because a time series of samples is necessary to detect trends of change in genetic diversity and species composition, archiving is a critical component of genetic monitoring. Here we discuss the collection, development, maintenance, and use of archives for genetic monitoring. This includes an overview of the genetic markers that facilitate effective monitoring, describes how tissue and DNA can be stored, and provides guidelines for proper practice.

Plasmid Vectors and Molecular Building Blocks for the Development of Genetic Manipulation Tools for Trypanosoma cruzi

PubMed Central

Bouvier, León A.; Cámara, María de los Milagros; Canepa, Gaspar E.; Miranda, Mariana R.; Pereira, Claudio A.

2013-01-01

The post genomic era revealed the need for developing better performing, easier to use and more sophisticated genetic manipulation tools for the study of Trypanosoma cruzi, the etiological agent of Chagas disease. In this work a series of plasmids that allow genetic manipulation of this protozoan parasite were developed. First of all we focused on useful tools to establish selection strategies for different strains and which can be employed as expression vectors. On the other hand molecular building blocks in the form of diverse selectable markers, modifiable fluorescent protein and epitope-tag coding sequences were produced. Both types of modules were harboured in backbone molecules conceived to offer multiple construction and sub-cloning strategies. These can be used to confer new properties to already available genetic manipulation tools or as starting points for whole novel designs. The performance of each plasmid and building block was determined independently. For illustration purposes, some simple direct practical applications were conducted. PMID:24205392

Tools for Genetic Studies in Experimental Populations of Polyploids.

PubMed

Bourke, Peter M; Voorrips, Roeland E; Visser, Richard G F; Maliepaard, Chris

2018-01-01

Polyploid organisms carry more than two copies of each chromosome, a condition rarely tolerated in animals but which occurs relatively frequently in the plant kingdom. One of the principal challenges faced by polyploid organisms is to evolve stable meiotic mechanisms to faithfully transmit genetic information to the next generation upon which the study of inheritance is based. In this review we look at the tools available to the research community to better understand polyploid inheritance, many of which have only recently been developed. Most of these tools are intended for experimental populations (rather than natural populations), facilitating genomics-assisted crop improvement and plant breeding. This is hardly surprising given that a large proportion of domesticated plant species are polyploid. We focus on three main areas: (1) polyploid genotyping; (2) genetic and physical mapping; and (3) quantitative trait analysis and genomic selection. We also briefly review some miscellaneous topics such as the mode of inheritance and the availability of polyploid simulation software. The current polyploid analytic toolbox includes software for assigning marker genotypes (and in particular, estimating the dosage of marker alleles in the heterozygous condition), establishing chromosome-scale linkage phase among marker alleles, constructing (short-range) haplotypes, generating linkage maps, performing genome-wide association studies (GWAS) and quantitative trait locus (QTL) analyses, and simulating polyploid populations. These tools can also help elucidate the mode of inheritance (disomic, polysomic or a mixture of both as in segmental allopolyploids) or reveal whether double reduction and multivalent chromosomal pairing occur. An increasing number of polyploids (or associated diploids) are being sequenced, leading to publicly available reference genome assemblies. Much work remains in order to keep pace with developments in genomic technologies. However, such technologies

Tools for Genetic Studies in Experimental Populations of Polyploids

PubMed Central

Bourke, Peter M.; Voorrips, Roeland E.; Visser, Richard G. F.; Maliepaard, Chris

2018-01-01

Polyploid organisms carry more than two copies of each chromosome, a condition rarely tolerated in animals but which occurs relatively frequently in the plant kingdom. One of the principal challenges faced by polyploid organisms is to evolve stable meiotic mechanisms to faithfully transmit genetic information to the next generation upon which the study of inheritance is based. In this review we look at the tools available to the research community to better understand polyploid inheritance, many of which have only recently been developed. Most of these tools are intended for experimental populations (rather than natural populations), facilitating genomics-assisted crop improvement and plant breeding. This is hardly surprising given that a large proportion of domesticated plant species are polyploid. We focus on three main areas: (1) polyploid genotyping; (2) genetic and physical mapping; and (3) quantitative trait analysis and genomic selection. We also briefly review some miscellaneous topics such as the mode of inheritance and the availability of polyploid simulation software. The current polyploid analytic toolbox includes software for assigning marker genotypes (and in particular, estimating the dosage of marker alleles in the heterozygous condition), establishing chromosome-scale linkage phase among marker alleles, constructing (short-range) haplotypes, generating linkage maps, performing genome-wide association studies (GWAS) and quantitative trait locus (QTL) analyses, and simulating polyploid populations. These tools can also help elucidate the mode of inheritance (disomic, polysomic or a mixture of both as in segmental allopolyploids) or reveal whether double reduction and multivalent chromosomal pairing occur. An increasing number of polyploids (or associated diploids) are being sequenced, leading to publicly available reference genome assemblies. Much work remains in order to keep pace with developments in genomic technologies. However, such technologies

Validation of Version 3.0 of the Breast Cancer Genetics Referral Screening Tool (B-RST™).

PubMed

Bellcross, Cecelia; Hermstad, April; Tallo, Christine; Stanislaw, Christine

2018-05-08

Despite increased awareness of hereditary breast and ovarian cancer among clinicians and the public, many BRCA1/2 mutation carriers remain unaware of their risk status. The Breast Cancer Genetics Referral Screening Tool (B-RST™) was created and validated to easily identify individuals at increased risk for hereditary breast and ovarian cancer for referral to cancer genetics services. The purpose of this study was to revise B-RST™ to maximize sensitivity against BRCA1/2 mutation status. We analyzed pedigrees of 277 individuals who had undergone BRCA1/2 testing to determine modifications to the B-RST™ 2.0 algorithm that would maximize sensitivity for mutations, while maintaining simplicity. We used McNemar's chi-square test to compare validation measures between the revised version (3.0) and the 2.0 version. Algorithmic changes made to B-RST™ 2.0 increased the sensitivity against BRCA1/2 mutation analysis from 71.1 to 94.0% (P < 0.0001). While specificity decreased, all screen-positive individuals were appropriate for cancer genetics referral, the primary purpose of the tool. Despite calls for BRCA1/2 population screening, there remains a critical need to identify those most at risk who should receive cancer genetics services. B-RST™ version 3.0 demonstrates high sensitivity for BRCA1/2 mutations, yet remains a simple and quick screening tool for at-risk individuals.

CRISPR therapeutic tools for complex genetic disorders and cancer (Review)

PubMed Central

Baliou, Stella; Adamaki, Maria; Kyriakopoulos, Anthony M.; Spandidos, Demetrios A.; Panayiotidis, Mihalis; Christodoulou, Ioannis; Zoumpourlis, Vassilis

2018-01-01

One of the fundamental discoveries in the field of biology is the ability to modulate the genome and to monitor the functional outputs derived from genomic alterations. In order to unravel new therapeutic options, scientists had initially focused on inducing genetic alterations in primary cells, in established cancer cell lines and mouse models using either RNA interference or cDNA overexpression or various programmable nucleases [zinc finger nucleases (ZNF), transcription activator-like effector nucleases (TALEN)]. Even though a huge volume of data was produced, its use was neither cheap nor accurate. Therefore, the clustered regularly interspaced short palindromic repeats (CRISPR) system was evidenced to be the next step in genome engineering tools. CRISPR-associated protein 9 (Cas9)-mediated genetic perturbation is simple, precise and highly efficient, empowering researchers to apply this method to immortalized cancerous cell lines, primary cells derived from mouse and human origins, xenografts, induced pluripotent stem cells, organoid cultures, as well as the generation of genetically engineered animal models. In this review, we assess the development of the CRISPR system and its therapeutic applications to a wide range of complex diseases (particularly distinct tumors), aiming at personalized therapy. Special emphasis is given to organoids and CRISPR screens in the design of innovative therapeutic approaches. Overall, the CRISPR system is regarded as an eminent genome engineering tool in therapeutics. We envision a new era in cancer biology during which the CRISPR-based genome engineering toolbox will serve as the fundamental conduit between the bench and the bedside; nonetheless, certain obstacles need to be addressed, such as the eradication of side-effects, maximization of efficiency, the assurance of delivery and the elimination of immunogenicity. PMID:29901119

Developing Molecular Genetic Tools to Facilitate Economic Production in Green Algae

DTIC Science & Technology

2012-09-10

Economic Production in Green Algae FA9550-10-1-0052 Georgianna, David, R Gimpel, Javier Hannon, Michael, J Mayfield, Stephen, P Prof. Stephen...Final Performance Report Project Title: Developing Molecular Genetic Tools to Facilitate Economic Production in Green Algae Award Number... ECONOMIC PRODUCTION IN GREEN ALGAE ABSTRACT It is now accepted that algae have enormous potential to generate economically viable and

Genetic characterization of some Romanian red wine grapevine varieties

NASA Astrophysics Data System (ADS)

Ghetea, Ligia Gabriela; Motoc, Rozalia Magda; Niculescu, Ana-Maria; Litescu, Simona Carmen; Duma, Virgil-Florin; Popescu, Carmen Florentina

2008-04-01

In our study we have considered three of the most valuable Romanian red wine grapevine cultivars: Feteasca neagra, Feteasca alba and Novac. We have chosen to study grapevine because grapes and wine are an important part of a healthy diet, and because red grapes have the highest content of proanthocyanidins, that act as antioxidants (free radical scavengers) in the human body. Proanthocyanidins possess anti-mutagenic, anti-tumor, anti-viral activities and they present many other confirmed or potential benefits. Genotyping method was applied in order to asses the genetic profile at 14 microsatellite loci, for two cultivars: Feteasca neagra and Feteasca alba. In order to achieve this, the HPLC-DAD method was used. The content of anthocyans in grape skin from two cultivars - Feteasca neagra and Novac - was measured. Microsatellite markers have been certified as powerful tools for assessing genetic identities and genetic relationships between grapevine gene pools. Genetic characterization of grapevine cultivars can certify their authenticity and purity, two features that have a direct effect on the quality and value of the finished product, the wine. In our country, this is the first attempt in order to establish a genetic profile for valuable Romanian origin grapevine varieties. In some of the 14 microsatellitic loci, Feteasca neagra and Feteasca alba cultivars presented allele size variants different from the values cited in the literature, proving that these cultivars belong to a geographical distinct gene pool. The content of anthocyans in Feteasca neagra grape skin was significantly higher than in Novac.

Value Innovation in Learner-Centered Design. How to Develop Valuable Learning Tools

ERIC Educational Resources Information Center

Breuer, Henning; Schwarz, Heinrich; Feller, Kristina; Matsumoto, Mitsuji

2014-01-01

This paper shows how to address technological, cultural and social transformations with empirically grounded innovation. Areas in transition such as higher education and learning techniques today bring about new needs and opportunities for innovative tools and services. But how do we find these tools? The paper argues for using a strategy of…

A facility monitoring system: The single most valuable and cost-effective tool available to an energy manager

DOE Office of Scientific and Technical Information (OSTI.GOV)

Holmes, W.A.

Energy engineering and management combines engineering problem-solving and financial management techniques to reduce utility costs. At present, substantial amounts of time and money are being spent in order to attempt to quantify energy consumption and costs and define opportunities for savings. Unfortunately, accurate verification of results is often overlooked. Advances in technology during the last few years have made the installation of a permanent, PC-based monitoring system possible for any facility, often for no more than the cost of a detailed study. By investing initially in a monitoring system rather than audits or studies, the actual consumption and cost datamore » will be available on a continuing basis and can be used to produce immediate operational savings, more accurately analyze opportunities requiring capital investments, and to verify actual savings resulting from changes. A permanent monitoring system, installed as the first step in a utility cost reduction effort, to identify where and how energy is used in a facility on a dynamic and real-time basis, can provide the most valuable and cost-effective tool available to an energy manager. The resulting data allows energy consumption patterns and utility costs to be understood and managed in the same manner as all other costs within a facility.« less

Transcriptome sequencing and microarray development for the woodrat (Neotoma spp.): custom genetic tools for exploring herbivore ecology.

PubMed

Malenke, J R; Milash, B; Miller, A W; Dearing, M D

2013-07-01

Massively parallel sequencing has enabled the creation of novel, in-depth genetic tools for nonmodel, ecologically important organisms. We present the de novo transcriptome sequencing, analysis and microarray development for a vertebrate herbivore, the woodrat (Neotoma spp.). This genus is of ecological and evolutionary interest, especially with respect to ingestion and hepatic metabolism of potentially toxic plant secondary compounds. We generated a liver transcriptome of the desert woodrat (Neotoma lepida) using the Roche 454 platform. The assembled contigs were well annotated using rodent references (99.7% annotation), and biotransformation function was reflected in the gene ontology. The transcriptome was used to develop a custom microarray (eArray, Agilent). We tested the microarray with three experiments: one across species with similar habitat (thus, dietary) niches, one across species with different habitat niches and one across populations within a species. The resulting one-colour arrays had high technical and biological quality. Probes designed from the woodrat transcriptome performed significantly better than functionally similar probes from the Norway rat (Rattus norvegicus). There were a multitude of expression differences across the woodrat treatments, many of which related to biotransformation processes and activities. The pattern and function of the differences indicate shared ecological pressures, and not merely phylogenetic distance, play an important role in shaping gene expression profiles of woodrat species and populations. The quality and functionality of the woodrat transcriptome and custom microarray suggest these tools will be valuable for expanding the scope of herbivore biology, as well as the exploration of conceptual topics in ecology. © 2013 John Wiley & Sons Ltd.

E-Portfolio, a Valuable Job Search Tool for College Students

ERIC Educational Resources Information Center

Yu, Ti

2012-01-01

Purpose: The purpose of this paper is to find answers to the following questions: How do employers think about e-portfolios? Do employers really see e-portfolios as a suitable hiring tool? Which factors in students' e-portfolios attract potential employers? Can e-portfolios be successfully used by students in their search for a job?…

DNA microarrays: a powerful genomic tool for biomedical and clinical research

PubMed Central

Trevino, Victor; Falciani, Francesco; Barrera-Saldaña, Hugo A.

2007-01-01

Among the many benefits of the Human Genome Project are new and powerful tools such as the genome-wide hybridization devices referred as microarrays. Initially designed to measure gene transcriptional levels, microarray technologies are now used for comparing other genome features among individuals and their tissues and cells. Results provide valuable information on disease subcategories, disease prognosis, and treatment outcome. Likewise, reveal differences in genetic makeup, regulatory mechanisms and subtle variations are approaching the era of personalized medicine. To understand this powerful tool, its versatility and how it is dramatically changing the molecular approach to biomedical and clinical research, this review describes the technology, its applications, a didactic step-by-step review of a typical microarray protocol, and a real experiment. Finally, it calls the attention of the medical community to integrate multidisciplinary teams, to take advantage of this technology and its expanding applications that in a slide reveals our genetic inheritance and destiny. PMID:17660860

Genetic Analysis of Digestive Physiology Using Fluorescent Phospholipid Reporters

NASA Astrophysics Data System (ADS)

Farber, Steven A.; Pack, Michael; Ho, Shiu-Ying; Johnson, Iain D.; Wagner, Daniel S.; Dosch, Roland; Mullins, Mary C.; Hendrickson, H. Stewart; Hendrickson, Elizabeth K.; Halpern, Marnie E.

2001-05-01

Zebrafish are a valuable model for mammalian lipid metabolism; larvae process lipids similarly through the intestine and hepatobiliary system and respond to drugs that block cholesterol synthesis in humans. After ingestion of fluorescently quenched phospholipids, endogenous lipase activity and rapid transport of cleavage products results in intense gall bladder fluorescence. Genetic screening identifies zebrafish mutants, such as fat free, that show normal digestive organ morphology but severely reduced phospholipid and cholesterol processing. Thus, fluorescent lipids provide a sensitive readout of lipid metabolism and are a powerful tool for identifying genes that mediate vertebrate digestive physiology.

Genetic diversity of Trichomonas vaginalis reinfection in HIV-positive women.

PubMed

Conrad, Melissa D; Kissinger, Patricia; Schmidt, Norine; Martin, David H; Carlton, Jane M

2013-09-01

Recently developed genotyping tools allow better understanding of Trichomonas vaginalis population genetics and epidemiology. These tools have yet to be applied to T vaginalis collected from HIV+ populations, where understanding the interaction between the pathogens is of great importance due to the correlation between T vaginalis infection and HIV transmission. The objectives of the study were twofold: first, to compare the genetic diversity and population structure of T vaginalis collected from HIV+ women with parasites from reference populations; second, to use the genetic markers to perform a case study demonstrating the usefulness of these techniques in investigating the mechanisms of repeat infections. Repository T vaginalis samples from a previously described treatment trial were genotyped at 11 microsatellite loci. Estimates of genetic diversity and population structure were determined using standard techniques and compared with previously reported estimates of global populations. Genotyping data were used in conjunction with behavioural data to evaluate mechanisms of repeat infections. T vaginalis from HIV+ women maintain many of the population genetic characteristics of parasites from global reference populations. Although there is evidence of reduced diversity and bias towards type 1 parasites in the HIV+ population, the populations share a two-type population structure and parasite haplotypes. Genotyping/behavioural data suggest that 36% (12/33) of repeat infections in HIV+ women can be attributed to treatment failure. T vaginalis infecting HIV+ women is not genetically distinct from T vaginalis infecting reference populations. Information from genotyping can be valuable for understanding mechanisms of repeat infections.

Genetic Code Analysis Toolkit: A novel tool to explore the coding properties of the genetic code and DNA sequences

NASA Astrophysics Data System (ADS)

Kraljić, K.; Strüngmann, L.; Fimmel, E.; Gumbel, M.

2018-01-01

The genetic code is degenerated and it is assumed that redundancy provides error detection and correction mechanisms in the translation process. However, the biological meaning of the code's structure is still under current research. This paper presents a Genetic Code Analysis Toolkit (GCAT) which provides workflows and algorithms for the analysis of the structure of nucleotide sequences. In particular, sets or sequences of codons can be transformed and tested for circularity, comma-freeness, dichotomic partitions and others. GCAT comes with a fertile editor custom-built to work with the genetic code and a batch mode for multi-sequence processing. With the ability to read FASTA files or load sequences from GenBank, the tool can be used for the mathematical and statistical analysis of existing sequence data. GCAT is Java-based and provides a plug-in concept for extensibility. Availability: Open source Homepage:http://www.gcat.bio/

A Valuable Tool in Predicting Poor Outcome due to Sepsis in Pediatric Intensive Care Unit: Tp-e/QT Ratio.

PubMed

Ozdemir, Rahmi; Isguder, Rana; Kucuk, Mehmet; Karadeniz, Cem; Ceylan, Gokhan; Katipoglu, Nagehan; Yilmazer, Murat Muhtar; Yozgat, Yilmaz; Mese, Timur; Agin, Hasan

2016-10-01

To assess the feasibility of 12-lead electrocardiographic (ECG) measures such as P wave dispersion (PWd), QT interval, QT dispersion (QTd), Tp-e interval, Tp-e/QT and Tp-e/QTc ratio in predicting poor outcome in patients diagnosed with sepsis in pediatric intensive care unit (PICU). Ninety-three patients diagnosed with sepsis, severe sepsis or septic shock and 103 age- and sex-matched healthy children were enrolled into the study. PWd, QT interval, QTd, Tp-e interval and Tp-e/QT, Tp-e/QTc ratios were obtained from a 12-lead electrocardiogram. PWd, QTd, Tp-e interval and Tp-e/QT, Tp-e/QTc ratios were significantly higher in septic patients compared with the controls. During the study period, 41 patients had died. In multivariate logistic regression analyses, only Tp-e/QT ratio was found to be an independent predictor of mortality. The ECG measurements can predict the poor outcome in patients with sepsis. The Tp-e/QT ratio may be a valuable tool in predicting mortality for patients with sepsis in the PICU. © The Author [2016]. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

EggLib: processing, analysis and simulation tools for population genetics and genomics

PubMed Central

2012-01-01

Background With the considerable growth of available nucleotide sequence data over the last decade, integrated and flexible analytical tools have become a necessity. In particular, in the field of population genetics, there is a strong need for automated and reliable procedures to conduct repeatable and rapid polymorphism analyses, coalescent simulations, data manipulation and estimation of demographic parameters under a variety of scenarios. Results In this context, we present EggLib (Evolutionary Genetics and Genomics Library), a flexible and powerful C++/Python software package providing efficient and easy to use computational tools for sequence data management and extensive population genetic analyses on nucleotide sequence data. EggLib is a multifaceted project involving several integrated modules: an underlying computationally efficient C++ library (which can be used independently in pure C++ applications); two C++ programs; a Python package providing, among other features, a high level Python interface to the C++ library; and the egglib script which provides direct access to pre-programmed Python applications. Conclusions EggLib has been designed aiming to be both efficient and easy to use. A wide array of methods are implemented, including file format conversion, sequence alignment edition, coalescent simulations, neutrality tests and estimation of demographic parameters by Approximate Bayesian Computation (ABC). Classes implementing different demographic scenarios for ABC analyses can easily be developed by the user and included to the package. EggLib source code is distributed freely under the GNU General Public License (GPL) from its website http://egglib.sourceforge.net/ where a full documentation and a manual can also be found and downloaded. PMID:22494792

EggLib: processing, analysis and simulation tools for population genetics and genomics.

PubMed

De Mita, Stéphane; Siol, Mathieu

2012-04-11

With the considerable growth of available nucleotide sequence data over the last decade, integrated and flexible analytical tools have become a necessity. In particular, in the field of population genetics, there is a strong need for automated and reliable procedures to conduct repeatable and rapid polymorphism analyses, coalescent simulations, data manipulation and estimation of demographic parameters under a variety of scenarios. In this context, we present EggLib (Evolutionary Genetics and Genomics Library), a flexible and powerful C++/Python software package providing efficient and easy to use computational tools for sequence data management and extensive population genetic analyses on nucleotide sequence data. EggLib is a multifaceted project involving several integrated modules: an underlying computationally efficient C++ library (which can be used independently in pure C++ applications); two C++ programs; a Python package providing, among other features, a high level Python interface to the C++ library; and the egglib script which provides direct access to pre-programmed Python applications. EggLib has been designed aiming to be both efficient and easy to use. A wide array of methods are implemented, including file format conversion, sequence alignment edition, coalescent simulations, neutrality tests and estimation of demographic parameters by Approximate Bayesian Computation (ABC). Classes implementing different demographic scenarios for ABC analyses can easily be developed by the user and included to the package. EggLib source code is distributed freely under the GNU General Public License (GPL) from its website http://egglib.sourceforge.net/ where a full documentation and a manual can also be found and downloaded.

Use of Study Guide as Intervention Tool in Enhancing Students' Motivation in Grade 8 Genetics Concepts

ERIC Educational Resources Information Center

Balan, Hazel R.

2018-01-01

Genetics is considered as one of the topics in science that students have difficulty and trouble in understanding. This study used study guide as an intervention tool to address the difficulties of students in learning genetics concepts. The main purpose of this study was to determine the perceptions of students on the effectiveness of study guide…

Invited review: Genetics and claw health: Opportunities to enhance claw health by genetic selection

USDA-ARS?s Scientific Manuscript database

Routine recording of claw health status at claw trimming of dairy cattle have been established in several countries, providing valuable data for genetic evaluation. In this review, issues related to genetic evaluation of claw health are examined, data sources, trait definitions and data validation p...

Genetic diversity of Trichomonas vaginalis reinfection in HIV-positive women

PubMed Central

Conrad, Melissa D; Kissinger, Patricia; Schmidt, Norine; Martin, David H; Carlton, Jane M

2013-01-01

Objectives Recently developed genotyping tools allow better understanding of Trichomonas vaginalis population genetics and epidemiology. These tools have yet to be applied to T vaginalis collected from HIV+ populations, where understanding the interaction between the pathogens is of great importance due to the correlation between T vaginalis infection and HIV transmission. The objectives of the study were twofold: first, to compare the genetic diversity and population structure of T vaginalis collected from HIV+ women with parasites from reference populations; second, to use the genetic markers to perform a case study demonstrating the usefulness of these techniques in investigating the mechanisms of repeat infections. Methods Repository T vaginalis samples from a previously described treatment trial were genotyped at 11 microsatellite loci. Estimates of genetic diversity and population structure were determined using standard techniques and compared with previously reported estimates of global populations. Genotyping data were used in conjunction with behavioural data to evaluate mechanisms of repeat infections. Results T vaginalis from HIV+ women maintain many of the population genetic characteristics of parasites from global reference populations. Although there is evidence of reduced diversity and bias towards type 1 parasites in the HIV+ population, the populations share a two-type population structure and parasite haplotypes. Genotyping/behavioural data suggest that 36% (12/33) of repeat infections in HIV+ women can be attributed to treatment failure. Conclusions T vaginalis infecting HIV+ women is not genetically distinct from T vaginalis infecting reference populations. Information from genotyping can be valuable for understanding mechanisms of repeat infections. PMID:23694936

Applications of colored petri net and genetic algorithms to cluster tool scheduling

NASA Astrophysics Data System (ADS)

Liu, Tung-Kuan; Kuo, Chih-Jen; Hsiao, Yung-Chin; Tsai, Jinn-Tsong; Chou, Jyh-Horng

2005-12-01

In this paper, we propose a method, which uses Coloured Petri Net (CPN) and genetic algorithm (GA) to obtain an optimal deadlock-free schedule and to solve re-entrant problem for the flexible process of the cluster tool. The process of the cluster tool for producing a wafer usually can be classified into three types: 1) sequential process, 2) parallel process, and 3) sequential parallel process. But these processes are not economical enough to produce a variety of wafers in small volume. Therefore, this paper will propose the flexible process where the operations of fabricating wafers are randomly arranged to achieve the best utilization of the cluster tool. However, the flexible process may have deadlock and re-entrant problems which can be detected by CPN. On the other hand, GAs have been applied to find the optimal schedule for many types of manufacturing processes. Therefore, we successfully integrate CPN and GAs to obtain an optimal schedule with the deadlock and re-entrant problems for the flexible process of the cluster tool.

Genetic diagnosis as a tool for personalized treatment of Duchenne muscular dystrophy.

PubMed

Bello, Luca; Pegoraro, Elena

2016-12-01

Accurate definition of genetic mutations causing Duchenne muscular dystrophy (DMD) has always been relevant in order to provide genetic counseling to patients and families, and helps to establish the prognosis in the case where the distinction between Duchenne, Becker, or intermediate muscular dystrophy is not obvious. As molecular treatments aimed at dystrophin restoration in DMD are increasingly available as commercialized drugs or within clinical trials, genetic diagnosis has become an indispensable tool in order to determine eligibility for these treatments. DMD patients in which multiplex ligation-dependent probe amplification (MLPA) or similar techniques show a deletion suitable to exon skipping of exons 44, 45, 51, or 53, may be currently treated with AONs targeting these exons, in the context of clinical trials, or, as is the case for exon 51 skipping in the United States, with the first commercialized drug (eteplirsen). Patients who test negative at MLPA, but in whom DMD gene sequencing shows a nonsense mutation, may be amenable for treatment with stop codon readthrough compounds such as ataluren. Novel molecular approaches such as CRISPR-Cas9 targeting of specific DMD mutations are still in the preclinical stages, but appear promising. In conclusion, an accurate genetic diagnosis represents the entrance into a new scenario of personalized medicine in DMD.

Evolutionary Determinants of Genetic Variation in Susceptibility to Infectious Diseases in Humans

PubMed Central

Baker, Christi; Antonovics, Janis

2012-01-01

Although genetic variation among humans in their susceptibility to infectious diseases has long been appreciated, little focus has been devoted to identifying patterns in levels of variation in susceptibility to different diseases. Levels of genetic variation in susceptibility associated with 40 human infectious diseases were assessed by a survey of studies on both pedigree-based quantitative variation, as well as studies on different classes of marker alleles. These estimates were correlated with pathogen traits, epidemiological characteristics, and effectiveness of the human immune response. The strongest predictors of levels of genetic variation in susceptibility were disease characteristics negatively associated with immune effectiveness. High levels of genetic variation were associated with diseases with long infectious periods and for which vaccine development attempts have been unsuccessful. These findings are consistent with predictions based on theoretical models incorporating fitness costs associated with the different types of resistance mechanisms. An appreciation of these observed patterns will be a valuable tool in directing future research given that genetic variation in disease susceptibility has large implications for vaccine development and epidemiology. PMID:22242158

The New Face of Genetics: Creating A Multimedia Educational Tool for the Twenty-First Century

NASA Astrophysics Data System (ADS)

Fan, Audrey

In the study of certain genetic conditions, it is important to understand the specific "dysmorphology" associated with them. This describes the unique anatomical manifestations of the genetic condition. Traditionally, students learn about dysmorphology by reading text descriptions or looking at photographs of affected individuals. The New Face of Genetics is a film project that aims to teach students dysmorphology by featuring people who have specific genetic conditions. The goal is to enhance students' understanding of these conditions as well as to impart the humanity and beauty of the people who appear in the film. Students will have the opportunity to see dysmorphic features on the animated human form as well as meet individuals who are living with genetic difference. The target audience includes genetic counseling students and other medical professionals. Three short films were made in this format to demonstrate how this type of educational tool can be made. The featured conditions were Marfan syndrome, Sturge-Weber syndrome and Joubert syndrome. Future work will be carried out by other genetic counseling students who will make additional films based on our templates. A compendium of approximately 20 films will be eventually completed and released to genetic counseling programs and medical schools.

m6ASNP: a tool for annotating genetic variants by m6A function.

PubMed

Jiang, Shuai; Xie, Yubin; He, Zhihao; Zhang, Ya; Zhao, Yuli; Chen, Li; Zheng, Yueyuan; Miao, Yanyan; Zuo, Zhixiang; Ren, Jian

2018-05-01

Large-scale genome sequencing projects have identified many genetic variants for diverse diseases. A major goal of these projects is to characterize these genetic variants to provide insight into their function and roles in diseases. N6-methyladenosine (m6A) is one of the most abundant RNA modifications in eukaryotes. Recent studies have revealed that aberrant m6A modifications are involved in many diseases. In this study, we present a user-friendly web server called "m6ASNP" that is dedicated to the identification of genetic variants that target m6A modification sites. A random forest model was implemented in m6ASNP to predict whether the methylation status of an m6A site is altered by the variants that surround the site. In m6ASNP, genetic variants in a standard variant call format (VCF) are accepted as the input data, and the output includes an interactive table that contains the genetic variants annotated by m6A function. In addition, statistical diagrams and a genome browser are provided to visualize the characteristics and to annotate the genetic variants. We believe that m6ASNP is a very convenient tool that can be used to boost further functional studies investigating genetic variants. The web server "m6ASNP" is implemented in JAVA and PHP and is freely available at [60].

Insights to Genetic Characterization Tools for Epidemiological Tracking of Francisella tularensis in Sweden

PubMed Central

Wahab, Tara; Birdsell, Dawn N.; Hjertqvist, Marika; Mitchell, Cedar L.; Wagner, David M.; Keim, Paul S.; Hedenström, Ingela; Löfdahl, Sven

2014-01-01

Tularaemia, caused by the bacterium Francisella tularensis, is endemic in Sweden and is poorly understood. The aim of this study was to evaluate the effectiveness of three different genetic typing systems to link a genetic type to the source and place of tularemia infection in Sweden. Canonical single nucleotide polymorphisms (canSNPs), MLVA including five variable number of tandem repeat loci and PmeI-PFGE were tested on 127 F. tularensis positive specimens collected from Swedish case-patients. All three typing methods identified two major genetic groups with near-perfect agreement. Higher genetic resolution was obtained with canSNP and MLVA compared to PFGE; F. tularensis samples were first assigned into ten phylogroups based on canSNPs followed by 33 unique MLVA types. Phylogroups were geographically analysed to reveal complex phylogeographic patterns in Sweden. The extensive phylogenetic diversity found within individual counties posed a challenge to linking specific genetic types with specific geographic locations. Despite this, a single phylogroup (B.22), defined by a SNP marker specific to a lone Swedish sequenced strain, did link genetic type with a likely geographic place. This result suggests that SNP markers, highly specific to a particular reference genome, may be found most frequently among samples recovered from the same location where the reference genome originated. This insight compels us to consider whole-genome sequencing (WGS) as the appropriate tool for effectively linking specific genetic type to geography. Comparing the WGS of an unknown sample to WGS databases of archived Swedish strains maximizes the likelihood of revealing those rare geographically informative SNPs. PMID:25401326

Donor liver histology--a valuable tool in graft selection.

PubMed

Flechtenmacher, Christa; Schirmacher, Peter; Schemmer, Peter

2015-07-01

Due to a tremendous organ shortage, livers from donors with extended criteria are increasingly considered for transplantation. Pathologists are more and more requested to evaluate these livers histopathologically using frozen sections at high urgency for acceptability. This article reviews the current knowledge on pre-transplant histology in liver transplantation. Prerequisites and conditions for proper pre-transplant evaluation of donor liver tissue are discussed as well as frozen section evaluation and reporting. Data sources include the relevant medical literature, web sites specialized in organ transplantation, and the authors' experiences in liver transplant centers. Pre-transplant histopathological evaluation is a time-effective, accurate, and reliable tool to assess liver quality from candidate deceased donors. Pre-transplant biopsies are of value in the selection of donor livers for transplantation, especially in case of extended criteria donors, and should be performed more frequently in order to avoid unnecessary loss of organs suitable for transplantation and transplantation of inappropriate organs. Correlation of histopathological findings with clinical conditions is essential and requires excellent communication between pathologists, surgeons, and the other members of the transplant team.

SPLICER - A GENETIC ALGORITHM TOOL FOR SEARCH AND OPTIMIZATION, VERSION 1.0 (MACINTOSH VERSION)

NASA Technical Reports Server (NTRS)

Wang, L.

1994-01-01

SPLICER is a genetic algorithm tool which can be used to solve search and optimization problems. Genetic algorithms are adaptive search procedures (i.e. problem solving methods) based loosely on the processes of natural selection and Darwinian "survival of the fittest." SPLICER provides the underlying framework and structure for building a genetic algorithm application. These algorithms apply genetically-inspired operators to populations of potential solutions in an iterative fashion, creating new populations while searching for an optimal or near-optimal solution to the problem at hand. SPLICER 1.0 was created using a modular architecture that includes a Genetic Algorithm Kernel, interchangeable Representation Libraries, Fitness Modules and User Interface Libraries, and well-defined interfaces between these components. The architecture supports portability, flexibility, and extensibility. SPLICER comes with all source code and several examples. For instance, a "traveling salesperson" example searches for the minimum distance through a number of cities visiting each city only once. Stand-alone SPLICER applications can be used without any programming knowledge. However, to fully utilize SPLICER within new problem domains, familiarity with C language programming is essential. SPLICER's genetic algorithm (GA) kernel was developed independent of representation (i.e. problem encoding), fitness function or user interface type. The GA kernel comprises all functions necessary for the manipulation of populations. These functions include the creation of populations and population members, the iterative population model, fitness scaling, parent selection and sampling, and the generation of population statistics. In addition, miscellaneous functions are included in the kernel (e.g., random number generators). Different problem-encoding schemes and functions are defined and stored in interchangeable representation libraries. This allows the GA kernel to be used with any

Groundnut improvement: use of genetic and genomic tools

PubMed Central

Janila, Pasupuleti; Nigam, S. N.; Pandey, Manish K.; Nagesh, P.; Varshney, Rajeev K.

2013-01-01

Groundnut (Arachis hypogaea L.), a self-pollinated legume is an important crop cultivated in 24 million ha world over for extraction of edible oil and food uses. The kernels are rich in oil (48–50%) and protein (25–28%), and are source of several vitamins, minerals, antioxidants, biologically active polyphenols, flavonoids, and isoflavones. Improved varieties of groundnut with high yield potential were developed and released for cultivation world over. The improved varieties belong to different maturity durations and possess resistance to diseases, tolerance to drought, enhanced oil content, and improved quality traits for food uses. Conventional breeding procedures along with the tools for phenotyping were largely used in groundnut improvement programs. Mutations were used to induce variability and wide hybridization was attempted to tap variability from wild species. Low genetic variability has been a bottleneck for groundnut improvement. The vast potential of wild species, reservoir of new alleles remains under-utilized. Development of linkage maps of groundnut during the last decade was followed by identification of markers and quantitative trait loci for the target traits. Consequently, the last decade has witnessed the deployment of molecular breeding approaches to complement the ongoing groundnut improvement programs in USA, China, India, and Japan. The other potential advantages of molecular breeding are the feasibility to target multiple traits for improvement and provide tools to tap new alleles from wild species. The first groundnut variety developed through marker-assisted back-crossing is a root-knot nematode-resistant variety, NemaTAM in USA. The uptake of molecular breeding approaches in groundnut improvement programs by NARS partners in India and many African countries is slow or needs to be initiated in part due to inadequate infrastructure, high genotyping costs, and human capacities. Availability of draft genome sequence for diploid (AA and

Multidisciplinary Design, Analysis, and Optimization Tool Development Using a Genetic Algorithm

NASA Technical Reports Server (NTRS)

Pak, Chan-gi; Li, Wesley

2009-01-01

Multidisciplinary design, analysis, and optimization using a genetic algorithm is being developed at the National Aeronautics and Space Administration Dryden Flight Research Center (Edwards, California) to automate analysis and design process by leveraging existing tools to enable true multidisciplinary optimization in the preliminary design stage of subsonic, transonic, supersonic, and hypersonic aircraft. This is a promising technology, but faces many challenges in large-scale, real-world application. This report describes current approaches, recent results, and challenges for multidisciplinary design, analysis, and optimization as demonstrated by experience with the Ikhana fire pod design.!

[Caenorhabditis elegans: a powerful tool for drug discovery].

PubMed

Jia, Xi-Hua; Cao, Cheng

2009-07-01

A simple model organism Caenorhabditis elegans has contributed substantially to the fundamental researches in biology. In an era of functional genomics, nematode worm has been developed into a multi-purpose tool that can be exploited to identify disease-causing or disease-associated genes, validate potential drug targets. This, coupled with its genetic amenability, low cost experimental manipulation and compatibility with high throughput screening in an intact physiological condition, makes the model organism into an effective toolbox for drug discovery. This review shows the unique features of C. elegans, how it can play a valuable role in our understanding of the molecular mechanism of human diseases and finding drug leads in drug development process.

Genetic modifications for personal enhancement: a defence.

PubMed

Murphy, Timothy F

2014-04-01

Bioconservative commentators argue that parents should not take steps to modify the genetics of their children even in the name of enhancement because of the damage they predict for values, identities and relationships. Some commentators have even said that adults should not modify themselves through genetic interventions. One commentator worries that genetic modifications chosen by adults for themselves will undermine moral agency, lead to less valuable experiences and fracture people's sense of self. These worries are not justified, however, since the effects of modification will not undo moral agency as such. Adults can still have valuable experiences, even if some prior choices no longer seem meaningful. Changes at the genetic level will not always, either, alienate people from their own sense of self. On the contrary, genetic modifications can help amplify choice, enrich lives and consolidate identities. Ultimately, there is no moral requirement that people value their contingent genetic endowment to the exclusion of changes important to them in their future genetic identities. Through weighing risks and benefits, adults also have the power to consent to, and assume the risks of, genetic modifications for themselves in a way not possible in prenatal genetic interventions.

Propagation method of saving valuable strains from a Mycobacterium liflandii infection in Western clawed frogs (Silurana tropicalis).

PubMed

Chai, Norin; Bronchain, Odile; Panteix, Gilles; Godreuil, Sylvain; de Medeiros, Christophe; Saunders, Richard; Bouts, Tim; de Luze, Amaury

2012-03-01

Mycobacterium liflandii has been responsible for an emerging infection reported in the international trade of Western clawed frogs (Silurana tropicalis). This study shows that this mycolactone-producing Mycobacterium (MPM) has expanded its distribution range to France. The results of this study suggest that the use of in vitro fertilization to maintain genetic lines could be a temporary solution for valuable S. tropicalis propagation.

'HoneySweet' plum - a valuable genetically engineered fruit-tree cultivar and germplasm resource

USDA-ARS?s Scientific Manuscript database

‘HoneySweet’ is a plum variety developed through genetic engineering to be highly resistant to plum pox potyvirus (PPV), the causal agent of sharka disease, that threatens stone-fruit industries world-wide and most specifically, in Europe. Field testing for over 15 years in Europe has demonstrated ...

TALENs and CRISPR/Cas9 fuel genetically engineered clinically relevant Xenopus tropicalis tumor models.

PubMed

Naert, Thomas; Van Nieuwenhuysen, Tom; Vleminckx, Kris

2017-01-01

The targeted nuclease revolution (TALENs, CRISPR/Cas9) now allows Xenopus researchers to rapidly generate custom on-demand genetic knockout models. These novel methods to perform reverse genetics are unprecedented and are fueling a wide array of human disease models within the aquatic diploid model organism Xenopus tropicalis (X. tropicalis). This emerging technology review focuses on the tools to rapidly generate genetically engineered X. tropicalis models (GEXM), with a focus on establishment of genuine genetic and clinically relevant cancer models. We believe that due to particular advantageous characteristics, outlined within this review, GEXM will become a valuable alternative animal model for modeling human cancer. Furthermore, we provide perspectives of how GEXM will be used as a platform for elucidation of novel therapeutic targets and for preclinical drug validation. Finally, we also discuss some future prospects on how the recent expansions and adaptations of the CRISPR/Cas9 toolbox might influence and push forward X. tropicalis cancer research. © 2017 Wiley Periodicals, Inc.

Governmentality, biopower, and the debate over genetic enhancement.

PubMed

McWhorter, Ladelle

2009-08-01

Although Foucault adamantly refused to make moral pronouncements or dictate moral principles or political programs to his readers, his work offers a number of tools and concepts that can help us develop our own ethical views and practices. One of these tools is genealogical analysis, and one of these concepts is "biopower." Specifically, this essay seeks to demonstrate that Foucault's concept of biopower and his genealogical method are valuable as we consider moral questions raised by genetic enhancement technologies. First, it examines contemporary debate over the development, marketing, and application of such technologies, suggesting that what passes for ethical deliberation is often little more than political maneuvering in a field where stakes are very high and public perceptions will play a crucial role in decisions about which technologies will be funded or disallowed. It goes on to argue that genuine ethical deliberation on these issues requires some serious investigation of their historical context. Accordingly, then, it takes up the oft-heard charge from critics that genetic enhancement technologies are continuous with twentieth-century eugenic projects or will usher in a new age of eugenics. Foucault explicitly links twentieth-century eugenics with the rise of biopower. Through review of some aspects of the twentieth-century eugenics movement alongside some of the rhetoric and claims of enhancement's modern-day proponents, the essay shows ways in which deployment of genetic enhancement technologies is and is not continuous with earlier deployments of biopower.

Next Generation Analytic Tools for Large Scale Genetic Epidemiology Studies of Complex Diseases

PubMed Central

Mechanic, Leah E.; Chen, Huann-Sheng; Amos, Christopher I.; Chatterjee, Nilanjan; Cox, Nancy J.; Divi, Rao L.; Fan, Ruzong; Harris, Emily L.; Jacobs, Kevin; Kraft, Peter; Leal, Suzanne M.; McAllister, Kimberly; Moore, Jason H.; Paltoo, Dina N.; Province, Michael A.; Ramos, Erin M.; Ritchie, Marylyn D.; Roeder, Kathryn; Schaid, Daniel J.; Stephens, Matthew; Thomas, Duncan C.; Weinberg, Clarice R.; Witte, John S.; Zhang, Shunpu; Zöllner, Sebastian; Feuer, Eric J.; Gillanders, Elizabeth M.

2012-01-01

Over the past several years, genome-wide association studies (GWAS) have succeeded in identifying hundreds of genetic markers associated with common diseases. However, most of these markers confer relatively small increments of risk and explain only a small proportion of familial clustering. To identify obstacles to future progress in genetic epidemiology research and provide recommendations to NIH for overcoming these barriers, the National Cancer Institute sponsored a workshop entitled “Next Generation Analytic Tools for Large-Scale Genetic Epidemiology Studies of Complex Diseases” on September 15–16, 2010. The goal of the workshop was to facilitate discussions on (1) statistical strategies and methods to efficiently identify genetic and environmental factors contributing to the risk of complex disease; and (2) how to develop, apply, and evaluate these strategies for the design, analysis, and interpretation of large-scale complex disease association studies in order to guide NIH in setting the future agenda in this area of research. The workshop was organized as a series of short presentations covering scientific (gene-gene and gene-environment interaction, complex phenotypes, and rare variants and next generation sequencing) and methodological (simulation modeling and computational resources and data management) topic areas. Specific needs to advance the field were identified during each session and are summarized. PMID:22147673

Multidisciplinary Design, Analysis, and Optimization Tool Development using a Genetic Algorithm

NASA Technical Reports Server (NTRS)

Pak, Chan-gi; Li, Wesley

2008-01-01

Multidisciplinary design, analysis, and optimization using a genetic algorithm is being developed at the National Aeronautics and Space A dministration Dryden Flight Research Center to automate analysis and design process by leveraging existing tools such as NASTRAN, ZAERO a nd CFD codes to enable true multidisciplinary optimization in the pr eliminary design stage of subsonic, transonic, supersonic, and hypers onic aircraft. This is a promising technology, but faces many challe nges in large-scale, real-world application. This paper describes cur rent approaches, recent results, and challenges for MDAO as demonstr ated by our experience with the Ikhana fire pod design.

Systems Genetics as a Tool to Identify Master Genetic Regulators in Complex Disease.

PubMed

Moreno-Moral, Aida; Pesce, Francesco; Behmoaras, Jacques; Petretto, Enrico

2017-01-01

Systems genetics stems from systems biology and similarly employs integrative modeling approaches to describe the perturbations and phenotypic effects observed in a complex system. However, in the case of systems genetics the main source of perturbation is naturally occurring genetic variation, which can be analyzed at the systems-level to explain the observed variation in phenotypic traits. In contrast with conventional single-variant association approaches, the success of systems genetics has been in the identification of gene networks and molecular pathways that underlie complex disease. In addition, systems genetics has proven useful in the discovery of master trans-acting genetic regulators of functional networks and pathways, which in many cases revealed unexpected gene targets for disease. Here we detail the central components of a fully integrated systems genetics approach to complex disease, starting from assessment of genetic and gene expression variation, linking DNA sequence variation to mRNA (expression QTL mapping), gene regulatory network analysis and mapping the genetic control of regulatory networks. By summarizing a few illustrative (and successful) examples, we highlight how different data-modeling strategies can be effectively integrated in a systems genetics study.

English Digital Dictionaries as Valuable Blended Learning Tools for Palestinian College Students

ERIC Educational Resources Information Center

Dwaik, Raghad A. A.

2015-01-01

Digital technology has become an indispensable aspect of foreign language learning around the globe especially in the case of college students who are often required to finish extensive reading assignments within a limited time period. Such pressure calls for the use of efficient tools such as digital dictionaries to help them achieve their…

ETHNOS: A versatile electronic tool for the development and curation of national genetic databases

PubMed Central

2010-01-01

National and ethnic mutation databases (NEMDBs) are emerging online repositories, recording extensive information about the described genetic heterogeneity of an ethnic group or population. These resources facilitate the provision of genetic services and provide a comprehensive list of genomic variations among different populations. As such, they enhance awareness of the various genetic disorders. Here, we describe the features of the ETHNOS software, a simple but versatile tool based on a flat-file database that is specifically designed for the development and curation of NEMDBs. ETHNOS is a freely available software which runs more than half of the NEMDBs currently available. Given the emerging need for NEMDB in genetic testing services and the fact that ETHNOS is the only off-the-shelf software available for NEMDB development and curation, its adoption in subsequent NEMDB development would contribute towards data content uniformity, unlike the diverse contents and quality of the available gene (locus)-specific databases. Finally, we allude to the potential applications of NEMDBs, not only as worldwide central allele frequency repositories, but also, and most importantly, as data warehouses of individual-level genomic data, hence allowing for a comprehensive ethnicity-specific documentation of genomic variation. PMID:20650823

ETHNOS : A versatile electronic tool for the development and curation of national genetic databases.

PubMed

van Baal, Sjozef; Zlotogora, Joël; Lagoumintzis, George; Gkantouna, Vassiliki; Tzimas, Ioannis; Poulas, Konstantinos; Tsakalidis, Athanassios; Romeo, Giovanni; Patrinos, George P

2010-06-01

National and ethnic mutation databases (NEMDBs) are emerging online repositories, recording extensive information about the described genetic heterogeneity of an ethnic group or population. These resources facilitate the provision of genetic services and provide a comprehensive list of genomic variations among different populations. As such, they enhance awareness of the various genetic disorders. Here, we describe the features of the ETHNOS software, a simple but versatile tool based on a flat-file database that is specifically designed for the development and curation of NEMDBs. ETHNOS is a freely available software which runs more than half of the NEMDBs currently available. Given the emerging need for NEMDB in genetic testing services and the fact that ETHNOS is the only off-the-shelf software available for NEMDB development and curation, its adoption in subsequent NEMDB development would contribute towards data content uniformity, unlike the diverse contents and quality of the available gene (locus)-specific databases. Finally, we allude to the potential applications of NEMDBs, not only as worldwide central allele frequency repositories, but also, and most importantly, as data warehouses of individual-level genomic data, hence allowing for a comprehensive ethnicity-specific documentation of genomic variation.

Competency-Based Education for the Molecular Genetic Pathology Fellow

PubMed Central

Talbert, Michael L.; Dunn, S. Terence; Hunt, Jennifer; Hillyard, David R.; Mirza, Imran; Nowak, Jan A.; Van Deerlin, Vivianna; Vnencak-Jones, Cindy L.

2009-01-01

The following report represents guidelines for competency-based fellowship training in Molecular Genetic Pathology (MGP) developed by the Association for Molecular Pathology Training and Education Committee and Directors of MGP Programs in the United States. The goals of the effort were to describe each of the Accreditation Council for Graduate Medical Education competencies as they apply to MGP fellowship training, provide a summary of goals and objectives, and recommend assessment tools. These guidelines are particularly pertinent to MGP training, which is a relatively new specialty that operates within a rapidly changing scientific and technological arena. It is hoped that this document will provide additional material for directors of existing MGP programs to consider for improvement of program objectives and enhancement of evaluation tools already in place. In addition, the guidelines should provide a valuable framework for the development of new MGP programs. PMID:19797613

Evolution and population genetics of exotic and reemerging pathogens: traditional and novel tools and approaches

Treesearch

N.J. Grünwald; E.M. Goss

2011-01-01

Given human population growth and accelerated global trade, the rate of emergence of exotic plant pathogens is bound to increase. Understanding the processes that lead to the emergence of new pathogens can help manage emerging epidemics. Novel tools for analyzing population genetic variation can be used to infer the evolutionary history of populations or species,...

Genetic Tool Development for a New Host for Biotechnology, the Thermotolerant Bacterium Bacillus coagulans▿ †

PubMed Central

Kovács, Ákos T.; van Hartskamp, Mariska; Kuipers, Oscar P.; van Kranenburg, Richard

2010-01-01

Bacillus coagulans has good potential as an industrial production organism for platform chemicals from renewable resources but has limited genetic tools available. Here, we present a targeted gene disruption system using the Cre-lox system, development of a LacZ reporter assay for monitoring gene transcription, and heterologous d-lactate dehydrogenase expression. PMID:20400555

Permanent foresty plots: a potentially valuable teaching resource in undergraduate biology porgrams for the Caribbean

Treesearch

H. Valles; C.M.S. Carrington

2016-01-01

There has been a recent proposal to change the way that biology is taught and learned in undergraduate biology programs in the USA so that students develop a better understanding of science and the natural world. Here, we use this new, recommended teaching– learning framework to assert that permanent forestry plots could be a valuable tool to help develop biology...

Are consumer surveys valuable as a service improvement tool in health services? A critical appraisal.

PubMed

Patwardhan, Anjali; Patwardhan, Prakash

2009-01-01

In the recent climate of consumerism and consumer focused care, health and social care needs to be more responsive than ever before. Consumer needs and preferences can be elicited with accepted validity and reliability only by strict methodological control, customerisation of the questionnaire and skilled interpretation. To construct, conduct, interpret and implement improved service provision, requires a trained work force and infrastructure. This article aims to appraise various aspects of consumer surveys and to assess their value as effective service improvement tools. The customer is the sole reason organisations exist. Consumer surveys are used worldwide as service and quality of care improvement tools by all types of service providers including health service providers. The article critically appraises the value of consumer surveys as service improvement tools in health services tool and its future applications. No one type of survey is the best or ideal. The key is the selection of the correct survey methodology, unique and customised for the particular type/aspect of care being evaluated. The method used should reflect the importance of the information required. Methodological rigor is essential for the effectiveness of consumer surveys as service improvement tools. Unfortunately so far there is no universal consensus on superiority of one particular methodology over another or any benefit of one specific methodology in a given situation. More training and some dedicated resource allocation is required to develop consumer surveys. More research is needed to develop specific survey methodology and evaluation techniques for improved validity and reliability of the surveys as service improvement tools. Measurement of consumer preferences/priorities, evaluation of services and key performance scores, is not easy. Consumer surveys seem impressive tools as they provide the customer a voice for change or modification. However, from a scientific point

The Relationship of Genetics, Nursing Practice, and Informatics Tools in 6-Mercaptopurine Dosing in Pediatric Oncology [Formula: see text].

PubMed

Haylett, Wendy J

An antileukemic agent prescribed for pediatric oncology patients during the maintenance phase of therapy for acute lymphoblastic leukemia, 6-mercaptopurine (6-MP), is highly influenced by genetic variations in the thiopurine S-methyltransferase enzyme. As such, 6-MP must be dosed so that patients with 1 or 2 inactive thiopurine S-methyltransferase alleles will not incur an increased risk for myelosuppression or other toxicities. Informatics tools such as clinical decision support systems are useful for the application of this and similar pharmacogenetics information to the realm of nursing and clinical practice for safe and effective patient care. This article will discuss pharmacogenetics and the associated use of 6-MP; present implications for nursing practice; identify informatics tools such as clinical decision support systems, which can greatly enhance the care of patients whose treatment is based on critical genetic information; and examine the relationship of genetics, nursing practice, and informatics for 6-MP dosing in pediatric oncology.

Astonishing advances in mouse genetic tools for biomedical research.

PubMed

Kaczmarczyk, Lech; Jackson, Walker S

2015-01-01

The humble house mouse has long been a workhorse model system in biomedical research. The technology for introducing site-specific genome modifications led to Nobel Prizes for its pioneers and opened a new era of mouse genetics. However, this technology was very time-consuming and technically demanding. As a result, many investigators continued to employ easier genome manipulation methods, though resulting models can suffer from overlooked or underestimated consequences. Another breakthrough, invaluable for the molecular dissection of disease mechanisms, was the invention of high-throughput methods to measure the expression of a plethora of genes in parallel. However, the use of samples containing material from multiple cell types could obfuscate data, and thus interpretations. In this review we highlight some important issues in experimental approaches using mouse models for biomedical research. We then discuss recent technological advances in mouse genetics that are revolutionising human disease research. Mouse genomes are now easily manipulated at precise locations thanks to guided endonucleases, such as transcription activator-like effector nucleases (TALENs) or the CRISPR/Cas9 system, both also having the potential to turn the dream of human gene therapy into reality. Newly developed methods of cell type-specific isolation of transcriptomes from crude tissue homogenates, followed by detection with next generation sequencing (NGS), are vastly improving gene regulation studies. Taken together, these amazing tools simplify the creation of much more accurate mouse models of human disease, and enable the extraction of hitherto unobtainable data.

Reproductive cloning and a (kind of) genetic fallacy.

PubMed

Levy, Neil; Lotz, Mianna

2005-06-01

Many people now believe that human reproductive cloning--once sufficiently safe and effective--should be permitted on the grounds that it will allow the otherwise infertile to have children that are biologically closely related to them. However, though it is widely believed that the possession of a close genetic link to our children is morally significant and valuable, we argue that such a view is erroneous. Moreover, the claim that the genetic link is valuable is pernicious; it tends to give rise to highly undesirable consequences, and therefore should be combated rather than pandered to. The emphasis on the genetic is unwarranted and unfortunate; rather than giving us moral reason to support reproductive cloning in the case of infertility, the fact that cloning requests are likely to be motivated by the genetic argument gives us reason to oppose its availability.

Genetic Diversity and Population Structure of Rice Varieties Cultivated in Temperate Regions.

PubMed

Reig-Valiente, Juan L; Viruel, Juan; Sales, Ester; Marqués, Luis; Terol, Javier; Gut, Marta; Derdak, Sophia; Talón, Manuel; Domingo, Concha

2016-12-01

current genetic resources available for temperate varieties of rice, providing a valuable tool for future association mapping studies.

Computer Simulation Is an Undervalued Tool for Genetic Analysis: A Historical View and Presentation of SHIMSHON – A Web-Based Genetic Simulation Package

PubMed Central

Greenberg, David A.

2011-01-01

Computer simulation methods are under-used tools in genetic analysis because simulation approaches have been portrayed as inferior to analytic methods. Even when simulation is used, its advantages are not fully exploited. Here, I present SHIMSHON, our package of genetic simulation programs that have been developed, tested, used for research, and used to generated data for Genetic Analysis Workshops (GAW). These simulation programs, now web-accessible, can be used by anyone to answer questions about designing and analyzing genetic disease studies for locus identification. This work has three foci: (1) the historical context of SHIMSHON's development, suggesting why simulation has not been more widely used so far. (2) Advantages of simulation: computer simulation helps us to understand how genetic analysis methods work. It has advantages for understanding disease inheritance and methods for gene searches. Furthermore, simulation methods can be used to answer fundamental questions that either cannot be answered by analytical approaches or cannot even be defined until the problems are identified and studied, using simulation. (3) I argue that, because simulation was not accepted, there was a failure to grasp the meaning of some simulation-based studies of linkage. This may have contributed to perceived weaknesses in linkage analysis; weaknesses that did not, in fact, exist. PMID:22189467

A preliminary assessment of genetic relationships among agronomically important cultivars of black pepper

PubMed Central

Joy, Nisha; Abraham, Z; Soniya, EV

2007-01-01

Background The impact of diseases such as Phytophthora foot rot and the replacement of unproductive cultivars by high yielding ones has brought about the disappearance of varieties in Piper species, like any other crop. Black pepper (King of spices), is a major spice crop consumed throughout the world. It is widely cultivated across various parts of the world apart from India. The different cultivars may be genetically related and could be a source of valuable genes for disease resistance and an increase in quantity and quality. Even though Western Ghats in India is believed to be the site of origin of this crop, numerous accessions from the NBPGR have not yet been evaluated. Our study aims to investigate the genetic relatedness in major cultivars of black pepper using Amplified Fragment Length Polymorphism. Results Amplified Fragment Length Polymorphic (AFLP) DNA analysis was performed in thirty popular cultivars of black pepper from National Bureau of Plant Genetic Resources (NBPGR), India. Fingerprint profiles were generated initially with, five different primer combinations, from which three primer pair combinations (EAGC/MCAA, EAGG/MCTA and EAGC/MCTG) gave consistent and scorable banding patterns. From 173 scorable markers, 158(> 90%) were polymorphic which shows there is considerable variation in the available germplasm. The dendrogram derived by unweighted pair group method analysis (UPGMA) grouped the accessions into three major clusters and four diverse cultivars with only 30% similarity. Karimunda, a widely grown and popular cultivar was unique in the fingerprint profiles obtained. Conclusion There are currently few fingerprinting studies using the valuable spice crop black pepper. We found considerable genetic variability among cultivars of black pepper. Fingerprinting analysis with AFLP proved to be an ideal tool for cultivar identification and phylogenetic studies. It shows the high level of polymorphism and the unique characterization of the major

The Perfect Neuroimaging-Genetics-Computation Storm: Collision of Petabytes of Data, Millions of Hardware Devices and Thousands of Software Tools

PubMed Central

Dinov, Ivo D.; Petrosyan, Petros; Liu, Zhizhong; Eggert, Paul; Zamanyan, Alen; Torri, Federica; Macciardi, Fabio; Hobel, Sam; Moon, Seok Woo; Sung, Young Hee; Jiang, Zhiguo; Labus, Jennifer; Kurth, Florian; Ashe-McNalley, Cody; Mayer, Emeran; Vespa, Paul M.; Van Horn, John D.; Toga, Arthur W.

2013-01-01

The volume, diversity and velocity of biomedical data are exponentially increasing providing petabytes of new neuroimaging and genetics data every year. At the same time, tens-of-thousands of computational algorithms are developed and reported in the literature along with thousands of software tools and services. Users demand intuitive, quick and platform-agnostic access to data, software tools, and infrastructure from millions of hardware devices. This explosion of information, scientific techniques, computational models, and technological advances leads to enormous challenges in data analysis, evidence-based biomedical inference and reproducibility of findings. The Pipeline workflow environment provides a crowd-based distributed solution for consistent management of these heterogeneous resources. The Pipeline allows multiple (local) clients and (remote) servers to connect, exchange protocols, control the execution, monitor the states of different tools or hardware, and share complete protocols as portable XML workflows. In this paper, we demonstrate several advanced computational neuroimaging and genetics case-studies, and end-to-end pipeline solutions. These are implemented as graphical workflow protocols in the context of analyzing imaging (sMRI, fMRI, DTI), phenotypic (demographic, clinical), and genetic (SNP) data. PMID:23975276

GAPscreener: An automatic tool for screening human genetic association literature in PubMed using the support vector machine technique

PubMed Central

Yu, Wei; Clyne, Melinda; Dolan, Siobhan M; Yesupriya, Ajay; Wulf, Anja; Liu, Tiebin; Khoury, Muin J; Gwinn, Marta

2008-01-01

Background Synthesis of data from published human genetic association studies is a critical step in the translation of human genome discoveries into health applications. Although genetic association studies account for a substantial proportion of the abstracts in PubMed, identifying them with standard queries is not always accurate or efficient. Further automating the literature-screening process can reduce the burden of a labor-intensive and time-consuming traditional literature search. The Support Vector Machine (SVM), a well-established machine learning technique, has been successful in classifying text, including biomedical literature. The GAPscreener, a free SVM-based software tool, can be used to assist in screening PubMed abstracts for human genetic association studies. Results The data source for this research was the HuGE Navigator, formerly known as the HuGE Pub Lit database. Weighted SVM feature selection based on a keyword list obtained by the two-way z score method demonstrated the best screening performance, achieving 97.5% recall, 98.3% specificity and 31.9% precision in performance testing. Compared with the traditional screening process based on a complex PubMed query, the SVM tool reduced by about 90% the number of abstracts requiring individual review by the database curator. The tool also ascertained 47 articles that were missed by the traditional literature screening process during the 4-week test period. We examined the literature on genetic associations with preterm birth as an example. Compared with the traditional, manual process, the GAPscreener both reduced effort and improved accuracy. Conclusion GAPscreener is the first free SVM-based application available for screening the human genetic association literature in PubMed with high recall and specificity. The user-friendly graphical user interface makes this a practical, stand-alone application. The software can be downloaded at no charge. PMID:18430222

GAPscreener: an automatic tool for screening human genetic association literature in PubMed using the support vector machine technique.

PubMed

Yu, Wei; Clyne, Melinda; Dolan, Siobhan M; Yesupriya, Ajay; Wulf, Anja; Liu, Tiebin; Khoury, Muin J; Gwinn, Marta

2008-04-22

Synthesis of data from published human genetic association studies is a critical step in the translation of human genome discoveries into health applications. Although genetic association studies account for a substantial proportion of the abstracts in PubMed, identifying them with standard queries is not always accurate or efficient. Further automating the literature-screening process can reduce the burden of a labor-intensive and time-consuming traditional literature search. The Support Vector Machine (SVM), a well-established machine learning technique, has been successful in classifying text, including biomedical literature. The GAPscreener, a free SVM-based software tool, can be used to assist in screening PubMed abstracts for human genetic association studies. The data source for this research was the HuGE Navigator, formerly known as the HuGE Pub Lit database. Weighted SVM feature selection based on a keyword list obtained by the two-way z score method demonstrated the best screening performance, achieving 97.5% recall, 98.3% specificity and 31.9% precision in performance testing. Compared with the traditional screening process based on a complex PubMed query, the SVM tool reduced by about 90% the number of abstracts requiring individual review by the database curator. The tool also ascertained 47 articles that were missed by the traditional literature screening process during the 4-week test period. We examined the literature on genetic associations with preterm birth as an example. Compared with the traditional, manual process, the GAPscreener both reduced effort and improved accuracy. GAPscreener is the first free SVM-based application available for screening the human genetic association literature in PubMed with high recall and specificity. The user-friendly graphical user interface makes this a practical, stand-alone application. The software can be downloaded at no charge.

Valuable water

NASA Astrophysics Data System (ADS)

Carlowicz, Michael

In some places, money flows with water. Studying both the water quality and property values around 22 lakes in south-central Maine, Kevin Boyle and Holly James of the University of Maine and Roy Bouchard of the Maine Department of Environmental Protection have found that good water quality makes waterfront property even more valuable. To gauge water quality, the researchers used Secchi disks to measure the clarity of the water at depth. They also reviewed 543 lakefront property sales between 1990 and 1994 to determine how values correlated with changing water conditions. The group also considered such factors as lake frontage, sizes of the houses and lots, and size of the lake.

Tying Profit to Performance: A Valuable Tool, But Use With Good Judgment

DTIC Science & Technology

2015-06-01

tool that ties profit to performance in a way that has been dem- onstrated to be a win-win for DoD and industry. PBL is...understood the definition of suc-cess: It was profit . If something made a profit for a business, it was good. If some- thing did not make a profit for a ... bankruptcy . Declining profits make it harder for businesses to raise capital or to invest for their futures. These

Using classical population genetics tools with heterochroneous data: time matters!

PubMed

Depaulis, Frantz; Orlando, Ludovic; Hänni, Catherine

2009-01-01

New polymorphism datasets from heterochroneous data have arisen thanks to recent advances in experimental and microbial molecular evolution, and the sequencing of ancient DNA (aDNA). However, classical tools for population genetics analyses do not take into account heterochrony between subsets, despite potential bias on neutrality and population structure tests. Here, we characterize the extent of such possible biases using serial coalescent simulations. We first use a coalescent framework to generate datasets assuming no or different levels of heterochrony and contrast most classical population genetic statistics. We show that even weak levels of heterochrony ( approximately 10% of the average depth of a standard population tree) affect the distribution of polymorphism substantially, leading to overestimate the level of polymorphism theta, to star like trees, with an excess of rare mutations and a deficit of linkage disequilibrium, which are the hallmark of e.g. population expansion (possibly after a drastic bottleneck). Substantial departures of the tests are detected in the opposite direction for more heterochroneous and equilibrated datasets, with balanced trees mimicking in particular population contraction, balancing selection, and population differentiation. We therefore introduce simple corrections to classical estimators of polymorphism and of the genetic distance between populations, in order to remove heterochrony-driven bias. Finally, we show that these effects do occur on real aDNA datasets, taking advantage of the currently available sequence data for Cave Bears (Ursus spelaeus), for which large mtDNA haplotypes have been reported over a substantial time period (22-130 thousand years ago (KYA)). Considering serial sampling changed the conclusion of several tests, indicating that neglecting heterochrony could provide significant support for false past history of populations and inappropriate conservation decisions. We therefore argue for systematically

Using Classical Population Genetics Tools with Heterochroneous Data: Time Matters!

PubMed Central

Depaulis, Frantz; Orlando, Ludovic; Hänni, Catherine

2009-01-01

Background New polymorphism datasets from heterochroneous data have arisen thanks to recent advances in experimental and microbial molecular evolution, and the sequencing of ancient DNA (aDNA). However, classical tools for population genetics analyses do not take into account heterochrony between subsets, despite potential bias on neutrality and population structure tests. Here, we characterize the extent of such possible biases using serial coalescent simulations. Methodology/Principal Findings We first use a coalescent framework to generate datasets assuming no or different levels of heterochrony and contrast most classical population genetic statistics. We show that even weak levels of heterochrony (∼10% of the average depth of a standard population tree) affect the distribution of polymorphism substantially, leading to overestimate the level of polymorphism θ, to star like trees, with an excess of rare mutations and a deficit of linkage disequilibrium, which are the hallmark of e.g. population expansion (possibly after a drastic bottleneck). Substantial departures of the tests are detected in the opposite direction for more heterochroneous and equilibrated datasets, with balanced trees mimicking in particular population contraction, balancing selection, and population differentiation. We therefore introduce simple corrections to classical estimators of polymorphism and of the genetic distance between populations, in order to remove heterochrony-driven bias. Finally, we show that these effects do occur on real aDNA datasets, taking advantage of the currently available sequence data for Cave Bears (Ursus spelaeus), for which large mtDNA haplotypes have been reported over a substantial time period (22–130 thousand years ago (KYA)). Conclusions/Significance Considering serial sampling changed the conclusion of several tests, indicating that neglecting heterochrony could provide significant support for false past history of populations and inappropriate

MOLECULAR GENETIC APPROACHES TO PEST AND NONTARGET POPULATION MONITORING

EPA Science Inventory

The U.S. Environmental Protection Agency has interest in a number of applications of genetic monitoring methodologies. Genetic monitoring in agroecosystems can provide valuable environmental information regarding both traditional and novel pesticides. One group of pesticides of...

Genetic algorithms

NASA Technical Reports Server (NTRS)

Wang, Lui; Bayer, Steven E.

1991-01-01

Genetic algorithms are mathematical, highly parallel, adaptive search procedures (i.e., problem solving methods) based loosely on the processes of natural genetics and Darwinian survival of the fittest. Basic genetic algorithms concepts are introduced, genetic algorithm applications are introduced, and results are presented from a project to develop a software tool that will enable the widespread use of genetic algorithm technology.

Quantitative genetic models of sexual conflict based on interacting phenotypes.

PubMed

Moore, Allen J; Pizzari, Tommaso

2005-05-01

Evolutionary conflict arises between reproductive partners when alternative reproductive opportunities are available. Sexual conflict can generate sexually antagonistic selection, which mediates sexual selection and intersexual coevolution. However, despite intense interest, the evolutionary implications of sexual conflict remain unresolved. We propose a novel theoretical approach to study the evolution of sexually antagonistic phenotypes based on quantitative genetics and the measure of social selection arising from male-female interactions. We consider the phenotype of one sex as both a genetically influenced evolving trait as well as the (evolving) social environment in which the phenotype of the opposite sex evolves. Several important points emerge from our analysis, including the relationship between direct selection on one sex and indirect effects through selection on the opposite sex. We suggest that the proposed approach may be a valuable tool to complement other theoretical approaches currently used to study sexual conflict. Most importantly, our approach highlights areas where additional empirical data can help clarify the role of sexual conflict in the evolutionary process.

The Stand-Alone Microprocessor System: A Valuable Tool in College Admissions and Recruitment.

ERIC Educational Resources Information Center

Garrett, Larry Neal

1983-01-01

The stand-alone microprocessor is seen as one innovative tool that can be used both in the organizational management of decline and in meeting specific organizational needs such as those of the admissions director and staff. The term "microprocessor" is defined. (MLW)

Using population genetic tools to develop a control strategy for feral cats (Felis catus) in Hawai'i

USGS Publications Warehouse

Hansen, H.; Hess, S.C.; Cole, D.; Banko, P.C.

2007-01-01

Population genetics can provide information about the demographics and dynamics of invasive species that is beneficial for developing effective control strategies. We studied the population genetics of feral cats on Hawai'i Island by microsatellite analysis to evaluate genetic diversity and population structure, assess gene flow and connectivity among three populations, identify potential source populations, characterise population dynamics, and evaluate sex-biased dispersal. High genetic diversity, low structure, and high number of migrants per generation supported high gene flow that was not limited spatially. Migration rates revealed that most migration occurred out of West Mauna Kea. Effective population size estimates indicated increasing cat populations despite control efforts. Despite high gene flow, relatedness estimates declined significantly with increased geographic distance and Bayesian assignment tests revealed the presence of three population clusters. Genetic structure and relatedness estimates indicated male-biased dispersal, primarily from Mauna Kea, suggesting that this population should be targeted for control. However, recolonisation seems likely, given the great dispersal ability that may not be inhibited by barriers such as lava flows. Genetic monitoring will be necessary to assess the effectiveness of future control efforts. Management of other invasive species may benefit by employing these population genetic tools. ?? CSIRO 2007.

Educating Tomorrow's Valuable Citizen.

ERIC Educational Resources Information Center

Burstyn, Joan N., Ed.

This collection of essays by various authors discusses the dilemmas that face those who would educate tomorrow's valuable citizens and describes the day-to-day commitment needed to maintain a community. The book gives guidelines for action through examples of current programs that provide a forum for civic discussion and public consensus on the…

Genetic variation in polyploid forage grass: Assessing the molecular genetic variability in the Paspalum genus

PubMed Central

2013-01-01

valuable tool for species identification in the initial assessment of germplasm as well as for characterization, conservation and successful species hybridization. PMID:23759066

An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology.

PubMed

Pennell, Matthew W; Harmon, Luke J

2013-06-01

Recent innovations in phylogenetic comparative methods (PCMs) have spurred a renaissance of research into the causes and consequences of large-scale patterns of biodiversity. In this paper, we review these advances. We also highlight the potential of comparative methods to integrate across fields and focus on three examples where such integration might be particularly valuable: quantitative genetics, community ecology, and paleobiology. We argue that PCMs will continue to be a key set of tools in evolutionary biology, shedding new light on how evolutionary processes have shaped patterns of biodiversity through deep time. © 2013 New York Academy of Sciences.

Genetic, genomic, and molecular tools for studying the protoploid yeast, L. waltii.

PubMed

Di Rienzi, Sara C; Lindstrom, Kimberly C; Lancaster, Ragina; Rolczynski, Lisa; Raghuraman, M K; Brewer, Bonita J

2011-02-01

Sequencing of the yeast Kluyveromyces waltii (recently renamed Lachancea waltii) provided evidence of a whole genome duplication event in the lineage leading to the well-studied Saccharomyces cerevisiae. While comparative genomic analyses of these yeasts have proven to be extremely instructive in modeling the loss or maintenance of gene duplicates, experimental tests of the ramifications following such genome alterations remain difficult. To transform L. waltii from an organism of the computational comparative genomic literature into an organism of the functional comparative genomic literature, we have developed genetic, molecular and genomic tools for working with L. waltii. In particular, we have characterized basic properties of L. waltii (growth, ploidy, molecular karyotype, mating type and the sexual cycle), developed transformation, cell cycle arrest and synchronization protocols, and have created centromeric and non-centromeric vectors as well as a genome browser for L. waltii. We hope that these tools will be used by the community to follow up on the ideas generated by sequence data and lead to a greater understanding of eukaryotic biology and genome evolution. 2010 John Wiley & Sons, Ltd.

Genetic, genomic, and molecular tools for studying the protoploid yeast, L. waltii

PubMed Central

Di Rienzi, Sara C.; Lindstrom, Kimberly C.; Lancaster, Ragina; Rolczynski, Lisa; Raghuraman, M. K.; Brewer, Bonita J.

2011-01-01

Sequencing of the yeast Kluyveromyces waltii (recently renamed Lachancea waltii) provided evidence of a whole genome duplication event in the lineage leading to the well-studied Saccharomyces cerevisiae. While comparative genomic analyses of these yeasts have proven to be extremely instructive in modeling the loss or maintenance of gene duplicates, experimental tests of the ramifications following such genome alterations remain difficult. To transform L. waltii from an organism of the computational comparative genomic literature into an organism of the functional comparative genomic literature, we have developed genetic, molecular and genomic tools for working with L. waltii. In particular, we have characterized basic properties of L. waltii (growth, ploidy, molecular karyotype, mating type and the sexual cycle), developed transformation, cell cycle arrest and synchronization protocols, and have created centromeric and non-centromeric vectors as well as a genome browser for L. waltii. We hope that these tools will be used by the community to follow up on the ideas generated by sequence data and lead to a greater understanding of eukaryotic biology and genome evolution. PMID:21246627

Preimplantation genetic testing for aneuploidy: what technology should you use and what are the differences?

PubMed

Brezina, Paul R; Anchan, Raymond; Kearns, William G

2016-07-01

The purpose of the review was to define the various diagnostic platforms currently available to perform preimplantation genetic testing for aneuploidy and describe in a clear and balanced manner the various strengths and weaknesses of these technologies. A systematic literature review was conducted. We used the terms "preimplantation genetic testing," "preimplantation genetic diagnosis," "preimplantation genetic screening," "preimplantation genetic diagnosis for aneuploidy," "PGD," "PGS," and "PGD-A" to search through PubMed, ScienceDirect, and Google Scholar from the year 2000 to April 2016. Bibliographies of articles were also searched for relevant studies. When possible, larger randomized controlled trials were used. However, for some emerging data, only data from meeting abstracts were available. PGS is emerging as one of the most valuable tools to enhance pregnancy success with assisted reproductive technologies. While all of the current diagnostic platforms currently available have various advantages and disadvantages, some platforms, such as next-generation sequencing (NGS), are capable of evaluating far more data points than has been previously possible. The emerging complexity of different technologies, especially with the utilization of more sophisticated tools such as NGS, requires an understanding by clinicians in order to request the best test for their patients.. Ultimately, the choice of which diagnostic platform is utilized should be individualized to the needs of both the clinic and the patient. Such a decision must incorporate the risk tolerance of both the patient and provider, fiscal considerations, and other factors such as the ability to counsel patients on their testing results and how these may or may not impact clinical outcomes.

Molecular genetics and genomics generate new insights into invertebrate pest invasions.

PubMed

Kirk, Heather; Dorn, Silvia; Mazzi, Dominique

2013-07-01

Invertebrate pest invasions and outbreaks are associated with high social, economic, and ecological costs, and their significance will intensify with an increasing pressure on agricultural productivity as a result of human population growth and climate change. New molecular genetic and genomic techniques are available and accessible, but have been grossly underutilized in studies of invertebrate pest invasions, despite that they are useful tools for applied pest management and for understanding fundamental features of pest invasions including pest population demographics and adaptation of pests to novel and/or changing environments. Here, we review current applications of molecular genetics and genomics in the study of invertebrate pest invasions and outbreaks, and we highlight shortcomings from the current body of research. We then discuss recent conceptual and methodological advances in the areas of molecular genetics/genomics and data analysis, and we highlight how these advances will further our understanding of the demographic, ecological, and evolutionary features of invertebrate pest invasions. We are now well equipped to use molecular data to understand invertebrate dispersal and adaptation, and this knowledge has valuable applications in agriculture at a time when these are critically required.

Phylogenic analysis and forensic genetic characterization of Chinese Uyghur group via autosomal multi STR markers

PubMed Central

Jin, Xiaoye; Wei, Yuanyuan; Chen, Jiangang; Kong, Tingting; Mu, Yuling; Guo, Yuxin; Dong, Qian; Xie, Tong; Meng, Haotian; Zhang, Meng; Li, Jianfei; Li, Xiaopeng; Zhu, Bofeng

2017-01-01

We investigated the allelic frequencies and forensic descriptive parameters of 23 autosomal short tandem repeat loci in a randomly selected sample of 1218 unrelated healthy Uyghur individuals residing in the Xinjiang Uyghur Autonomous Region, northwest China. A total of 281 alleles at these loci were identified and their corresponding allelic frequencies ranged from 0.0004 to 0.5390. The combined match probability and combined probability of exclusion of all loci were 5.192 × 10−29 and 0.9999999996594, respectively. The results of population genetic study manifested that Uyghur had close relationships with those contiguous populations, such as Xibe and Hui groups. In a word, these autosomal short tandem repeat loci were highly informative in Uyghur group and the multiplex PCR system could be used as a valuable tool for forensic caseworks and population genetic analysis. PMID:29088750

Phylogenic analysis and forensic genetic characterization of Chinese Uyghur group via autosomal multi STR markers.

PubMed

Jin, Xiaoye; Wei, Yuanyuan; Chen, Jiangang; Kong, Tingting; Mu, Yuling; Guo, Yuxin; Dong, Qian; Xie, Tong; Meng, Haotian; Zhang, Meng; Li, Jianfei; Li, Xiaopeng; Zhu, Bofeng

2017-09-26

We investigated the allelic frequencies and forensic descriptive parameters of 23 autosomal short tandem repeat loci in a randomly selected sample of 1218 unrelated healthy Uyghur individuals residing in the Xinjiang Uyghur Autonomous Region, northwest China. A total of 281 alleles at these loci were identified and their corresponding allelic frequencies ranged from 0.0004 to 0.5390. The combined match probability and combined probability of exclusion of all loci were 5.192 × 10 -29 and 0.9999999996594, respectively. The results of population genetic study manifested that Uyghur had close relationships with those contiguous populations, such as Xibe and Hui groups. In a word, these autosomal short tandem repeat loci were highly informative in Uyghur group and the multiplex PCR system could be used as a valuable tool for forensic caseworks and population genetic analysis.

Combined measurement of plasma cystatin C and low-density lipoprotein cholesterol: A valuable tool for evaluating progressive supranuclear palsy.

PubMed

Weng, Ruihui; Wei, Xiaobo; Yu, Bin; Zhu, Shuzhen; Yang, Xiaohua; Xie, Fen; Zhang, Mahui; Jiang, Ying; Feng, Zhong-Ping; Sun, Hong-Shuo; Xia, Ying; Jin, Kunlin; Chan, Piu; Wang, Qing; Gao, Xiaoya

2018-07-01

Progressive supranuclear palsy (PSP) was previously thought as a cause of atypical Parkinsonism. Although Cystatin C (Cys C) and low-density cholesterol lipoprotein-C (LDL-C) are known to play critical roles in Parkinsonism, it is unknown whether they can be used as markers to distinguish PSP patients from healthy subjects and to determine disease severity. We conducted a cross-sectional study to determine plasma Cys C/HDL/LDL-C levels of 40 patients with PSP and 40 healthy age-matched controls. An extended battery of motor and neuropsychological tests, including the PSP-Rating Scale (PSPRS), the Non-Motor Symptoms Scale (NMSS), Geriatric Depression Scale (GDS) and Mini-Mental State Examination (MMSE), was used to evaluate the disease severity. Receiver operating characteristic (ROC) curves were adopted to assess the prognostic accuracy of Cys C/LDL-C levels in distinguishing PSP from healthy subjects. Patients with PSP exhibited significantly higher plasma levels of Cys C and lower LDL-C. The levels of plasma Cys C were positively and inversely correlated with the PSPRS/NMSS and MMSE scores, respectively. The LDL-C/HDL-C ratio was positively associated with PSPRS/NMSS and GDS scores. The ROC curve for the combination of Cys C and LDL-C yielded a better accuracy for distinguishing PSP from healthy subjects than the separate curves for each parameter. Plasma Cys C and LDL-C may be valuable screening tools for differentiating PSP from healthy subjects; while they could be useful for the PSP intensifies and severity evaluation. A better understanding of Cys C and LDL-C may yield insights into the pathogenesis of PSP. Copyright © 2018 Elsevier Ltd. All rights reserved.

“Real time” genetic manipulation: a new tool for ecological field studies

PubMed Central

Schäfer, Martin; Brütting, Christoph; Gase, Klaus; Reichelt, Michael; Baldwin, Ian; Meldau, Stefan

2014-01-01

Summary Field experiments with transgenic plants often reveal the functional significance of genetic traits important for plant performance in their natural environments. Until now, only constitutive overexpression, ectopic expression and gene silencing methods have been used to analyze gene-related phenotypes in natural habitats. These methods do not allow sufficient control over gene expression to study ecological interactions in real-time, genetic traits playing essential roles in development, or dose-dependent effects. We applied the sensitive dexamethasone (DEX)-inducible pOp6/LhGR expression system to the ecological model plant Nicotiana attenuata and established a lanolin-based DEX application method to facilitate ectopic gene expression and RNAi mediated gene silencing in the field and under challenging conditions (e.g. high temperature, wind and UV radiation). Fully established field-grown plants were used to silence phytoene desaturase and thereby cause photobleaching only in specific plant sectors, and to activate expression of the cytokinin (CK) biosynthesis gene isopentenyl transferase (ipt). We used ipt expression to analyze the role of CK’s in both the glasshouse and field to understand resistance to the native herbivore Tupiocoris notatus, which attack plants at small spatial scales. By spatially restricting ipt expression and elevating CK levels in single leaves, T. notatus damage increased, demonstrating CK’s role in this plant-herbivore interaction at a small scale. As the arena of most ecological interactions is highly constrained in time and space, these tools will advance the genetic analysis of dynamic traits that matter for plant performance in nature. PMID:23906159

Nationwide genetic testing towards eliminating Lafora disease from Miniature Wirehaired Dachshunds in the United Kingdom.

PubMed

Ahonen, Saija; Seath, Ian; Rusbridge, Clare; Holt, Susan; Key, Gill; Wang, Travis; Wang, Peixiang; Minassian, Berge A

2018-01-01

Canine DNA-testing has become an important tool in purebred dog breeding and many breeders use genetic testing results when planning their breeding strategies. In addition, information obtained from testing of hundreds dogs in one breed gives valuable information about the breed-wide genotype frequency of disease associated allele. Lafora disease is a late onset, recessively inherited genetic disease which is diagnosed in Miniature Wirehaired Dachshunds (MWHD). It is one of the most severe forms of canine epilepsy leading to neurodegeneration and, frequently euthanasia within a few years of diagnosis. Canine Lafora disease is caused by a dodecamer repeat expansion mutation in the NHLRC1 gene and a DNA test is available to identify homozygous dogs at risk, carriers and dogs free of the mutation. Blood samples were collected from 733 MWHDs worldwide, mostly of UK origin, for canine Lafora disease testing. Among the tested MWHD population 7.0% were homozygous for the mutation and at risk for Lafora disease. In addition, 234 dogs were heterozygous, indicating a carrier frequency of 31.9% in the tested population. Among the tested MWHDs, the mutant allele frequency was 0.2. In addition, data from the tested dogs over 6 years (2012-2017) indicated that the frequency of the homozygous and carrier dogs has decreased from 10.4% to 2.7% and 41.5% to 25.7%, respectively among MWHDs tested. As a consequence, the frequency of dogs free of the mutation has increased from 48.1% to 71.6%. This study provides valuable data for the MWHD community and shows that the DNA test is a useful tool for the breeders to prevent occurrence of Lafora disease in MWHDs. DNA testing has, over 6 years, helped to decrease the frequency of carriers and dogs at risk. Additionally, the DNA test can continue to be used to slowly eradicate the disease-causing mutation in the breed. However, this should be done carefully, over time, to avoid further compromising the genetic diversity of the breed. The

Expanding the scope of site-specific recombinases for genetic and metabolic engineering.

PubMed

Gaj, Thomas; Sirk, Shannon J; Barbas, Carlos F

2014-01-01

Site-specific recombinases are tremendously valuable tools for basic research and genetic engineering. By promoting high-fidelity DNA modifications, site-specific recombination systems have empowered researchers with unprecedented control over diverse biological functions, enabling countless insights into cellular structure and function. The rigid target specificities of many sites-specific recombinases, however, have limited their adoption in fields that require highly flexible recognition abilities. As a result, intense effort has been directed toward altering the properties of site-specific recombination systems by protein engineering. Here, we review key developments in the rational design and directed molecular evolution of site-specific recombinases, highlighting the numerous applications of these enzymes across diverse fields of study. © 2013 Wiley Periodicals, Inc.

Expanding the Scope of Site-Specific Recombinases for Genetic and Metabolic Engineering

PubMed Central

Gaj, Thomas; Sirk, Shannon J.; Barbas, Carlos F.

2014-01-01

Site-specific recombinases are tremendously valuable tools for basic research and genetic engineering. By promoting high-fidelity DNA modifications, site-specific recombination systems have empowered researchers with unprecedented control over diverse biological functions, enabling countless insights into cellular structure and function. The rigid target specificities of many sites-specific recombinases, however, have limited their adoption in fields that require highly flexible recognition abilities. As a result, intense effort has been directed toward altering the properties of site-specific recombination systems by protein engineering. Here, we review key developments in the rational design and directed molecular evolution of site-specific recombinases, highlighting the numerous applications of these enzymes across diverse fields of study. PMID:23982993

Telegenetics use in presymptomatic genetic counselling: patient evaluations on satisfaction and quality of care

PubMed Central

Otten, Ellen; Birnie, Erwin; Ranchor, Adelita V; van Langen, Irene M

2016-01-01

In recent years, online counselling has been introduced in clinical genetics to increase patients' access to care and to reduce time and cost for both patients and professionals. Most telegenetics reports so far evaluated online oncogenetic counselling at remote health centres in regions with large travelling distances, generally showing positive patient outcomes. We think online counselling – including the use of supportive tools that are also available during in-person counselling – of presymptomatic patients in their homes can also be feasible and valuable for patients in relatively small regions. We performed a single-centre pilot study of online genetic counselling for 57 patients who were presymptomatic cardiogenetic (n=17), presymptomatic oncogenetic (n=34) and prenatal (3 couples). One-third of presymptomatic patients we approached consented to online counselling. Patient evaluations of practical aspects, satisfaction and psychological outcomes were assessed and compared with a matched control group. Patients managed to fulfil the preparations, were significantly more satisfied with their counsellor and counselling session than controls and were satisfied with the online counselling more than they expected to be beforehand. Psychological outcomes (decreased anxiety and increased control) did not differ with control patients. Technical problems occurred in almost half of online sessions. Nonetheless, online counselling in patients' homes proved to be feasible and was appreciated by a substantial part of presymptomatic patients at our genetics centre in the Netherlands. Based on these outcomes, we conclude online counselling can be a valuable addition to existing counselling options in regular patient care. PMID:26173963

Incorporating Social Media into your Support Tool Box: Points to Consider from Genetics-Based Communities.

PubMed

Rocha, Heather Mae; Savatt, Juliann M; Riggs, Erin Rooney; Wagner, Jennifer K; Faucett, W Andrew; Martin, Christa Lese

2018-04-01

Patients with newly-described or rare genetic findings are turning to social media to find and connect with others. Blogs, Facebook groups, and Twitter have all been reported as tools for patients to connect with one another. However, the preferences for social media use and privacy among patients, their families, and these communities have not been well characterized. To explore preferences about privacy and membership guidelines, an online survey was administered to two web-based patient registries, Simons Variation in Individuals Project ( www.simonsvipconnect.org ) and GenomeConnect ( www.genomeconnect.org ). Over a three-month period, invitations were sent to 2524 individuals and 103 responses (4%) were received and analyzed. Responses indicate that Facebook is the most popular resource accessed within this sample population (99%). Participants used social media to look for information about their diagnosis or test results (83%), read posts from rare disease groups or organizations (73%), participate in conversations about their diagnosis (67%), and connect with others to find support (58%). Focusing on privacy issues in social media, respondents indicate that membership and access impact the level of comfort in sharing personal or medical information. Nearly 60% of respondents felt uncomfortable sharing photos or medical information within a public Facebook group, whereas only 12% of respondents felt uncomfortable sharing in private group targeted to families alone. Using this preliminary data concerning social media use and privacy, we developed points for genetic counselors to incorporate when discussing available support resources for patients with a new, or rare, genetic diagnosis or genetic test result. Genetic counselors are trained to provide anticipatory guidance to families adapting to new genetic information, and are well-equipped to help patients consider their preferences about using social media as a source of information and support.

Advantages of using molecular coancestry in the removal of introgressed genetic material

PubMed Central

2013-01-01

Background When introgression of undesired exogenous genetic material occurs in a population intended to remain pure, actions are necessary to recover the original background. It has been shown that genome-wide information can replace pedigree information for different objectives and is a valuable tool in the fields of genetic conservation and breeding. In this simulation study, molecular information provided by 50 000 SNP was used to minimise the molecular coancestry between individuals of an admixed population and the foreign individuals that originally introgressed a native population in order to remove the exogenous DNA. Results This management method, which detects the ‘purest’ individuals to be used as parents for the next generation, allowed recovery of the native genetic background to a great extent in all simulated scenarios. However, it also caused an increase in inbreeding larger than expected because of the lower number of individuals selected as parents and the higher coancestry between them. In scenarios involving several introgression events the method was more efficient than in those involving a single introgression event because part of the genetic information was mixed with the native genetic material for a shorter period. Conclusions Genome-wide information can be used to identify the purest individuals via the minimisation of molecular coancestry between individuals of the admixed and exogenous populations. Removal of the undesired genetic material is more efficient with a molecular-based approach than with a pedigree-based approach. PMID:23634969

Genetic diversity based on 28S rDNA sequences among populations of Culex quinquefasciatus collected at different locations in Tamil Nadu, India.

PubMed

Sakthivelkumar, S; Ramaraj, P; Veeramani, V; Janarthanan, S

2015-09-01

The basis of the present study was to distinguish the existence of any genetic variability among populations of Culex quinquefasciatus which would be a valuable tool in the management of mosquito control programmes. In the present study, population of Cx. quinquefasciatus collected at different locations in Tamil Nadu were analyzed for their genetic variation based on 28S rDNA D2 region nucleotide sequences. A high degree of genetic polymorphism was detected in the sequences of D2 region of 28S rDNA on the predicted secondary structures in spite of high nucleotide sequence similarity. The findings based on secondary structure using rDNA sequences suggested the existence of a complex genotypic diversity of Cx. quinquefasciatus population collected at different locations of Tamil Nadu, India. This complexity in genetic diversity in a single mosquito population collected at different locations is considered an important issue towards their influence and nature of vector potential of these mosquitoes.

Differential Targeting of Unpaired Bases within Duplex DNA by the Natural Compound Clerocidin: A Valuable Tool to Dissect DNA Secondary Structure

PubMed Central

Nadai, Matteo; Palù, Giorgio; Palumbo, Manlio; Richter, Sara N.

2012-01-01

Non-canonical DNA structures have been postulated to mediate protein-nucleic acid interactions and to function as intermediates in the generation of frame-shift mutations when errors in DNA replication occur, which result in a variety of diseases and cancers. Compounds capable of binding to non-canonical DNA conformations may thus have significant diagnostic and therapeutic potential. Clerocidin is a natural diterpenoid which has been shown to selectively react with single-stranded bases without targeting the double helix. Here we performed a comprehensive analysis on several non-canonical DNA secondary structures, namely mismatches, nicks, bulges, hairpins, with sequence variations in both the single-stranded region and the double-stranded flanking segment. By analysis of clerocidin reactivity, we were able to identify the exposed reactive residues which provided information on both the secondary structure and the accessibility of the non-paired sites. Mismatches longer than 1 base were necessary to be reached by clerocidin reactive groups, while 1-base nicks were promptly targeted by clerocidin; in hairpins, clerocidin reactivity increased with the length of the hairpin loop, while, interestingly, reactivity towards bulges reached a maximum in 3-base-long bulges and declined in longer bulges. Electrophoretic mobility shift analysis demonstrated that bulges longer than 3 bases (i.e. 5- and 7-bases) folded or stacked on the duplex region therefore being less accessible by the compound. Clerocidin thus represents a new valuable diagnostic tool to dissect DNA secondary structures. PMID:23285245

Differential targeting of unpaired bases within duplex DNA by the natural compound clerocidin: a valuable tool to dissect DNA secondary structure.

PubMed

Nadai, Matteo; Palù, Giorgio; Palumbo, Manlio; Richter, Sara N

2012-01-01

Non-canonical DNA structures have been postulated to mediate protein-nucleic acid interactions and to function as intermediates in the generation of frame-shift mutations when errors in DNA replication occur, which result in a variety of diseases and cancers. Compounds capable of binding to non-canonical DNA conformations may thus have significant diagnostic and therapeutic potential. Clerocidin is a natural diterpenoid which has been shown to selectively react with single-stranded bases without targeting the double helix. Here we performed a comprehensive analysis on several non-canonical DNA secondary structures, namely mismatches, nicks, bulges, hairpins, with sequence variations in both the single-stranded region and the double-stranded flanking segment. By analysis of clerocidin reactivity, we were able to identify the exposed reactive residues which provided information on both the secondary structure and the accessibility of the non-paired sites. Mismatches longer than 1 base were necessary to be reached by clerocidin reactive groups, while 1-base nicks were promptly targeted by clerocidin; in hairpins, clerocidin reactivity increased with the length of the hairpin loop, while, interestingly, reactivity towards bulges reached a maximum in 3-base-long bulges and declined in longer bulges. Electrophoretic mobility shift analysis demonstrated that bulges longer than 3 bases (i.e. 5- and 7-bases) folded or stacked on the duplex region therefore being less accessible by the compound. Clerocidin thus represents a new valuable diagnostic tool to dissect DNA secondary structures.

A new comprehension and communication tool: a valuable resource for internationally educated occupational therapists.

PubMed

Nguyen, Tram; Baptiste, Sue; Jung, Bonny; Wilkins, Seanne

2014-06-01

The need was identified for a way to assess internationally educated occupational therapists’ skills in understanding and communicating professional terminology used in occupational therapy practice. The project aim was to develop and validate such a resource. A scenario-based assessment was developed using a three-phase process for tool development. The development process involved completion of a literature scan of professional terminology used in occupational therapy practice; selection of terms and concepts commonly used in occupational therapy practice; and, creation of practice-based scenarios illustrating key concepts complete with rating rubrics. An advisory group provided oversight, and a sample of internationally educated occupational therapists completed pilot and validity testing. The initial findings showed the assessment to be easy to complete and sensitive to testing understanding of the defined terms. The final outcome is an assessment tool that has broad application for occupational therapists wishing to enter professional practice in a new country. © 2013 Occupational Therapy Australia.

Local Genetic Correlation Gives Insights into the Shared Genetic Architecture of Complex Traits.

PubMed

Shi, Huwenbo; Mancuso, Nicholas; Spendlove, Sarah; Pasaniuc, Bogdan

2017-11-02

Although genetic correlations between complex traits provide valuable insights into epidemiological and etiological studies, a precise quantification of which genomic regions disproportionately contribute to the genome-wide correlation is currently lacking. Here, we introduce ρ-HESS, a technique to quantify the correlation between pairs of traits due to genetic variation at a small region in the genome. Our approach requires GWAS summary data only and makes no distributional assumption on the causal variant effect sizes while accounting for linkage disequilibrium (LD) and overlapping GWAS samples. We analyzed large-scale GWAS summary data across 36 quantitative traits, and identified 25 genomic regions that contribute significantly to the genetic correlation among these traits. Notably, we find 6 genomic regions that contribute to the genetic correlation of 10 pairs of traits that show negligible genome-wide correlation, further showcasing the power of local genetic correlation analyses. Finally, we report the distribution of local genetic correlations across the genome for 55 pairs of traits that show putative causal relationships. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Genetic homogeneity in Juglans nigra(Juglanaceae) at nuclear microsatellites

Treesearch

Erin R. Victory; Jeffrey C. Glaubitz; Olin E., Jr. Rhodes; Keith E. Woeste

2006-01-01

Broad-scale studies of genetic structure and diversity are indicative of the recent evolutionary history of a species and are relevant to conservation efforts. We have estimated current levels of genetic diversity and population structure for black walnut (Juglans nigra L.), a highly valuable timber species, in the central hardwood region of the...

The Tracking Meteogram, an AWIPS II Tool for Time-Series Analysis

NASA Technical Reports Server (NTRS)

Burks, Jason Eric; Sperow, Ken

2015-01-01

A new tool has been developed for the National Weather Service (NWS) Advanced Weather Interactive Processing System (AWIPS) II through collaboration between NASA's Short-term Prediction Research and Transition (SPoRT) and the NWS Meteorological Development Laboratory (MDL). Referred to as the "Tracking Meteogram", the tool aids NWS forecasters in assessing meteorological parameters associated with moving phenomena. The tool aids forecasters in severe weather situations by providing valuable satellite and radar derived trends such as cloud top cooling rates, radial velocity couplets, reflectivity, and information from ground-based lightning networks. The Tracking Meteogram tool also aids in synoptic and mesoscale analysis by tracking parameters such as the deepening of surface low pressure systems, changes in surface or upper air temperature, and other properties. The tool provides a valuable new functionality and demonstrates the flexibility and extensibility of the NWS AWIPS II architecture. In 2014, the operational impact of the tool was formally evaluated through participation in the NOAA/NWS Operations Proving Ground (OPG), a risk reduction activity to assess performance and operational impact of new forecasting concepts, tools, and applications. Performance of the Tracking Meteogram Tool during the OPG assessment confirmed that it will be a valuable asset to the operational forecasters. This presentation reviews development of the Tracking Meteogram tool, performance and feedback acquired during the OPG activity, and future goals for continued support and extension to other application areas.

A high-density SNP genetic linkage map for the silver-lipped pearl oyster, Pinctada maxima: a valuable resource for gene localisation and marker-assisted selection.

PubMed

Jones, David B; Jerry, Dean R; Khatkar, Mehar S; Raadsma, Herman W; Zenger, Kyall R

2013-11-20

map for any pearl oyster species. It provides an essential genomic tool facilitating studies investigating the genomic architecture of complex trait variation and identifying quantitative trait loci for economically important traits useful in genetic selection programs within the P. maxima pearling industry. Furthermore, this map provides a foundation for further research aiming to improve our understanding of the dynamic process of biomineralization, and pearl oyster evolution and synteny.

Sunflower genetic, genomic, and ecological resources

USDA-ARS?s Scientific Manuscript database

Long a major focus of genetic research and breeding, sunflowers (Helianthus) are emerging as an increasingly important experimental system for ecological and evolutionary studies. Here we review the various attributes of wild and domesticated sunflowers that make them valuable for ecological experim...

Advances in the genetic dissection of plant cell walls: tools and resources available in Miscanthus

PubMed Central

Slavov, Gancho; Allison, Gordon; Bosch, Maurice

2013-01-01

Tropical C4 grasses from the genus Miscanthus are believed to have great potential as biomass crops. However, Miscanthus species are essentially undomesticated, and genetic, molecular and bioinformatics tools are in very early stages of development. Furthermore, similar to other crops targeted as lignocellulosic feedstocks, the efficient utilization of biomass is hampered by our limited knowledge of the structural organization of the plant cell wall and the underlying genetic components that control this organization. The Institute of Biological, Environmental and Rural Sciences (IBERS) has assembled an extensive collection of germplasm for several species of Miscanthus. In addition, an integrated, multidisciplinary research programme at IBERS aims to inform accelerated breeding for biomass productivity and composition, while also generating fundamental knowledge. Here we review recent advances with respect to the genetic characterization of the cell wall in Miscanthus. First, we present a summary of recent and on-going biochemical studies, including prospects and limitations for the development of powerful phenotyping approaches. Second, we review current knowledge about genetic variation for cell wall characteristics of Miscanthus and illustrate how phenotypic data, combined with high-density arrays of single-nucleotide polymorphisms, are being used in genome-wide association studies to generate testable hypotheses and guide biological discovery. Finally, we provide an overview of the current knowledge about the molecular biology of cell wall biosynthesis in Miscanthus and closely related grasses, discuss the key conceptual and technological bottlenecks, and outline the short-term prospects for progress in this field. PMID:23847628

Enterovirus A71 DNA-Launched Infectious Clone as a Robust Reverse Genetic Tool

PubMed Central

Tan, Chee Wah; Tee, Han Kang; Lee, Michelle Hui Pheng; Sam, I-Ching; Chan, Yoke Fun

2016-01-01

Enterovirus A71 (EV-A71) causes major outbreaks of hand, foot and mouth disease, and is occasionally associated with neurological complications and death in children. Reverse genetics is widely used in the field of virology for functional study of viral genes. For EV-A71, such tools are limited to clones that are transcriptionally controlled by T7/SP6 bacteriophage promoter. This is often time-consuming and expensive. Here, we describe the development of infectious plasmid DNA-based EV-A71 clones, for which EV-A71 genome expression is under transcriptional control by the CMV-intermediate early promoter and SV40 transcriptional-termination signal. Transfection of this EV-A71 infectious DNA produces good virus yield similar to in vitro-transcribed EV-A71 infectious RNA, 6.4 and 5.8 log10PFU/ml, respectively. Infectious plasmid with enhanced green fluorescence protein and Nano luciferase reporter genes also produced good virus titers, with 4.3 and 5.0 log10 PFU/ml, respectively. Another infectious plasmid with both CMV and T7 promoters was also developed for easy manipulation of in vitro transcription or direct plasmid transfection. Transfection with either dual-promoter infectious plasmid DNA or infectious RNA derived from this dual-promoter clone produced infectious viral particles. Incorporation of hepatitis delta virus ribozyme, which yields precise 3’ ends of the DNA-launched EV-A71 genomic transcripts, increased infectious viral production. In contrast, the incorporation of hammerhead ribozyme in the DNA-launched EV-A71 resulted in lower virus yield, but improved the virus titers for T7 promoter-derived infectious RNA. This study describes rapid and robust reverse genetic tools for EV-A71. PMID:27617744

Eukaryotic and prokaryotic promoter databases as valuable tools in exploring the regulation of gene transcription: a comprehensive overview.

PubMed

Majewska, Małgorzata; Wysokińska, Halina; Kuźma, Łukasz; Szymczyk, Piotr

2018-02-20

The complete exploration of the regulation of gene expression remains one of the top-priority goals for researchers. As the regulation is mainly controlled at the level of transcription by promoters, study on promoters and findings are of great importance. This review summarizes forty selected databases that centralize experimental and theoretical knowledge regarding the organization of promoters, interacting transcription factors (TFs) and microRNAs (miRNAs) in many eukaryotic and prokaryotic species. The presented databases offer researchers valuable support in elucidating the regulation of gene transcription. Copyright © 2017 Elsevier B.V. All rights reserved.

Australian endemic pest tephritids: genetic, molecular and microbial tools for improved Sterile Insect Technique

PubMed Central

2014-01-01

Among Australian endemic tephritid fruit flies, the sibling species Bactrocera tryoni and Bactrocera neohumeralis have been serious horticultural pests since the introduction of horticulture in the nineteenth century. More recently, Bactrocera jarvisi has also been declared a pest in northern Australia. After several decades of genetic research there is now a range of classical and molecular genetic tools that can be used to develop improved Sterile Insect Technique (SIT) strains for control of these pests. Four-way crossing strategies have the potential to overcome the problem of inbreeding in mass-reared strains of B. tryoni. The ability to produce hybrids between B. tryoni and the other two species in the laboratory has proved useful for the development of genetically marked strains. The identification of Y-chromosome markers in B. jarvisi means that male and female embryos can be distinguished in any strain that carries a B. jarvisi Y chromosome. This has enabled the study of homologues of the sex-determination genes during development of B jarvisi and B. tryoni, which is necessary for the generation of genetic-sexing strains. Germ-line transformation has been established and a draft genome sequence for B. tryoni released. Transcriptomes from various species, tissues and developmental stages, to aid in identification of manipulation targets for improving SIT, have been assembled and are in the pipeline. Broad analyses of the microbiome have revealed a metagenome that is highly variable within and across species and defined by the environment. More specific analyses detected Wolbachia at low prevalence in the tropics but absent in temperate regions, suggesting a possible role for this endosymbiont in future control strategies. PMID:25470996

Development of the first consensus genetic map of intermediate wheatgrass (Thinopyrum intermedium) using genotyping-by-sequencing.

PubMed

Kantarski, Traci; Larson, Steve; Zhang, Xiaofei; DeHaan, Lee; Borevitz, Justin; Anderson, James; Poland, Jesse

2017-01-01

Development of the first consensus genetic map of intermediate wheatgrass gives insight into the genome and tools for molecular breeding. Intermediate wheatgrass (Thinopyrum intermedium) has been identified as a candidate for domestication and improvement as a perennial grain, forage, and biofuel crop and is actively being improved by several breeding programs. To accelerate this process using genomics-assisted breeding, efficient genotyping methods and genetic marker reference maps are needed. We present here the first consensus genetic map for intermediate wheatgrass (IWG), which confirms the species' allohexaploid nature (2n = 6x = 42) and homology to Triticeae genomes. Genotyping-by-sequencing was used to identify markers that fit expected segregation ratios and construct genetic maps for 13 heterogeneous parents of seven full-sib families. These maps were then integrated using a linear programming method to produce a consensus map with 21 linkage groups containing 10,029 markers, 3601 of which were present in at least two populations. Each of the 21 linkage groups contained between 237 and 683 markers, cumulatively covering 5061 cM (2891 cM--Kosambi) with an average distance of 0.5 cM between each pair of markers. Through mapping the sequence tags to the diploid (2n = 2x = 14) barley reference genome, we observed high colinearity and synteny between these genomes, with three homoeologous IWG chromosomes corresponding to each of the seven barley chromosomes, and mapped translocations that are known in the Triticeae. The consensus map is a valuable tool for wheat breeders to map important disease-resistance genes within intermediate wheatgrass. These genomic tools can help lead to rapid improvement of IWG and development of high-yielding cultivars of this perennial grain that would facilitate the sustainable intensification of agricultural systems.

Tooth dentin defects reflect genetic disorders affecting bone mineralization

PubMed Central

Vital, S. Opsahl; Gaucher, C.; Bardet, C.; Rowe, P.S.; George, A.; Linglart, A.; Chaussain, C.

2012-01-01

Several genetic disorders affecting bone mineralization may manifest during dentin mineralization. Dentin and bone are similar in several aspects, especially pertaining to the composition of the extracellular matrix (ECM) which is secreted by well-differentiated odontoblasts and osteoblasts, respectively. However, unlike bone, dentin is not remodelled and is not involved in the regulation of calcium and phosphate metabolism. In contrast to bone, teeth are accessible tissues with the shedding of deciduous teeth and the extractions of premolars and third molars for orthodontic treatment. The feasibility of obtaining dentin makes this a good model to study biomineralization in physiological and pathological conditions. In this review, we focus on two genetic diseases that disrupt both bone and dentin mineralization. Hypophosphatemic rickets is related to abnormal secretory proteins involved in the ECM organization of both bone and dentin, as well as in the calcium and phosphate metabolism. Osteogenesis imperfecta affects proteins involved in the local organization of the ECM. In addition, dentin examination permits evaluation of the effects of the systemic treatment prescribed to hypophosphatemic patients during growth. In conclusion, dentin constitutes a valuable tool for better understanding of the pathological processes affecting biomineralization. PMID:22296718

Genetic diversity of neotropical primates: phylogeny, population genetics, and animal models for infectious diseases.

PubMed

Moreira, M A M; Bonvicino, C R; Soares, M A; Seuánez, H N

2010-01-01

The classification of neotropical primates has been controversial, and different arrangements have been proposed based on disparate taxonomic criteria and on the traits selected for elucidating phylogenetic reconstructions, like morphologic characters, nuclear DNA and mitochondrial DNA. Population studies of some neotropical primates have been useful for assessing their extant genetic variability and for understanding their social structure and dynamics. Finally, neotropical primates have become valuable models for some human infectious deseases, especially for HIV studies related to viral resistance. In this review, we comment on these aspects that make neotropical primates a group of highly valuable species for basic and applied research. Copyright 2010 S. Karger AG, Basel.

454-pyrosequencing: A tool for discovery and biomarker development

USDA-ARS?s Scientific Manuscript database

The Roche GS-FLX (454) sequencer has made possible what was thought impossible just a few years ago: sequence >1 million high-quality nucleotide reads (mean 400 bp) in less than 12 h. This technology provides valuable species-specific sequence information, and is a valuable tool to discover and und...

SMART – Sunflower Mutant population And Reverse genetic Tool for crop improvement

PubMed Central

2013-01-01

Background Sunflower (Helianthus annuus L.) is an important oilseed crop grown widely in various areas of the world. Classical genetic studies have been extensively undertaken for the improvement of this particular oilseed crop. Pertaining to this endeavor, we developed a “chemically induced mutated genetic resource for detecting SNP by TILLING” in sunflower to create new traits. Results To optimize the EMS mutagenesis, we first conducted a “kill curve” analysis with a range of EMS dose from 0.5% to 3%. Based on the observed germination rate, a 50% survival rate i.e. LD50, treatment with 0.6% EMS for 8 hours was chosen to generate 5,000 M2 populations, out of which, 4,763 M3 plants with fertile seed set. Phenotypic characterization of the 5,000 M2 mutagenised lines were undertaken to assess the mutagenesis quality and to identify traits of interest. In the M2 population, about 1.1% of the plants showed phenotypic variations. The sunflower TILLING platform was setup using Endo-1-nuclease as mismatch detection system coupled with an eight fold DNA pooling strategy. As proof-of-concept, we screened the M2 population for induced mutations in two genes related to fatty acid biosynthesis, FatA an acyl-ACP thioesterase and SAD the stearoyl-ACP desaturase and identified a total of 26 mutations. Conclusion Based on the TILLING of FatA and SAD genes, we calculated the overall mutation rate to one mutation every 480 kb, similar to other report for this crop so far. As sunflower is a plant model for seed oil biosynthesis, we anticipate that the developed genetic resource will be a useful tool to identify novel traits for sunflower crop improvement. PMID:23496999

Genetic linkage map and comparative genome analysis for the estuarine Atlantic killifish (Fundulus heteroclitus)

EPA Pesticide Factsheets

Genetic linkage maps are valuable tools in evolutionary biology; however, their availability for wild populations is extremely limited. Fundulus heteroclitus (Atlantic killifish) is a non-migratory estuarine fish that exhibits high allelic and phenotypic diversity partitioned among subpopulations that reside in disparate environmental conditions. An ideal candidate model organism for studying gene-environment interactions, the molecular toolbox for F. heteroclitus is limited. We identified hundreds of novel microsatellites which, when combined with existing microsatellites and single nucleotide polymorphisms (SNPs), were used to construct the first genetic linkage map for this species. By integrating independent linkage maps from three genetic crosses, we developed a consensus map containing 24 linkage groups, consistent with the number of chromosomes reported for this species. These linkage groups span 2300 centimorgans (cM) of recombinant genomic space, intermediate in size relative to the current linkage maps for the teleosts, medaka and zebrafish. Comparisons between fish genomes support a high degree of synteny between the consensus F. heteroclitus linkage map and the medaka and (to a lesser extent) zebrafish physical genome assemblies.This dataset is associated with the following publication:Waits , E., J. Martinson , B. Rinner, S. Morris, D. Proestou, D. Champlin , and D. Nacci. Genetic linkage map and comparative genome analysis for the estuarine Atlanti

A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna.

PubMed

Dukić, Marinela; Berner, Daniel; Roesti, Marius; Haag, Christoph R; Ebert, Dieter

2016-10-13

Recombination rate is an essential parameter for many genetic analyses. Recombination rates are highly variable across species, populations, individuals and different genomic regions. Due to the profound influence that recombination can have on intraspecific diversity and interspecific divergence, characterization of recombination rate variation emerges as a key resource for population genomic studies and emphasises the importance of high-density genetic maps as tools for studying genome biology. Here we present such a high-density genetic map for Daphnia magna, and analyse patterns of recombination rate across the genome. A F2 intercross panel was genotyped by Restriction-site Associated DNA sequencing to construct the third-generation linkage map of D. magna. The resulting high-density map included 4037 markers covering 813 scaffolds and contigs that sum up to 77 % of the currently available genome draft sequence (v2.4) and 55 % of the estimated genome size (238 Mb). Total genetic length of the map presented here is 1614.5 cM and the genome-wide recombination rate is estimated to 6.78 cM/Mb. Merging genetic and physical information we consistently found that recombination rate estimates are high towards the peripheral parts of the chromosomes, while chromosome centres, harbouring centromeres in D. magna, show very low recombination rate estimates. Due to its high-density, the third-generation linkage map for D. magna can be coupled with the draft genome assembly, providing an essential tool for genome investigation in this model organism. Thus, our linkage map can be used for the on-going improvements of the genome assembly, but more importantly, it has enabled us to characterize variation in recombination rate across the genome of D. magna for the first time. These new insights can provide a valuable assistance in future studies of the genome evolution, mapping of quantitative traits and population genetic studies.

Valuable use of computer-aided surgery in congenital bony aural atresia.

PubMed

Caversaccio, Marco; Romualdez, Joel; Baechler, Richard; Nolte, Lutz-Peter; Kompis, Martin; Häusler, Rudolf

2003-04-01

Congenital aural atresia repair is difficult owing to unpredictable anatomy. Benefits may be gained from computer-aided surgery (CAS), but its exact role has yet to be clearly defined. This is a retrospective study of 18 patients with bony type C (Schuknecht classification) congenital atresia. In the first group (n = 9), repair was performed with CAS while in the second group (n = 9), similar intervention was applied without CAS. Intra- and post-operative clinical and audiological findings were compared. CAS computed tomography (CT) images correlated well with intra-operative findings giving the surgeon more security and reducing operative time by 25 minutes. In our estimation, CAS is valuable for type C congenital aural atresia repair. It serves as an educational tool and as a guide for the experienced surgeon in critical situations where anatomical landmarks are distorted and where access is limited.

Optimization of Processing Parameters in ECM of Die Tool Steel Using Nanofluid by Multiobjective Genetic Algorithm.

PubMed

Sathiyamoorthy, V; Sekar, T; Elango, N

2015-01-01

Formation of spikes prevents achievement of the better material removal rate (MRR) and surface finish while using plain NaNO3 aqueous electrolyte in electrochemical machining (ECM) of die tool steel. Hence this research work attempts to minimize the formation of spikes in the selected workpiece of high carbon high chromium die tool steel using copper nanoparticles suspended in NaNO3 aqueous electrolyte, that is, nanofluid. The selected influencing parameters are applied voltage and electrolyte discharge rate with three levels and tool feed rate with four levels. Thirty-six experiments were designed using Design Expert 7.0 software and optimization was done using multiobjective genetic algorithm (MOGA). This tool identified the best possible combination for achieving the better MRR and surface roughness. The results reveal that voltage of 18 V, tool feed rate of 0.54 mm/min, and nanofluid discharge rate of 12 lit/min would be the optimum values in ECM of HCHCr die tool steel. For checking the optimality obtained from the MOGA in MATLAB software, the maximum MRR of 375.78277 mm(3)/min and respective surface roughness Ra of 2.339779 μm were predicted at applied voltage of 17.688986 V, tool feed rate of 0.5399705 mm/min, and nanofluid discharge rate of 11.998816 lit/min. Confirmatory tests showed that the actual performance at the optimum conditions was 361.214 mm(3)/min and 2.41 μm; the deviation from the predicted performance is less than 4% which proves the composite desirability of the developed models.

Facebook: A Potentially Valuable Educational Tool?

ERIC Educational Resources Information Center

Voivonta, Theodora; Avraamidou, Lucy

2018-01-01

This paper is concerned with the educational value of Facebook and specifically how it can be used in formal educational settings. As such, it provides a review of existing literature of how Facebook is used in higher education paying emphasis on the scope of its use and the outcomes achieved. As evident in existing literature, Facebook has been…

Lasers: A Valuable Tool for Chemists.

ERIC Educational Resources Information Center

Findsen, E. W.; Ondrias, M. R.

1986-01-01

Discusses the properties of laser light, reviews types of lasers, presents operating principles, and considers mechanical aspects of laser light production. Applications reviewed include spectroscopy, photochemical reaction initiation, and investigation of biological processes involving porphyrins. (JM)

Software For Genetic Algorithms

NASA Technical Reports Server (NTRS)

Wang, Lui; Bayer, Steve E.

1992-01-01

SPLICER computer program is genetic-algorithm software tool used to solve search and optimization problems. Provides underlying framework and structure for building genetic-algorithm application program. Written in Think C.

LocusExplorer: a user-friendly tool for integrated visualization of human genetic association data and biological annotations.

PubMed

Dadaev, Tokhir; Leongamornlert, Daniel A; Saunders, Edward J; Eeles, Rosalind; Kote-Jarai, Zsofia

2016-03-15

: In this article, we present LocusExplorer, a data visualization and exploration tool for genetic association data. LocusExplorer is written in R using the Shiny library, providing access to powerful R-based functions through a simple user interface. LocusExplorer allows users to simultaneously display genetic, statistical and biological data for humans in a single image and allows dynamic zooming and customization of the plot features. Publication quality plots may then be produced in a variety of file formats. LocusExplorer is open source and runs through R and a web browser. It is available at www.oncogenetics.icr.ac.uk/LocusExplorer/ or can be installed locally and the source code accessed from https://github.com/oncogenetics/LocusExplorer tokhir.dadaev@icr.ac.uk. © The Author 2015. Published by Oxford University Press.

A reverse genetics approach identifies novel mutants in light responses and anthocyanin metabolism in petunia.

PubMed

Berenschot, Amanda S; Quecini, Vera

2014-01-01

Flower color and plant architecture are important commercially valuable features for ornamental petunias (Petunia x hybrida Vilm.). Photoperception and light signaling are the major environmental factors controlling anthocyanin and chlorophyll biosynthesis and shade-avoidance responses in higher plants. The genetic regulators of these processes were investigated in petunia by in silico analyses and the sequence information was used to devise a reverse genetics approach to probe mutant populations. Petunia orthologs of photoreceptor, light-signaling components and anthocyanin metabolism genes were identified and investigated for functional conservation by phylogenetic and protein motif analyses. The expression profiles of photoreceptor gene families and of transcription factors regulating anthocyanin biosynthesis were obtained by bioinformatic tools. Two mutant populations, generated by an alkalyting agent and by gamma irradiation, were screened using a phenotype-independent, sequence-based method by high-throughput PCR-based assay. The strategy allowed the identification of novel mutant alleles for anthocyanin biosynthesis (CHALCONE SYNTHASE) and regulation (PH4), and for light signaling (CONSTANS) genes.

Breast cancer genetic testing: more than a medical management tool.

PubMed

Schroeder, Dawn; Conroy, Sherrill A

2015-10-01

Knowing whether a harmful hereditary mutation exists in BRCA1 and BRCA2 can enable women to make informed decisions regarding surveillance and surgery options to manage risk. Given the attention in the media about BRCA genetic testing, nurses need to revisit how this knowledge may affect a woman's sense of self and the forces that may influence this decision. This article aims to understand how complex the decision to undergo genetic testing may be for some women by exploring the impact of genetic knowledge on the self, changes to customary definitions for health and illness, and ethical issues and social forces that may influence genetic testing decisions. A review of the literature was undertaken to understand how genetic knowledge may alter meanings attached to the breast and how health is defined, and to identify ethical concerns and social forces that may affect a woman's decision to undergo or decline an offer for genetic testing. An understanding and awareness of the potential benefits and harms of BRCA1 and BRCA2 genetic testing, as well as the social forces that may influence a woman's decision to undergo or decline an offer for genetic testing and the commitment to remain open to the uniqueness of each woman's situation, may enhance the nurse-patient relationship and result in a decision that is ethically in the best interest of the patient.

Ravens reconcile after aggressive conflicts with valuable partners.

PubMed

Fraser, Orlaith N; Bugnyar, Thomas

2011-03-25

Reconciliation, a post-conflict affiliative interaction between former opponents, is an important mechanism for reducing the costs of aggressive conflict in primates and some other mammals as it may repair the opponents' relationship and reduce post-conflict distress. Opponents who share a valuable relationship are expected to be more likely to reconcile as for such partners the benefits of relationship repair should outweigh the risk of renewed aggression. In birds, however, post-conflict behavior has thus far been marked by an apparent absence of reconciliation, suggested to result either from differing avian and mammalian strategies or because birds may not share valuable relationships with partners with whom they engage in aggressive conflict. Here, we demonstrate the occurrence of reconciliation in a group of captive subadult ravens (Corvus corax) and show that it is more likely to occur after conflicts between partners who share a valuable relationship. Furthermore, former opponents were less likely to engage in renewed aggression following reconciliation, suggesting that reconciliation repairs damage caused to their relationship by the preceding conflict. Our findings suggest not only that primate-like valuable relationships exist outside the pair bond in birds, but that such partners may employ the same mechanisms in birds as in primates to ensure that the benefits afforded by their relationships are maintained even when conflicts of interest escalate into aggression. These results provide further support for a convergent evolution of social strategies in avian and mammalian species.

Fetal magnetic resonance imaging (MRI): a tool for a better understanding of normal and abnormal brain development.

PubMed

Saleem, Sahar N

2013-07-01

Knowledge of the anatomy of the developing fetal brain is essential to detect abnormalities and understand their pathogenesis. Capability of magnetic resonance imaging (MRI) to visualize the brain in utero and to differentiate between its various tissues makes fetal MRI a potential diagnostic and research tool for the developing brain. This article provides an approach to understand the normal and abnormal brain development through schematic interpretation of fetal brain MR images. MRI is a potential screening tool in the second trimester of pregnancies in fetuses at risk for brain anomalies and helps in describing new brain syndromes with in utero presentation. Accurate interpretation of fetal MRI can provide valuable information that helps genetic counseling, facilitates management decisions, and guides therapy. Fetal MRI can help in better understanding the pathogenesis of fetal brain malformations and can support research that could lead to disease-specific interventions.

Molecular markers: a potential resource for ginger genetic diversity studies.

PubMed

Ismail, Nor Asiah; Rafii, M Y; Mahmud, T M M; Hanafi, M M; Miah, Gous

2016-12-01

Ginger is an economically important and valuable plant around the world. Ginger is used as a food, spice, condiment, medicine and ornament. There is available information on biochemical aspects of ginger, but few studies have been reported on its molecular aspects. The main objective of this review is to accumulate the available molecular marker information and its application in diverse ginger studies. This review article was prepared by combing material from published articles and our own research. Molecular markers allow the identification and characterization of plant genotypes through direct access to hereditary material. In crop species, molecular markers are applied in different aspects and are useful in breeding programs. In ginger, molecular markers are commonly used to identify genetic variation and classify the relatedness among varieties, accessions, and species. Consequently, it provides important input in determining resourceful management strategies for ginger improvement programs. Alternatively, a molecular marker could function as a harmonizing tool for documenting species. This review highlights the application of molecular markers (isozyme, RAPD, AFLP, SSR, ISSR and others such as RFLP, SCAR, NBS and SNP) in genetic diversity studies of ginger species. Some insights on the advantages of the markers are discussed. The detection of genetic variation among promising cultivars of ginger has significance for ginger improvement programs. This update of recent literature will help researchers and students select the appropriate molecular markers for ginger-related research.

Human genetics as a tool to identify progranulin regulators.

PubMed

Nicholson, Alexandra M; Finch, NiCole A; Rademakers, Rosa

2011-11-01

Frontotemporal lobar degeneration (FTLD) is a common neurodegenerative disorder that predominantly affects individuals under the age of 65. It is known that the most common pathological subtype is FTLD with TAR DNA-binding protein 43 inclusions (FTLD-TDP). FTLD has a strong genetic component with about 50% of cases having a positive family history. Mutations identified in the progranulin gene (GRN) have been shown to cause FTLD-TDP as a result of progranulin haploinsufficiency. These findings suggest a progranulin-dependent mechanism in this pathological FTLD subtype. Thus, identifying regulators of progranulin levels is essential for new therapies and treatments for FTLD and related disorders. In this review, we discuss the role of genetic studies in identifying progranulin regulators, beginning with the discovery of pathogenic GRN mutations and additional GRN risk variants. We also cover more recent genetic advances, including the detection of variants in the transmembrane protein 106 B gene that increase FTLD-TDP risk presumably by modulating progranulin levels and the identification of a potential progranulin receptor, sortilin. This review highlights the importance of genetic studies in the context of FTLD and further emphasizes the need for future genetic and cell biology research to continue the effort in finding a cure for progranulin-related diseases.

HUMAN GENETICS AS A TOOL TO IDENTIFY PROGRANULIN REGULATORS

PubMed Central

Nicholson, Alexandra M.; Finch, NiCole A.; Rademakers, Rosa

2012-01-01

Frontotemporal lobar degeneration (FTLD) is a common neurodegenerative disorder that predominantly affects individuals under the age of 65. It is known that the most common pathological subtype is FTLD with TAR DNA-binding protein 43 inclusions (FTLD-TDP). FTLD has a strong genetic component with about 50% of cases having a positive family history. Mutations identified in the progranulin gene (GRN) have been shown to cause FTLD-TDP as a result of progranulin haploinsufficiency. These findings suggest a progranulin-dependent mechanism in this pathological FTLD subtype. Thus, identifying regulators of progranulin levels is essential for new therapies and treatments for FTLD and related disorders. In this review, we discuss the role of genetic studies in identifying progranulin regulators, beginning with the discovery of pathogenic GRN mutations and additional GRN risk variants. We also cover more recent genetic advances, including the detection of variants in the transmembrane protein 106 B gene that increase FTLD-TDP risk presumably by modulating progranulin levels and the identification of a potential progranulin receptor, sortilin. This review highlights the importance of genetic studies in the context of FTLD and further emphasizes the need for future genetic and cell biology research to continue the effort in finding a cure for progranulin-related diseases. PMID:21626010

The Genetic Drift Inventory: A Tool for Measuring What Advanced Undergraduates Have Mastered about Genetic Drift

ERIC Educational Resources Information Center

Price, Rebecca M.; Andrews, Tessa C.; McElhinny, Teresa L.; Mead, Louise S.; Abraham, Joel K.; Thanukos, Anna; Perez, Kathryn E.

2014-01-01

Understanding genetic drift is crucial for a comprehensive understanding of biology, yet it is difficult to learn because it combines the conceptual challenges of both evolution and randomness. To help assess strategies for teaching genetic drift, we have developed and evaluated the Genetic Drift Inventory (GeDI), a concept inventory that measures…

Genetic Diversity and Population Structure of Broomcorn Millet (Panicum miliaceum L.) Cultivars and Landraces in China Based on Microsatellite Markers

PubMed Central

Liu, Minxuan; Xu, Yue; He, Jihong; Zhang, Shuang; Wang, Yinyue; Lu, Ping

2016-01-01

Broomcorn millet (Panicum miliaceum L.), one of the first domesticated crops, has been grown in Northern China for at least 10,000 years. The species is presently a minor crop, and evaluation of its genetic diversity has been very limited. In this study, we analyzed the genetic diversity of 88 accessions of broomcorn millet collected from various provinces of China. Amplification with 67 simple sequence repeat (SSR) primers revealed moderate levels of diversity in the investigated accessions. A total of 179 alleles were detected, with an average of 2.7 alleles per locus. Polymorphism information content and expected heterozygosity ranged from 0.043 to 0.729 (mean = 0.376) and 0.045 to 0.771 (mean = 0.445), respectively. Cluster analysis based on the unweighted pair group method of mathematical averages separated the 88 accessions into four groups at a genetic similarity level of 0.633. A genetic structure assay indicated a close correlation between geographical regions and genetic diversity. The uncovered information will be valuable for defining gene pools and developing breeding programs for broomcorn millet. Furthermore, the millet-specific SSR markers developed in this study should serve as useful tools for assessment of genetic diversity and elucidation of population structure in broomcorn millet. PMID:26985894

Application of the High Resolution Melting analysis for genetic mapping of Sequence Tagged Site markers in narrow-leafed lupin (Lupinus angustifolius L.).

PubMed

Kamel, Katarzyna A; Kroc, Magdalena; Święcicki, Wojciech

2015-01-01

Sequence tagged site (STS) markers are valuable tools for genetic and physical mapping that can be successfully used in comparative analyses among related species. Current challenges for molecular markers genotyping in plants include the lack of fast, sensitive and inexpensive methods suitable for sequence variant detection. In contrast, high resolution melting (HRM) is a simple and high-throughput assay, which has been widely applied in sequence polymorphism identification as well as in the studies of genetic variability and genotyping. The present study is the first attempt to use the HRM analysis to genotype STS markers in narrow-leafed lupin (Lupinus angustifolius L.). The sensitivity and utility of this method was confirmed by the sequence polymorphism detection based on melting curve profiles in the parental genotypes and progeny of the narrow-leafed lupin mapping population. Application of different approaches, including amplicon size and a simulated heterozygote analysis, has allowed for successful genetic mapping of 16 new STS markers in the narrow-leafed lupin genome.

Gametic embryogenesis and haploid technology as valuable support to plant breeding.

PubMed

Germanà, Maria Antonietta

2011-05-01

Plant breeding is focused on continuously increasing crop production to meet the needs of an ever-growing world population, improving food quality to ensure a long and healthy life and address the problems of global warming and environment pollution, together with the challenges of developing novel sources of biofuels. The breeders' search for novel genetic combinations, with which to select plants with improved traits to satisfy both farmers and consumers, is endless. About half of the dramatic increase in crop yield obtained in the second half of the last century has been achieved thanks to the results of genetic improvement, while the residual advance has been due to the enhanced management techniques (pest and disease control, fertilization, and irrigation). Biotechnologies provide powerful tools for plant breeding, and among these ones, tissue culture, particularly haploid and doubled haploid technology, can effectively help to select superior plants. In fact, haploids (Hs), which are plants with gametophytic chromosome number, and doubled haploids (DHs), which are haploids that have undergone chromosome duplication, represent a particularly attractive biotechnological method to accelerate plant breeding. Currently, haploid technology, making possible through gametic embryogenesis the single-step development of complete homozygous lines from heterozygous parents, has already had a huge impact on agricultural systems of many agronomically important crops, representing an integral part in their improvement programmes. The aim of this review was to provide some background, recent advances, and future prospective on the employment of haploid technology through gametic embryogenesis as a powerful tool to support plant breeding.

Problem solving with genetic algorithms and Splicer

NASA Technical Reports Server (NTRS)

Bayer, Steven E.; Wang, Lui

1991-01-01

Genetic algorithms are highly parallel, adaptive search procedures (i.e., problem-solving methods) loosely based on the processes of population genetics and Darwinian survival of the fittest. Genetic algorithms have proven useful in domains where other optimization techniques perform poorly. The main purpose of the paper is to discuss a NASA-sponsored software development project to develop a general-purpose tool for using genetic algorithms. The tool, called Splicer, can be used to solve a wide variety of optimization problems and is currently available from NASA and COSMIC. This discussion is preceded by an introduction to basic genetic algorithm concepts and a discussion of genetic algorithm applications.

Recommendations for developing and applying genetic tools to assess and manage biological invasions in marine ecosystems

PubMed Central

Darling, John A.; Galil, Bella S.; Carvalho, Gary R.; Rius, Marc; Viard, Frédérique; Piraino, Stefano

2018-01-01

The European Union’s Marine Strategy Framework Directive (MSFD) aims to adopt integrated ecosystem management approaches to achieve or maintain “Good Environmental Status” for marine waters, habitats and resources, including mitigation of the negative effects of non-indigenous species (NIS). The Directive further seeks to promote broadly standardized monitoring efforts and assessment of temporal trends in marine ecosystem condition, incorporating metrics describing the distribution and impacts of NIS. Accomplishing these goals will require application of advanced tools for NIS surveillance and risk assessment, particularly given known challenges associated with surveying and monitoring with traditional methods. In the past decade, a host of methods based on nucleic acids (DNA and RNA) analysis have been developed or advanced that promise to dramatically enhance capacity in assessing and managing NIS. However, ensuring that these rapidly evolving approaches remain accessible and responsive to the needs of resource managers remains a challenge. This paper provides recommendations for future development of these genetic tools for assessment and management of NIS in marine systems, within the context of the explicit requirements of the MSFD. Issues considered include technological innovation, methodological standardization, data sharing and collaboration, and the critical importance of shared foundational resources, particularly integrated taxonomic expertise. Though the recommendations offered here are not exhaustive, they provide a basis for future intentional (and international) collaborative development of a genetic toolkit for NIS research, capable of fulfilling the immediate and long term goals of marine ecosystem and resource conservation. PMID:29681680

Genetic Code Expansion: A Powerful Tool for Understanding the Physiological Consequences of Oxidative Stress Protein Modifications.

PubMed

Porter, Joseph J; Mehl, Ryan A

2018-01-01

Posttranslational modifications resulting from oxidation of proteins (Ox-PTMs) are present intracellularly under conditions of oxidative stress as well as basal conditions. In the past, these modifications were thought to be generic protein damage, but it has become increasingly clear that Ox-PTMs can have specific physiological effects. It is an arduous task to distinguish between the two cases, as multiple Ox-PTMs occur simultaneously on the same protein, convoluting analysis. Genetic code expansion (GCE) has emerged as a powerful tool to overcome this challenge as it allows for the site-specific incorporation of an Ox-PTM into translated protein. The resulting homogeneously modified protein products can then be rigorously characterized for the effects of individual Ox-PTMs. We outline the strengths and weaknesses of GCE as they relate to the field of oxidative stress and Ox-PTMs. An overview of the Ox-PTMs that have been genetically encoded and applications of GCE to the study of Ox-PTMs, including antibody validation and therapeutic development, is described.

Next generation DNA sequencing technology delivers valuable genetic markers for the genomic orphan legume species, Bituminaria bituminosa

PubMed Central

2011-01-01

Background Bituminaria bituminosa is a perennial legume species from the Canary Islands and Mediterranean region that has potential as a drought-tolerant pasture species and as a source of pharmaceutical compounds. Three botanical varieties have previously been identified in this species: albomarginata, bituminosa and crassiuscula. B. bituminosa can be considered a genomic 'orphan' species with very few genomic resources available. New DNA sequencing technologies provide an opportunity to develop high quality molecular markers for such orphan species. Results 432,306 mRNA molecules were sampled from a leaf transcriptome of a single B. bituminosa plant using Roche 454 pyrosequencing, resulting in an average read length of 345 bp (149.1 Mbp in total). Sequences were assembled into 3,838 isotigs/contigs representing putatively unique gene transcripts. Gene ontology descriptors were identified for 3,419 sequences. Raw sequence reads containing simple sequence repeat (SSR) motifs were identified, and 240 primer pairs flanking these motifs were designed. Of 87 primer pairs developed this way, 75 (86.2%) successfully amplified primarily single fragments by PCR. Fragment analysis using 20 primer pairs in 79 accessions of B. bituminosa detected 130 alleles at 21 SSR loci. Genetic diversity analyses confirmed that variation at these SSR loci accurately reflected known taxonomic relationships in original collections of B. bituminosa and provided additional evidence that a division of the botanical variety bituminosa into two according to geographical origin (Mediterranean region and Canary Islands) may be appropriate. Evidence of cross-pollination was also found between botanical varieties within a B. bituminosa breeding programme. Conclusions B. bituminosa can no longer be considered a genomic orphan species, having now a large (albeit incomplete) repertoire of expressed gene sequences that can serve as a resource for future genetic studies. This experimental approach was

Storytelling: a leadership and educational tool.

PubMed

Kowalski, Karren

2015-06-01

A powerful tool that leaders and educators can use to engage the listeners-both staff and learners-is storytelling. Stories demonstrate important points, valuable lessons, and the behaviors that are preferred by the leader. Copyright 2015, SLACK Incorporated.

Tracing the Tiger: Population Genetics Provides Valuable Insights into the Aedes (Stegomyia) albopictus Invasion of the Australasian Region

PubMed Central

Beebe, Nigel W.; Ambrose, Luke; Hill, Lydia A.; Davis, Joseph B.; Hapgood, George; Cooper, Robert D.; Russell, Richard C.; Ritchie, Scott A.; Reimer, Lisa J.; Lobo, Neil F.; Syafruddin, Din; van den Hurk, Andrew F.

2013-01-01

Background The range of the Asian tiger mosquito Aedes albopictus is expanding globally, raising the threat of emerging and re-emerging arbovirus transmission risks including dengue and chikungunya. Its detection in Papua New Guinea's (PNG) southern Fly River coastal region in 1988 and 1992 placed it 150 km from mainland Australia. However, it was not until 12 years later that it appeared on the Torres Strait Islands. We hypothesized that the extant PNG population expanded into the Torres Straits as an indirect effect of drought-proofing the southern Fly River coastal villages in response to El Nino-driven climate variability in the region (via the rollout of rainwater tanks and water storage containers). Methodology/Principal Findings Examination of the mosquito's mitochondrial DNA cytochrome oxidase I (COI) sequences and 13 novel nuclear microsatellites revealed evidence of substantial intermixing between PNG's southern Fly region and Torres Strait Island populations essentially compromising any island eradication attempts due to potential of reintroduction. However, two genetically distinct populations were identified in this region comprising the historically extant PNG populations and the exotic introduced population. Both COI sequence data and microsatellites showed the introduced population to have genetic affinities to populations from Timor Leste and Jakarta in the Indonesian region. Conclusions/Significance The Ae. albopictus invasion into the Australian region was not a range expansion out of PNG as suspected, but founded by other, genetically distinct population(s), with strong genetic affinities to populations sampled from the Indonesian region. We now suspect that the introduction of Ae. albopictus into the Australian region was driven by widespread illegal fishing activity originating from the Indonesian region during this period. Human sea traffic is apparently shuttling this mosquito between islands in the Torres Strait and the southern PNG

Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools.

PubMed

Dufresne, France; Stift, Marc; Vergilino, Roland; Mable, Barbara K

2014-01-01

Despite the importance of polyploidy and the increasing availability of new genomic data, there remain important gaps in our knowledge of polyploid population genetics. These gaps arise from the complex nature of polyploid data (e.g. multiple alleles and loci, mixed inheritance patterns, association between ploidy and mating system variation). Furthermore, many of the standard tools for population genetics that have been developed for diploids are often not feasible for polyploids. This review aims to provide an overview of the state-of-the-art in polyploid population genetics and to identify the main areas where further development of molecular techniques and statistical theory is required. We review commonly used molecular tools (amplified fragment length polymorphism, microsatellites, Sanger sequencing, next-generation sequencing and derived technologies) and their challenges associated with their use in polyploid populations: that is, allele dosage determination, null alleles, difficulty of distinguishing orthologues from paralogues and copy number variation. In addition, we review the approaches that have been used for population genetic analysis in polyploids and their specific problems. These problems are in most cases directly associated with dosage uncertainty and the problem of inferring allele frequencies and assumptions regarding inheritance. This leads us to conclude that for advancing the field of polyploid population genetics, most priority should be given to development of new molecular approaches that allow efficient dosage determination, and to further development of analytical approaches to circumvent dosage uncertainty and to accommodate 'flexible' modes of inheritance. In addition, there is a need for more simulation-based studies that test what kinds of biases could result from both existing and novel approaches. © 2013 John Wiley & Sons Ltd.

Live-cell imaging of cell signaling using genetically encoded fluorescent reporters.

PubMed

Ni, Qiang; Mehta, Sohum; Zhang, Jin

2018-01-01

Synergistic advances in fluorescent protein engineering and live-cell imaging techniques in recent years have fueled the concurrent development and application of genetically encoded fluorescent reporters that are tailored for tracking signaling dynamics in living systems over multiple length and time scales. These biosensors are uniquely suited for this challenging task, owing to their specificity, sensitivity, and versatility, as well as to the noninvasive and nondestructive nature of fluorescence and the power of genetic encoding. Over the past 10 years, a growing number of fluorescent reporters have been developed for tracking a wide range of biological signals in living cells and animals, including second messenger and metabolite dynamics, enzyme activation and activity, and cell cycle progression and neuronal activity. Many of these biosensors are gaining wide use and are proving to be indispensable for unraveling the complex biological functions of individual signaling molecules in their native environment, the living cell, shedding new light on the structural and molecular underpinnings of cell signaling. In this review, we highlight recent advances in protein engineering that are likely to help expand and improve the design and application of these valuable tools. We then turn our focus to specific examples of live-cell imaging using genetically encoded fluorescent reporters as an important platform for advancing our understanding of G protein-coupled receptor signaling and neuronal activity. © 2017 Federation of European Biochemical Societies.

Remote Sensing: A valuable tool in the Forest Service decision making process. [in Utah

NASA Technical Reports Server (NTRS)

Stanton, F. L.

1975-01-01

Forest Service studies for integrating remotely sensed data into existing information systems highlight a need to: (1) re-examine present methods of collecting and organizing data, (2) develop an integrated information system for rapidly processing and interpreting data, (3) apply existing technological tools in new ways, and (4) provide accurate and timely information for making right management decisions. The Forest Service developed an integrated information system using remote sensors, microdensitometers, computer hardware and software, and interactive accessories. Their efforts substantially reduce the time it takes for collecting and processing data.

Analysis of genetic diversity of rapeseed genetic resources in Japan and core collection construction

PubMed Central

Chen, Ruikun; Hara, Takashi; Ohsawa, Ryo; Yoshioka, Yosuke

2017-01-01

Diversity analysis of rapeseed accessions preserved in the Japanese Genebank can provide valuable information for breeding programs. In this study, 582 accessions were genotyped with 30 SSR markers covering all 19 rapeseed chromosomes. These markers amplified 311 alleles (10.37 alleles per marker; range, 3–39). The genetic diversity of Japanese accessions was lower than that of overseas accessions. Analysis of molecular variance indicated significant genetic differentiation between Japanese and overseas accessions. Small but significant differences were found among geographical groups in Japan, and genetic differentiation tended to increase with geographical distance. STRUCTURE analysis indicated the presence of two main genetic clusters in the NARO rapeseed collection. With the membership probabilities threshold, 227 accessions mostly originating from overseas were assigned to one subgroup, and 276 accessions mostly originating from Japan were assigned to the other subgroup. The remaining 79 accessions are assigned to admixed group. The core collection constructed comprises 96 accessions of diverse origin. It represents the whole collection well and thus it may be useful for rapeseed genetic research and breeding programs. The core collection improves the efficiency of management, evaluation, and utilization of genetic resources. PMID:28744177

Hemodynamic exercise testing. A valuable tool in the selection of cardiac transplantation candidates.

PubMed

Chomsky, D B; Lang, C C; Rayos, G H; Shyr, Y; Yeoh, T K; Pierson, R N; Davis, S F; Wilson, J R

1996-12-15

Peak exercise oxygen consumption (Vo2), a noninvasive index of peak exercise cardiac output (CO), is widely used to select candidates for heart transplantation. However, peak exercise Vo2 can be influenced by noncardiac factors such as deconditioning, motivation, or body composition and may yield misleading prognostic information. Direct measurement of the CO response to exercise may avoid this problem and more accurately predict prognosis. Hemodynamic and ventilatory responses to maximal treadmill exercise were measured in 185 ambulatory patients with chronic heart failure who had been referred for cardiac transplantation (mean left ventricular ejection fraction, 22 +/- 7%; mean peak Vo2, 12.9 +/- 3.0 mL. min-1.kg-1). CO response to exercise was normal in 83 patients and reduced in 102. By univariate analysis, patients with normal CO responses had a better 1-year survival rate (95%) than did those with reduced CO responses (72%) (P < .0001). Survival in patients with peak Vo2 of > 14 mL.min-1.kg-1 (88%) was not different from that of patients with peak Vo2 of < or = 14 mL.min-1.kg-1 (79%) (P = NS). However, survival was worse in patients with peak Vo2 of < or = 10 mL.min-1.kg-1 (52%) versus those with peak Vo2 of > 10 mL.min-1.kg-1 (89%) (P < .0001). By Cox regression analysis, exercise CO response was the strongest independent predictor of survival (risk ratio, 4.3), with peak Vo2 dichotomized at 10 mL. min-1.kg-1 (risk ratio, 3.3) as the only other independent predictor. Patients with reduced CO responses and peak Vo2 of < or = 10 mL.min-1.kg-1 had an extremely poor 1-year survival rate (38%). Both CO response to exercise and peak exercise Vo2 provide valuable independent prognostic information in ambulatory patients with heart failure. These variables should be used in combination to select potential heart transplantation candidates.

[Epilepsy-new diagnostic tools, old drugs? : Therapeutic consequences of epilepsy genetics].

PubMed

Tacke, M; Neubauer, B A; Gerstl, L; Roser, T; Rémi, J; Borggraefe, I

2017-12-01

Recent advances in the field of epilepsy genetics have led to an increased fraction of patients with epilepsies where the etiology of the disease could be identified. Nevertheless, there is some criticism regarding the use of epilepsy genetics because in many cases the identification of a pathogenetic mutation does not lead to an adaptation of therapy or to an improved prognosis. In addition, the interpretation of genetic results might be complicated due to the considerable numbers of variants of unclear significance. This publication presents the arguments in favour of a broad use of genetic investigations for children with epilepsies. Several diseases where a genetic diagnosis does in fact have direct therapeutic consequences are mentioned. In addition, the indirect impact of an established etiology, encompassing the avoidance of unnecessary diagnostic measures, possibility of genetic counselling, and the easing of the psychologic burden for the caregivers, should not be underestimated. The arguments in favour of broad genetic diagnostics prevail notwithstanding the lack of relevant new developments regarding the therapy.

Genetical Genomics Identifies the Genetic Architecture for Growth and Weevil Resistance in Spruce

PubMed Central

Porth, Ilga; White, Richard; Jaquish, Barry; Alfaro, René; Ritland, Carol; Ritland, Kermit

2012-01-01

In plants, relationships between resistance to herbivorous insect pests and growth are typically controlled by complex interactions between genetically correlated traits. These relationships often result in tradeoffs in phenotypic expression. In this study we used genetical genomics to elucidate genetic relationships between tree growth and resistance to white pine terminal weevil (Pissodes strobi Peck.) in a pedigree population of interior spruce (Picea glauca, P. engelmannii and their hybrids) that was growing at Vernon, B.C. and segregating for weevil resistance. Genetical genomics uses genetic perturbations caused by allelic segregation in pedigrees to co-locate quantitative trait loci (QTLs) for gene expression and quantitative traits. Bark tissue of apical leaders from 188 trees was assayed for gene expression using a 21.8K spruce EST-spotted microarray; the same individuals were genotyped for 384 SNP markers for the genetic map. Many of the expression QTLs (eQTL) co-localized with resistance trait QTLs. For a composite resistance phenotype of six attack and oviposition traits, 149 positional candidate genes were identified. Resistance and growth QTLs also overlapped with eQTL hotspots along the genome suggesting that: 1) genetic pleiotropy of resistance and growth traits in interior spruce was substantial, and 2) master regulatory genes were important for weevil resistance in spruce. These results will enable future work on functional genetic studies of insect resistance in spruce, and provide valuable information about candidate genes for genetic improvement of spruce. PMID:22973444

Genetics and neuropsychology: A merger whose time has come.

PubMed

Kremen, William S; Panizzon, Matthew S; Cannon, Tyrone D

2016-01-01

Genetics and neuropsychology have historically been 2 rather distant and unrelated fields. With the very rapid advances that have been taking place in genetics, research and treatment of disorders of cognition in the 21st century are likely to be increasingly informed by individual differences in genetics and epigenetics. Although neuropsychologists are not expected to become geneticists, it is our view that increased training in genetics should become more central to training in neuropsychology. This relationship should not be unidirectional. Here we note ways in which an understanding of genetics and epigenetics can inform neuropsychology. On the other hand, given the complexity of cognitive phenotypes, neuropsychology can also play a valuable role in informing and refining genetic studies. Greater integration of the 2 should advance both fields. (c) 2015 APA, all rights reserved).

Genetics and Neuropsychology: A Merger Whose Time Has Come

PubMed Central

Kremen, William S.; Panizzon, Matthew S.; Cannon, Tyrone D.

2016-01-01

Genetics and neuropsychology have historically been two rather distant and unrelated fields. With the very rapid advances that have been taking place in genetics, research and treatment of disorders of cognition in the 21st century are likely to be increasingly informed by individual differences in genetics and epigenetics. Although neuropsychologists are not expected to become geneticists, it is our view that increased training in genetics should become more central to training in neuropsychology. This relationship should not be unidirectional. Here we note ways in which an understanding of genetics and epigenetics can inform neuropsychology. On the other hand, given the complexity of cognitive phenotypes, neuropsychology can also play a valuable role in informing and refining genetic studies. Greater integration of the two should advance both fields. PMID:26710091

Invited review: Genetics and claw health: Opportunities to enhance claw health by genetic selection.

PubMed

Heringstad, B; Egger-Danner, C; Charfeddine, N; Pryce, J E; Stock, K F; Kofler, J; Sogstad, A M; Holzhauer, M; Fiedler, A; Müller, K; Nielsen, P; Thomas, G; Gengler, N; de Jong, G; Ødegård, C; Malchiodi, F; Miglior, F; Alsaaod, M; Cole, J B

2018-06-01

Routine recording of claw health status at claw trimming of dairy cattle has been established in several countries, providing valuable data for genetic evaluation. In this review, we examine issues related to genetic evaluation of claw health; discuss data sources, trait definitions, and data validation procedures; and present a review of genetic parameters, possible indicator traits, and status of genetic and genomic evaluations for claw disorders. Different sources of data and traits can be used to describe claw health. Severe cases of claw disorders can be identified by veterinary diagnoses. Data from lameness and locomotion scoring, activity information from sensors, and feet and leg conformation traits are used as auxiliary traits. The most reliable and comprehensive information is data from regular hoof trimming. In genetic evaluation, claw disorders are usually defined as binary traits, based on whether or not the claw disorder was present (recorded) at least once during a defined time period. The traits can be specific disorders, composite traits, or overall claw health. Data validation and editing criteria are needed to ensure reliable data at the trimmer, herd, animal, and record levels. Different strategies have been chosen, reflecting differences in herd sizes, data structures, management practices, and recording systems among countries. Heritabilities of the most commonly analyzed claw disorders based on data from routine claw trimming were generally low, with ranges of linear model estimates from 0.01 to 0.14, and threshold model estimates from 0.06 to 0.39. Estimated genetic correlations among claw disorders varied from -0.40 to 0.98. The strongest genetic correlations were found among sole hemorrhage (SH), sole ulcer (SU), and white line disease (WL), and between digital/interdigital dermatitis (DD/ID) and heel horn erosion (HHE). Genetic correlations between DD/ID and HHE on the one hand and SH, SU, or WL on the other hand were, in most cases, low

Variant effect prediction tools assessed using independent, functional assay-based datasets: implications for discovery and diagnostics.

PubMed

Mahmood, Khalid; Jung, Chol-Hee; Philip, Gayle; Georgeson, Peter; Chung, Jessica; Pope, Bernard J; Park, Daniel J

2017-05-16

Genetic variant effect prediction algorithms are used extensively in clinical genomics and research to determine the likely consequences of amino acid substitutions on protein function. It is vital that we better understand their accuracies and limitations because published performance metrics are confounded by serious problems of circularity and error propagation. Here, we derive three independent, functionally determined human mutation datasets, UniFun, BRCA1-DMS and TP53-TA, and employ them, alongside previously described datasets, to assess the pre-eminent variant effect prediction tools. Apparent accuracies of variant effect prediction tools were influenced significantly by the benchmarking dataset. Benchmarking with the assay-determined datasets UniFun and BRCA1-DMS yielded areas under the receiver operating characteristic curves in the modest ranges of 0.52 to 0.63 and 0.54 to 0.75, respectively, considerably lower than observed for other, potentially more conflicted datasets. These results raise concerns about how such algorithms should be employed, particularly in a clinical setting. Contemporary variant effect prediction tools are unlikely to be as accurate at the general prediction of functional impacts on proteins as reported prior. Use of functional assay-based datasets that avoid prior dependencies promises to be valuable for the ongoing development and accurate benchmarking of such tools.

Characterization of Planctomyces limnophilus and development of genetic tools for its manipulation establish it as a model species for the phylum Planctomycetes.

PubMed

Jogler, Christian; Glöckner, Frank Oliver; Kolter, Roberto

2011-08-15

Planctomycetes represent a remarkable clade in the domain Bacteria because they play crucial roles in global carbon and nitrogen cycles and display cellular structures that closely parallel those of eukaryotic cells. Studies on Planctomycetes have been hampered by the lack of genetic tools, which we developed for Planctomyces limnophilus.

Native xylose-inducible promoter expands the genetic tools for the biomass-degrading, extremely thermophilic bacterium Caldicellulosiruptor bescii.

PubMed

Williams-Rhaesa, Amanda M; Awuku, Nanaakua K; Lipscomb, Gina L; Poole, Farris L; Rubinstein, Gabriel M; Conway, Jonathan M; Kelly, Robert M; Adams, Michael W W

2018-07-01

Regulated control of both homologous and heterologous gene expression is essential for precise genetic manipulation and metabolic engineering of target microorganisms. However, there are often no options available for inducible promoters when working with non-model microorganisms. These include extremely thermophilic, cellulolytic bacteria that are of interest for renewable lignocellulosic conversion to biofuels and chemicals. In fact, improvements to the genetic systems in these organisms often cease once transformation is achieved. This present study expands the tools available for genetically engineering Caldicellulosiruptor bescii, the most thermophilic cellulose-degrader known growing up to 90 °C on unpretreated plant biomass. A native xylose-inducible (P xi ) promoter was utilized to control the expression of the reporter gene (ldh) encoding lactate dehydrogenase. The P xi -ldh construct resulted in a both increased ldh expression (20-fold higher) and lactate dehydrogenase activity (32-fold higher) in the presence of xylose compared to when glucose was used as a substrate. Finally, lactate production during growth of the recombinant C. bescii strain was proportional to the initial xylose concentration, showing that tunable expression of genes is now possible using this xylose-inducible system. This study represents a major step in the use of C. bescii as a potential platform microorganism for biotechnological applications using renewable biomass.

Discrete mixture modeling to address genetic heterogeneity in time-to-event regression

PubMed Central

Eng, Kevin H.; Hanlon, Bret M.

2014-01-01

Motivation: Time-to-event regression models are a critical tool for associating survival time outcomes with molecular data. Despite mounting evidence that genetic subgroups of the same clinical disease exist, little attention has been given to exploring how this heterogeneity affects time-to-event model building and how to accommodate it. Methods able to diagnose and model heterogeneity should be valuable additions to the biomarker discovery toolset. Results: We propose a mixture of survival functions that classifies subjects with similar relationships to a time-to-event response. This model incorporates multivariate regression and model selection and can be fit with an expectation maximization algorithm, we call Cox-assisted clustering. We illustrate a likely manifestation of genetic heterogeneity and demonstrate how it may affect survival models with little warning. An application to gene expression in ovarian cancer DNA repair pathways illustrates how the model may be used to learn new genetic subsets for risk stratification. We explore the implications of this model for censored observations and the effect on genomic predictors and diagnostic analysis. Availability and implementation: R implementation of CAC using standard packages is available at https://gist.github.com/programeng/8620b85146b14b6edf8f Data used in the analysis are publicly available. Contact: kevin.eng@roswellpark.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24532723

Genetic Code Expansion: A Powerful Tool for Understanding the Physiological Consequences of Oxidative Stress Protein Modifications

PubMed Central

2018-01-01

Posttranslational modifications resulting from oxidation of proteins (Ox-PTMs) are present intracellularly under conditions of oxidative stress as well as basal conditions. In the past, these modifications were thought to be generic protein damage, but it has become increasingly clear that Ox-PTMs can have specific physiological effects. It is an arduous task to distinguish between the two cases, as multiple Ox-PTMs occur simultaneously on the same protein, convoluting analysis. Genetic code expansion (GCE) has emerged as a powerful tool to overcome this challenge as it allows for the site-specific incorporation of an Ox-PTM into translated protein. The resulting homogeneously modified protein products can then be rigorously characterized for the effects of individual Ox-PTMs. We outline the strengths and weaknesses of GCE as they relate to the field of oxidative stress and Ox-PTMs. An overview of the Ox-PTMs that have been genetically encoded and applications of GCE to the study of Ox-PTMs, including antibody validation and therapeutic development, is described. PMID:29849913

Construction of a high-density, high-resolution genetic map and its integration with BAC-based physical map in channel catfish

PubMed Central

Li, Yun; Liu, Shikai; Qin, Zhenkui; Waldbieser, Geoff; Wang, Ruijia; Sun, Luyang; Bao, Lisui; Danzmann, Roy G.; Dunham, Rex; Liu, Zhanjiang

2015-01-01

Construction of genetic linkage map is essential for genetic and genomic studies. Recent advances in sequencing and genotyping technologies made it possible to generate high-density and high-resolution genetic linkage maps, especially for the organisms lacking extensive genomic resources. In the present work, we constructed a high-density and high-resolution genetic map for channel catfish with three large resource families genotyped using the catfish 250K single-nucleotide polymorphism (SNP) array. A total of 54,342 SNPs were placed on the linkage map, which to our knowledge had the highest marker density among aquaculture species. The estimated genetic size was 3,505.4 cM with a resolution of 0.22 cM for sex-averaged genetic map. The sex-specific linkage maps spanned a total of 4,495.1 cM in females and 2,593.7 cM in males, presenting a ratio of 1.7 : 1 between female and male in recombination fraction. After integration with the previously established physical map, over 87% of physical map contigs were anchored to the linkage groups that covered a physical length of 867 Mb, accounting for ∼90% of the catfish genome. The integrated map provides a valuable tool for validating and improving the catfish whole-genome assembly and facilitates fine-scale QTL mapping and positional cloning of genes responsible for economically important traits. PMID:25428894

Spectroscopy applied to feed additives of the European Union Reference Laboratory: a valuable tool for traceability.

PubMed

Omar, Jone; Slowikowski, Boleslaw; Boix, Ana; von Holst, Christoph

2017-08-01

Feed additives need to be authorised to be placed on the market according to Regulation (EU) No. 1831/2003. Next to laying down the procedural requirements, the regulation creates the European Union Reference Laboratory for Feed Additives (EURL-FA) and requires that applicants send samples to the EURL-FA. Once authorised, the characteristics of the marketed feed additives should correspond to those deposited in the sample bank of the EURL-FA. For this purpose, the submitted samples were subjected to near-infrared (NIR) and Raman spectroscopy for spectral characterisation. These techniques have the valuable potential of characterising the feed additives in a non-destructive manner without any complicated sample preparation. This paper describes the capability of spectroscopy for a rapid characterisation of products to establish whether specific authorisation criteria are met. This study is based on the analysis of feed additive samples from different categories and functional groups, namely products containing (1) selenium, (2) zinc and manganese, (3) vitamins and (4) essential oils such as oregano and thyme oil. The use of chemometrics turned out to be crucial, especially in cases where the differentiation of spectra by visual inspection was very difficult.

Effective elimination of chimeric tissue in transgenics for the stable genetic transformation of lesquerella fendleri

USDA-ARS?s Scientific Manuscript database

In order to improve the potential of Lesquerella fendleri as a valuable industrial oilseed crop, a stable genetic transformation system was developed. Genetic transformation was performed by inoculating leaf segments with an Agrobacterium tumefaciens strain AGL1 carrying binary vector pCAMBIA 1301.1...

Environmental DNA from Residual Saliva for Efficient Noninvasive Genetic Monitoring of Brown Bears (Ursus arctos)

PubMed Central

Wheat, Rachel E.; Allen, Jennifer M.; Miller, Sophie D. L.; Wilmers, Christopher C.; Levi, Taal

2016-01-01

Noninvasive genetic sampling is an important tool in wildlife ecology and management, typically relying on hair snaring or scat sampling techniques, but hair snaring is labor and cost intensive, and scats yield relatively low quality DNA. New approaches utilizing environmental DNA (eDNA) may provide supplementary, cost-effective tools for noninvasive genetic sampling. We tested whether eDNA from residual saliva on partially-consumed Pacific salmon (Oncorhynchus spp.) carcasses might yield suitable DNA quality for noninvasive monitoring of brown bears (Ursus arctos). We compared the efficiency of monitoring brown bear populations using both fecal DNA and salivary eDNA collected from partially-consumed salmon carcasses in Southeast Alaska. We swabbed a range of tissue types from 156 partially-consumed salmon carcasses from a midseason run of lakeshore-spawning sockeye (O. nerka) and a late season run of stream-spawning chum (O. keta) salmon in 2014. We also swabbed a total of 272 scats from the same locations. Saliva swabs collected from the braincases of salmon had the best amplification rate, followed by swabs taken from individual bite holes. Saliva collected from salmon carcasses identified unique individuals more quickly and required much less labor to locate than scat samples. Salmon carcass swabbing is a promising method to aid in efficient and affordable monitoring of bear populations, and suggests that the swabbing of food remains or consumed baits from other animals may be an additional cost-effective and valuable tool in the study of the ecology and population biology of many elusive and/or wide-ranging species. PMID:27828988

Microsatellite data analysis for population genetics

USDA-ARS?s Scientific Manuscript database

Theories and analytical tools of population genetics have been widely applied for addressing various questions in the fields of ecological genetics, conservation biology, and any context where the role of dispersal or gene flow is important. Underlying much of population genetics is the analysis of ...

A Highly Thermostable Kanamycin Resistance Marker Expands the Tool Kit for Genetic Manipulation of Caldicellulosiruptor bescii

PubMed Central

Lipscomb, Gina L.; Conway, Jonathan M.; Blumer-Schuette, Sara E.; Kelly, Robert M.

2016-01-01

ABSTRACT Caldicellulosiruptor bescii, an anaerobic Gram-positive bacterium with an optimal growth temperature of 78°C, is the most thermophilic cellulose degrader known. It is of great biotechnological interest, as it efficiently deconstructs nonpretreated lignocellulosic plant biomass. Currently, its genetic manipulation relies on a mutant uracil auxotrophic background strain that contains a random deletion in the pyrF genome region. The pyrF gene serves as a genetic marker to select for uracil prototrophy, and it can also be counterselected for loss via resistance to the compound 5-fluoroorotic acid (5-FOA). To expand the C. bescii genetic tool kit, kanamycin resistance was developed as a selection for genetic manipulation. A codon-optimized version of the highly thermostable kanamycin resistance gene (named Cbhtk) allowed the use of kanamycin selection to obtain transformants of either replicating or integrating vector constructs in C. bescii. These strains showed resistance to kanamycin at concentrations >50 μg · ml−1, whereas wild-type C. bescii was sensitive to kanamycin at 10 μg · ml−1. In addition, placement of the Cbhtk marker between homologous recombination regions in an integrating vector allowed direct selection of a chromosomal mutation using both kanamycin and 5-FOA. Furthermore, the use of kanamycin selection enabled the targeted deletion of the pyrE gene in wild-type C. bescii, generating a uracil auxotrophic genetic background strain resistant to 5-FOA. The pyrE gene functioned as a counterselectable marker, like pyrF, and was used together with Cbhtk in the ΔpyrE background strain to delete genes encoding lactate dehydrogenase and the CbeI restriction enzyme. IMPORTANCE Caldicellulosiruptor bescii is a thermophilic anaerobic bacterium with an optimal growth temperature of 78°C, and it has the ability to efficiently deconstruct nonpretreated lignocellulosic plant biomass. It is, therefore, of biotechnological interest for genetic

Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach.

PubMed

Steggles, L Jason; Banks, Richard; Shaw, Oliver; Wipat, Anil

2007-02-01

New developments in post-genomic technology now provide researchers with the data necessary to study regulatory processes in a holistic fashion at multiple levels of biological organization. One of the major challenges for the biologist is to integrate and interpret these vast data resources to gain a greater understanding of the structure and function of the molecular processes that mediate adaptive and cell cycle driven changes in gene expression. In order to achieve this biologists require new tools and techniques to allow pathway related data to be modelled and analysed as network structures, providing valuable insights which can then be validated and investigated in the laboratory. We propose a new technique for constructing and analysing qualitative models of genetic regulatory networks based on the Petri net formalism. We take as our starting point the Boolean network approach of treating genes as binary switches and develop a new Petri net model which uses logic minimization to automate the construction of compact qualitative models. Our approach addresses the shortcomings of Boolean networks by providing access to the wide range of existing Petri net analysis techniques and by using non-determinism to cope with incomplete and inconsistent data. The ideas we present are illustrated by a case study in which the genetic regulatory network controlling sporulation in the bacterium Bacillus subtilis is modelled and analysed. The Petri net model construction tool and the data files for the B. subtilis sporulation case study are available at http://bioinf.ncl.ac.uk/gnapn.

Valuable human capital: the aging health care worker.

PubMed

Collins, Sandra K; Collins, Kevin S

2006-01-01

With the workforce growing older and the supply of younger workers diminishing, it is critical for health care managers to understand the factors necessary to capitalize on their vintage employees. Retaining this segment of the workforce has a multitude of benefits including the preservation of valuable intellectual capital, which is necessary to ensure that health care organizations maintain their competitive advantage in the consumer-driven market. Retaining the aging employee is possible if health care managers learn the motivators and training differences associated with this category of the workforce. These employees should be considered a valuable resource of human capital because without their extensive expertise, intense loyalty and work ethic, and superior customer service skills, health care organizations could suffer severe economic repercussions in the near future.

The Genetic Drift Inventory: A Tool for Measuring What Advanced Undergraduates Have Mastered about Genetic Drift

PubMed Central

Price, Rebecca M.; Andrews, Tessa C.; McElhinny, Teresa L.; Mead, Louise S.; Abraham, Joel K.; Thanukos, Anna; Perez, Kathryn E.

2014-01-01

Understanding genetic drift is crucial for a comprehensive understanding of biology, yet it is difficult to learn because it combines the conceptual challenges of both evolution and randomness. To help assess strategies for teaching genetic drift, we have developed and evaluated the Genetic Drift Inventory (GeDI), a concept inventory that measures upper-division students’ understanding of this concept. We used an iterative approach that included extensive interviews and field tests involving 1723 students across five different undergraduate campuses. The GeDI consists of 22 agree–disagree statements that assess four key concepts and six misconceptions. Student scores ranged from 4/22 to 22/22. Statements ranged in mean difficulty from 0.29 to 0.80 and in discrimination from 0.09 to 0.46. The internal consistency, as measured with Cronbach's alpha, ranged from 0.58 to 0.88 across five iterations. Test–retest analysis resulted in a coefficient of stability of 0.82. The true–false format means that the GeDI can test how well students grasp key concepts central to understanding genetic drift, while simultaneously testing for the presence of misconceptions that indicate an incomplete understanding of genetic drift. The insights gained from this testing will, over time, allow us to improve instruction about this key component of evolution. PMID:24591505

Genetics of eosinophilic esophagitis

PubMed Central

Kottyan, LC; Rothenberg, ME

2017-01-01

Eosinophilic esophagitis (EoE) is a chronic, allergic disease associated with marked mucosal eosinophil accumulation. EoE disease risk is multifactorial and includes environmental and genetic factors. This review will focus on the contribution of genetic variation to EoE risk, as well as the experimental tools and statistical methodology used to identify EoE risk loci. Specific disease-risk loci that are shared between EoE and other allergic diseases (TSLP, LRRC32) or unique to EoE (CAPN14), as well as Mendellian Disorders associated with EoE, will be reviewed in the context of the insight that they provide into the molecular pathoetiology of EoE. We will also discuss the clinical opportunities that genetic analyses provide in the form of decision support tools, molecular diagnostics, and novel therapeutic approaches. PMID:28224995

Genetics of eosinophilic esophagitis.

PubMed

Kottyan, L C; Rothenberg, M E

2017-05-01

Eosinophilic esophagitis (EoE) is a chronic, allergic disease associated with marked mucosal eosinophil accumulation. EoE disease risk is multifactorial and includes environmental and genetic factors. This review will focus on the contribution of genetic variation to EoE risk, as well as the experimental tools and statistical methodology used to identify EoE risk loci. Specific disease-risk loci that are shared between EoE and other allergic diseases (TSLP, LRRC32) or unique to EoE (CAPN14), as well as Mendellian Disorders associated with EoE, will be reviewed in the context of the insight that they provide into the molecular pathoetiology of EoE. We will also discuss the clinical opportunities that genetic analyses provide in the form of decision support tools, molecular diagnostics, and novel therapeutic approaches.

Educational websites--Bioinformatics Tools II.

PubMed

Lomberk, Gwen

2009-01-01

In this issue, the highlighted websites are a continuation of a series of educational websites; this one in particular from a couple of years ago, Bioinformatics Tools [Pancreatology 2005;5:314-315]. These include sites that are valuable resources for many research needs in genomics and proteomics. Bioinformatics has become a laboratory tool to map sequences to databases, develop models of molecular interactions, evaluate structural compatibilities, describe differences between normal and disease-associated DNA, identify conserved motifs within proteins, and chart extensive signaling networks, all in silico. Copyright 2008 S. Karger AG, Basel and IAP.

Genetic Modifiers and Oligogenic Inheritance

PubMed Central

Kousi, Maria; Katsanis, Nicholas

2015-01-01

Despite remarkable progress in the identification of mutations that drive genetic disorders, progress in understanding the effect of genetic background on the penetrance and expressivity of causal alleles has been modest, in part because of the methodological challenges in identifying genetic modifiers. Nonetheless, the progressive discovery of modifier alleles has improved both our interpretative ability and our analytical tools to dissect such phenomena. In this review, we analyze the genetic properties and behaviors of modifiers as derived from studies in patient populations and model organisms and we highlight conceptual and technological tools used to overcome some of the challenges inherent in modifier mapping and cloning. Finally, we discuss how the identification of these modifiers has facilitated the elucidation of biological pathways and holds the potential to improve the clinical predictive value of primary causal mutations and to develop novel drug targets. PMID:26033081

Precocious flowering of juvenile citrus induced by a viral vector based on Citrus leaf blotch virus: a new tool for genetics and breeding.

PubMed

Velázquez, Karelia; Agüero, Jesús; Vives, María C; Aleza, Pablo; Pina, José A; Moreno, Pedro; Navarro, Luis; Guerri, José

2016-10-01

The long juvenile period of citrus trees (often more than 6 years) has hindered genetic improvement by traditional breeding methods and genetic studies. In this work, we have developed a biotechnology tool to promote transition from the vegetative to the reproductive phase in juvenile citrus plants by expression of the Arabidopsis thaliana or citrus FLOWERING LOCUS T (FT) genes using a Citrus leaf blotch virus-based vector (clbvINpr-AtFT and clbvINpr-CiFT, respectively). Citrus plants of different genotypes graft inoculated with either of these vectors started flowering within 4-6 months, with no alteration of the plant architecture, leaf, flower or fruit morphology in comparison with noninoculated adult plants. The vector did not integrate in or recombine with the plant genome nor was it pollen or vector transmissible, albeit seed transmission at low rate was detected. The clbvINpr-AtFT is very stable, and flowering was observed over a period of at least 5 years. Precocious flowering of juvenile citrus plants after vector infection provides a helpful and safe tool to dramatically speed up genetic studies and breeding programmes. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Genetic construction of recombinant Pseudomonas chlororaphis for improved glycerol utilization

USDA-ARS?s Scientific Manuscript database

The objective of this study is to improve by genetic engineering the glycerol metabolic capability of Pseudomonas chlororaphis which is capable of producing commercially valuable biodegradable poly(hydroxyalkanoate) (PHA) and biosurfactant rhamnolipids (RLs). In the study, glycerol uptake facilitat...

Genetic counseling and testing for Alzheimer disease: Joint practice guidelines of the American College of Medical Genetics and the National Society of Genetic Counselors

PubMed Central

Goldman, Jill S.; Hahn, Susan E.; Catania, Jennifer Williamson; LaRusse-Eckert, Susan; Butson, Melissa Barber; Rumbaugh, Malia; Strecker, Michelle N.; Roberts, J. Scott; Burke, Wylie; Mayeux, Richard; Bird, Thomas

2012-01-01

Alzheimer disease is the most common cause of dementia. It occurs worldwide and affects all ethnic groups. The incidence of Alzheimer disease is increasing due, in part, to increased life expectancy and the aging baby boomer generation. The average lifetime risk of developing Alzheimer disease is 10–12%. This risk at least doubles with the presence of a first-degree relative with the disorder. Despite its limited utility, patients express concern over their risk and, in some instances, request testing. Furthermore, research has demonstrated that testing individuals for apoli-poprotein E can be valuable and safe in certain contexts. However, because of the complicated genetic nature of the disorder, few clinicians are prepared to address the genetic risks of Alzheimer disease with their patients. Given the increased awareness in family history thanks to family history campaigns, the increasing incidence of Alzheimer disease, and the availability of direct to consumer testing, patient requests for information is increasing. This practice guideline provides clinicians with a framework for assessing their patients’ genetic risk for Alzheimer disease, identifying which individuals may benefit from genetic testing, and providing the key elements of genetic counseling for AD. PMID:21577118

Genetic counseling and testing for Alzheimer disease: joint practice guidelines of the American College of Medical Genetics and the National Society of Genetic Counselors.

PubMed

Goldman, Jill S; Hahn, Susan E; Catania, Jennifer Williamson; LaRusse-Eckert, Susan; Butson, Melissa Barber; Rumbaugh, Malia; Strecker, Michelle N; Roberts, J Scott; Burke, Wylie; Mayeux, Richard; Bird, Thomas

2011-06-01

Alzheimer disease is the most common cause of dementia. It occurs worldwide and affects all ethnic groups. The incidence of Alzheimer disease is increasing due, in part, to increased life expectancy and the aging baby boomer generation. The average lifetime risk of developing Alzheimer disease is 10-12%. This risk at least doubles with the presence of a first-degree relative with the disorder. Despite its limited utility, patients express concern over their risk and, in some instances, request testing. Furthermore, research has demonstrated that testing individuals for apolipoprotein E can be valuable and safe in certain contexts. However, because of the complicated genetic nature of the disorder, few clinicians are prepared to address the genetic risks of Alzheimer disease with their patients. Given the increased awareness in family history thanks to family history campaigns, the increasing incidence of Alzheimer disease, and the availability of direct to consumer testing, patient requests for information is increasing. This practice guideline provides clinicians with a framework for assessing their patients' genetic risk for Alzheimer disease, identifying which individuals may benefit from genetic testing, and providing the key elements of genetic counseling for AD.

A mutational approach for the detection of genetic factors affecting seed size in maize.

PubMed

Sangiorgio, Stefano; Carabelli, Laura; Gabotti, Damiano; Manzotti, Priscilla Sofia; Persico, Martina; Consonni, Gabriella; Gavazzi, Giuseppe

2016-12-01

Genes influencing seed size. The designation emp (empty pericarp) refers to a group of defective kernel mutants that exhibit a drastic reduction in endosperm tissue production. They allow the isolation of genes controlling seed development and affecting seed size. Nine independently isolated emp mutants have been analyzed in this study and in all cases longitudinal sections of mature seeds revealed the absence of morphogenesis in the embryo proper, an observation that correlates with their failure to germinate. Complementation tests with the nine emp mutants, crossed inter se in all pairwise combinations, identified complementing and non-complementing pairs in the F 1 progenies. Data were then validated in the F 2 /F 3 generations. Mutant chromosomal location was also established. Overall our study has identified two novel emp genes and a novel allele at the previously identified emp4 gene. The introgression of single emp mutants in a different genetic background revealed the existence of a cryptic genetic variation (CGV) recognizable as a variable increase in the endosperm tissue. The unmasking of CGV by introducing single mutants in different genetic backgrounds is the result of the interaction of the emp mutants with a suppressor that has no obvious phenotype of its own and is present in the genetic background of the inbred lines into which the emp mutants were transferred. On the basis of these results, emp mutants could be used as tools for the detection of genetic factors that enhance the amount of endosperm tissue in the maize kernel and which could thus become valuable targets to exploit in future breeding programs.

Genetic Design Automation: engineering fantasy or scientific renewal?

PubMed Central

Lux, Matthew W.; Bramlett, Brian W.; Ball, David A.; Peccoud, Jean

2013-01-01

Synthetic biology aims to make genetic systems more amenable to engineering, which has naturally led to the development of Computer-Aided Design (CAD) tools. Experimentalists still primarily rely on project-specific ad-hoc workflows instead of domain-specific tools, suggesting that CAD tools are lagging behind the front line of the field. Here, we discuss the scientific hurdles that have limited the productivity gains anticipated from existing tools. We argue that the real value of efforts to develop CAD tools is the formalization of genetic design rules that determine the complex relationships between genotype and phenotype. PMID:22001068

Genetic modification of the human germ line: The reasons why this project has no future.

PubMed

Morange, Michel

2015-01-01

Modification of the human germ line has remained a distant but valuable objective for most biologists since the emergence of genetics (and even before). To study the historical transformations of this project, I have selected three periods - the 1930s, at the pinnacle of eugenics, around 1974 when molecular biology triumphed, and today - and have adopted three criteria to estimate the feasibility of this project: the state of scientific knowledge, the existence of suitable tools, and societal demands. Although the long-awaited techniques to modify the germ line are now available, I will show that most of the expectations behind this project have disappeared, or are considered as being reachable by highly different strategies. Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Response to selection while maximizing genetic variance in small populations.

PubMed

Cervantes, Isabel; Gutiérrez, Juan Pablo; Meuwissen, Theo H E

2016-09-20

Rare breeds represent a valuable resource for future market demands. These populations are usually well-adapted, but their low census compromises the genetic diversity and future of these breeds. Since improvement of a breed for commercial traits may also confer higher probabilities of survival for the breed, it is important to achieve good responses to artificial selection. Therefore, efficient genetic management of these populations is essential to ensure that they respond adequately to genetic selection in possible future artificial selection scenarios. Scenarios that maximize the maximum genetic variance in a unique population could be a valuable option. The aim of this work was to study the effect of the maximization of genetic variance to increase selection response and improve the capacity of a population to adapt to a new environment/production system. We simulated a random scenario (A), a full-sib scenario (B), a scenario applying the maximum variance total (MVT) method (C), a MVT scenario with a restriction on increases in average inbreeding (D), a MVT scenario with a restriction on average individual increases in inbreeding (E), and a minimum coancestry scenario (F). Twenty replicates of each scenario were simulated for 100 generations, followed by 10 generations of selection. Effective population size was used to monitor the outcomes of these scenarios. Although the best response to selection was achieved in scenarios B and C, they were discarded because they are unpractical. Scenario A was also discarded because of its low response to selection. Scenario D yielded less response to selection and a smaller effective population size than scenario E, for which response to selection was higher during early generations because of the moderately structured population. In scenario F, response to selection was slightly higher than in Scenario E in the last generations. Application of MVT with a restriction on individual increases in inbreeding resulted in the

Recent advances in genetic modification systems for Actinobacteria.

PubMed

Deng, Yu; Zhang, Xi; Zhang, Xiaojuan

2017-03-01

Actinobacteria are extremely important to human health, agriculture, and forests. Because of the vast differences of the characteristics of Actinobacteria, a lot of genetic tools have been developed for efficiently manipulating the genetics. Although there are a lot of successful examples of engineering Actinobacteria, they are still more difficult to be genetically manipulated than other model microorganisms such as Saccharomyces cerevisiae, Escherichia coli, and Bacillus subtilis etc. due to the diverse genomics and biochemical machinery. Here, we review the methods to introduce heterologous DNA into Actinobacteria and the available genetic modification tools. The trends and problems existing in engineering Actinobacteria are also covered.

An Evaluation of Teaching Introductory Geomorphology Using Computer-based Tools.

ERIC Educational Resources Information Center

Wentz, Elizabeth A.; Vender, Joann C.; Brewer, Cynthia A.

1999-01-01

Compares student reactions to traditional teaching methods and an approach where computer-based tools (GEODe CD-ROM and GIS-based exercises) were either integrated with or replaced the traditional methods. Reveals that the students found both of these tools valuable forms of instruction when used in combination with the traditional methods. (CMK)

A role for molecular genetics in biological conservation.

PubMed Central

O'Brien, S J

1994-01-01

The recognition of recent accelerated depletion of species as a consequence of human industrial development has spawned a wide interest in identifying threats to endangered species. In addition to ecological and demographic perils, it has become clear that small populations that narrowly survive demographic contraction may undergo close inbreeding, genetic drift, and loss of overall genomic variation due to allelic loss or reduction to homozygosity. I review here the consequences of such genetic depletion revealed by applying molecular population genetic analysis to four endangered mammals: African cheetah, lion, Florida panther, and humpback whale. The accumulated genetic results, combined with physiological, ecological, and ethological data, provide a multifaceted perspective of the process of species diminution. An emerging role of population genetics, phylogenetics, and phylogeography as indicators of a population's natural history and its future prognosis provides valuable data of use in the development of conservation management plans for endangered species. PMID:7912434

pTcGW plasmid vectors 1.1 version: a versatile tool for Trypanosoma cruzi gene characterisation

PubMed Central

Kugeratski, Fernanda G; Batista, Michel; Inoue, Alexandre Haruo; Ramos, Bruno Dias; Krieger, Marco Aurelio; Marchini/, Fabricio K

2015-01-01

The functional characterisation of thousands of Trypanosoma cruzi genes remains a challenge. Reverse genetics approaches compatible with high-throughput cloning strategies can provide the tool needed to tackle this challenge. We previously published the pTcGW platform, composed by plasmid vectors carrying different options of N-terminal fusion tags based on Gateway® technology. Here, we present an improved 1.1 version of pTcGW vectors, which is characterised by a fully flexible structure allowing an easy customisation of each element of the vectors in a single cloning step. Additionally, both N and C-terminal fusions are available with new tag options for protein complexes purification. Three of the newly created vectors were successfully used to determine the cellular localisation of four T. cruzi proteins. The 1.1 version of pTcGW platform can be used in a variety of assays, such as protein overexpression, identification of protein-protein interaction and protein localisation. This powerful and versatile tool allows adding valuable functional information to T. cruzi genes and is freely available for scientific community. PMID:26200713

Conservation genetics of managed ungulate populations

USGS Publications Warehouse

Scribner, Kim T.

1993-01-01

Natural populations of many species are increasingly impacted by human activities. Perturbations are particularly pronunced for large ungulates due in part to sport and commercial harvest, to reductions and fragmentation of native habitat, and as the result of reintroductions. These perturbations affect population size, sex and age composition, and population breeding structure, and as a consequence affect the levels and partitioning of genetic variation. Three case histories highlighting long-term ecological genetic research on mule deer Odocoileus hemionus (Rafinesque, 1817), white-tailed deer O. virginianus (Zimmermann, 1780), and Alpine ibex Capra i. ibex Linnaeus, 1758 are presented. Joint examinations of population ecological and genetic data from several populations of each species reveal: (1) that populations are not in genetic equilibrium, but that allele frequencies and heterozygosity change dramatically over time and among cohorts produced in successive years, (2) populations are genetically structured over short and large geographic distances reflecting local breeding structure and patterns of gene flow, respectively; however, this structure is quite dynamic over time, due in part to population exploitation, and (3) restocking programs are often undertaken with small numbers of founding individuals resulting in dramatic declines in levels of genetic variability and increasing levels of genetic differentiation among populations due to genetic drift. Genetic characteristics have and will continue to provide valuable indirect sources of information relating enviromental and human perturbations to changes in population processes.

A survey of tools for variant analysis of next-generation genome sequencing data

PubMed Central

Pabinger, Stephan; Dander, Andreas; Fischer, Maria; Snajder, Rene; Sperk, Michael; Efremova, Mirjana; Krabichler, Birgit; Speicher, Michael R.; Zschocke, Johannes

2014-01-01

Recent advances in genome sequencing technologies provide unprecedented opportunities to characterize individual genomic landscapes and identify mutations relevant for diagnosis and therapy. Specifically, whole-exome sequencing using next-generation sequencing (NGS) technologies is gaining popularity in the human genetics community due to the moderate costs, manageable data amounts and straightforward interpretation of analysis results. While whole-exome and, in the near future, whole-genome sequencing are becoming commodities, data analysis still poses significant challenges and led to the development of a plethora of tools supporting specific parts of the analysis workflow or providing a complete solution. Here, we surveyed 205 tools for whole-genome/whole-exome sequencing data analysis supporting five distinct analytical steps: quality assessment, alignment, variant identification, variant annotation and visualization. We report an overview of the functionality, features and specific requirements of the individual tools. We then selected 32 programs for variant identification, variant annotation and visualization, which were subjected to hands-on evaluation using four data sets: one set of exome data from two patients with a rare disease for testing identification of germline mutations, two cancer data sets for testing variant callers for somatic mutations, copy number variations and structural variations, and one semi-synthetic data set for testing identification of copy number variations. Our comprehensive survey and evaluation of NGS tools provides a valuable guideline for human geneticists working on Mendelian disorders, complex diseases and cancers. PMID:23341494

Genovar: a detection and visualization tool for genomic variants.

PubMed

Jung, Kwang Su; Moon, Sanghoon; Kim, Young Jin; Kim, Bong-Jo; Park, Kiejung

2012-05-08

Along with single nucleotide polymorphisms (SNPs), copy number variation (CNV) is considered an important source of genetic variation associated with disease susceptibility. Despite the importance of CNV, the tools currently available for its analysis often produce false positive results due to limitations such as low resolution of array platforms, platform specificity, and the type of CNV. To resolve this problem, spurious signals must be separated from true signals by visual inspection. None of the previously reported CNV analysis tools support this function and the simultaneous visualization of comparative genomic hybridization arrays (aCGH) and sequence alignment. The purpose of the present study was to develop a useful program for the efficient detection and visualization of CNV regions that enables the manual exclusion of erroneous signals. A JAVA-based stand-alone program called Genovar was developed. To ascertain whether a detected CNV region is a novel variant, Genovar compares the detected CNV regions with previously reported CNV regions using the Database of Genomic Variants (DGV, http://projects.tcag.ca/variation) and the Single Nucleotide Polymorphism Database (dbSNP). The current version of Genovar is capable of visualizing genomic data from sources such as the aCGH data file and sequence alignment format files. Genovar is freely accessible and provides a user-friendly graphic user interface (GUI) to facilitate the detection of CNV regions. The program also provides comprehensive information to help in the elimination of spurious signals by visual inspection, making Genovar a valuable tool for reducing false positive CNV results. http://genovar.sourceforge.net/.

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

PubMed

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.

MixFit: Methodology for Computing Ancestry-Related Genetic Scores at the Individual Level and Its Application to the Estonian and Finnish Population Studies.

PubMed

Haller, Toomas; Leitsalu, Liis; Fischer, Krista; Nuotio, Marja-Liisa; Esko, Tõnu; Boomsma, Dorothea Irene; Kyvik, Kirsten Ohm; Spector, Tim D; Perola, Markus; Metspalu, Andres

2017-01-01

Ancestry information at the individual level can be a valuable resource for personalized medicine, medical, demographical and history research, as well as for tracing back personal history. We report a new method for quantitatively determining personal genetic ancestry based on genome-wide data. Numerical ancestry component scores are assigned to individuals based on comparisons with reference populations. These comparisons are conducted with an existing analytical pipeline making use of genotype phasing, similarity matrix computation and our addition-multidimensional best fitting by MixFit. The method is demonstrated by studying Estonian and Finnish populations in geographical context. We show the main differences in the genetic composition of these otherwise close European populations and how they have influenced each other. The components of our analytical pipeline are freely available computer programs and scripts one of which was developed in house (available at: www.geenivaramu.ee/en/tools/mixfit).

Genetic design automation: engineering fantasy or scientific renewal?

PubMed

Lux, Matthew W; Bramlett, Brian W; Ball, David A; Peccoud, Jean

2012-02-01

The aim of synthetic biology is to make genetic systems more amenable to engineering, which has naturally led to the development of computer-aided design (CAD) tools. Experimentalists still primarily rely on project-specific ad hoc workflows instead of domain-specific tools, which suggests that CAD tools are lagging behind the front line of the field. Here, we discuss the scientific hurdles that have limited the productivity gains anticipated from existing tools. We argue that the real value of efforts to develop CAD tools is the formalization of genetic design rules that determine the complex relationships between genotype and phenotype. Copyright © 2011 Elsevier Ltd. All rights reserved.

Advanced technologies for genetically manipulating the silkworm Bombyx mori, a model Lepidopteran insect

PubMed Central

Xu, Hanfu; O'Brochta, David A.

2015-01-01

Genetic technologies based on transposon-mediated transgenesis along with several recently developed genome-editing technologies have become the preferred methods of choice for genetically manipulating many organisms. The silkworm, Bombyx mori, is a Lepidopteran insect of great economic importance because of its use in silk production and because it is a valuable model insect that has greatly enhanced our understanding of the biology of insects, including many agricultural pests. In the past 10 years, great advances have been achieved in the development of genetic technologies in B. mori, including transposon-based technologies that rely on piggyBac-mediated transgenesis and genome-editing technologies that rely on protein- or RNA-guided modification of chromosomes. The successful development and application of these technologies has not only facilitated a better understanding of B. mori and its use as a silk production system, but also provided valuable experiences that have contributed to the development of similar technologies in non-model insects. This review summarizes the technologies currently available for use in B. mori, their application to the study of gene function and their use in genetically modifying B. mori for biotechnology applications. The challenges, solutions and future prospects associated with the development and application of genetic technologies in B. mori are also discussed. PMID:26108630

Winemaking and Bioprocesses Strongly Shaped the Genetic Diversity of the Ubiquitous Yeast Torulaspora delbrueckii

PubMed Central

Comte, Guillaume; Panfili, Aurélie; Delcamp, Adline; Salin, Franck; Marullo, Philippe; Bely, Marina

2014-01-01

The yeast Torulaspora delbrueckii is associated with several human activities including oenology, bakery, distillery, dairy industry, etc. In addition to its biotechnological applications, T. delbrueckii is frequently isolated in natural environments (plant, soil, insect). T. delbrueckii is thus a remarkable ubiquitous yeast species with both wild and anthropic habitats, and appears to be a perfect yeast model to search for evidence of human domestication. For that purpose, we developed eight microsatellite markers that were used for the genotyping of 110 strains from various substrates and geographical origins. Microsatellite analysis showed four genetic clusters: two groups contained most nature strains from Old World and Americas respectively, and two clusters were associated with winemaking and other bioprocesses. Analysis of molecular variance (AMOVA) confirmed that human activities significantly shaped the genetic variability of T. delbrueckii species. Natural isolates are differentiated on the basis of geographical localisation, as expected for wild population. The domestication of T. delbrueckii probably dates back to the Roman Empire for winemaking (∼1900 years ago), and to the Neolithic era for bioprocesses (∼4000 years ago). Microsatellite analysis also provided valuable data regarding the life-cycle of the species, suggesting a mostly diploid homothallic life. In addition to population genetics and ecological studies, the microsatellite tool will be particularly useful for further biotechnological development of T. delbrueckii strains for winemaking and other bioprocesses. PMID:24718638

Winemaking and bioprocesses strongly shaped the genetic diversity of the ubiquitous yeast Torulaspora delbrueckii.

PubMed

Albertin, Warren; Chasseriaud, Laura; Comte, Guillaume; Panfili, Aurélie; Delcamp, Adline; Salin, Franck; Marullo, Philippe; Bely, Marina

2014-01-01

The yeast Torulaspora delbrueckii is associated with several human activities including oenology, bakery, distillery, dairy industry, etc. In addition to its biotechnological applications, T. delbrueckii is frequently isolated in natural environments (plant, soil, insect). T. delbrueckii is thus a remarkable ubiquitous yeast species with both wild and anthropic habitats, and appears to be a perfect yeast model to search for evidence of human domestication. For that purpose, we developed eight microsatellite markers that were used for the genotyping of 110 strains from various substrates and geographical origins. Microsatellite analysis showed four genetic clusters: two groups contained most nature strains from Old World and Americas respectively, and two clusters were associated with winemaking and other bioprocesses. Analysis of molecular variance (AMOVA) confirmed that human activities significantly shaped the genetic variability of T. delbrueckii species. Natural isolates are differentiated on the basis of geographical localisation, as expected for wild population. The domestication of T. delbrueckii probably dates back to the Roman Empire for winemaking (∼ 1900 years ago), and to the Neolithic era for bioprocesses (∼ 4000 years ago). Microsatellite analysis also provided valuable data regarding the life-cycle of the species, suggesting a mostly diploid homothallic life. In addition to population genetics and ecological studies, the microsatellite tool will be particularly useful for further biotechnological development of T. delbrueckii strains for winemaking and other bioprocesses.

Ani s 11-Like Protein Is a Pepsin- and Heat-Resistant Major Allergen of Anisakis spp. and a Valuable Tool for Anisakis Allergy Component-Resolved Diagnosis.

PubMed

Carballeda-Sangiao, Noelia; Rodríguez-Mahillo, Ana I; Careche, Mercedes; Navas, Alfonso; Caballero, Teresa; Dominguez-Ortega, Javier; Jurado-Palomo, Jesús; González-Muñoz, Miguel

2016-01-01

Anisakis simplex is a fish parasite responsible for gastrointestinal and allergic symptoms in humans. The Ani s 11-like protein has been proposed as an Anisakis allergen because its primary structure is similar to that of Ani s 11. The aims of this work were to analyse the frequency of detection of the Ani s 11-like protein and assess its diagnostic value. rAni s 11-like protein, rAni s 5 and rAni s 4 were expressed in Escherichia coli and rAni s 1 was produced in Pichia pastoris. Recombinant allergen detection patterns in 37 Anisakis-sensitised patients were determined. The stability to pepsin digestion and heat treatment of rAni s 11-like protein was also analysed by IgE immunoblotting. Ani s 11-like protein is a major allergen detected by 78% of Anisakis-allergic patients, and 13.5% of patients detect only the rAni s 11-like allergen. This allergen is heat stable because it retains its capability of binding IgE after boiling for 30 min and it is resistant to pepsin digestion for 120 min. These data indicate that the Ani s 11-like protein is a pepsin- and heat-resistant major allergen (Ani s 11.0201) of Anisakis spp. and a valuable tool for Anisakis allergy component-resolved diagnosis. © 2016 S. Karger AG, Basel.

Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice

PubMed Central

Yang, Wanneng; Guo, Zilong; Huang, Chenglong; Duan, Lingfeng; Chen, Guoxing; Jiang, Ni; Fang, Wei; Feng, Hui; Xie, Weibo; Lian, Xingming; Wang, Gongwei; Luo, Qingming; Zhang, Qifa; Liu, Qian; Xiong, Lizhong

2014-01-01

Even as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques, traditional plant phenotyping lags far behind. Here we develop a high-throughput rice phenotyping facility (HRPF) to monitor 13 traditional agronomic traits and 2 newly defined traits during the rice growth period. Using genome-wide association studies (GWAS) of the 15 traits, we identify 141 associated loci, 25 of which contain known genes such as the Green Revolution semi-dwarf gene, SD1. Based on a performance evaluation of the HRPF and GWAS results, we demonstrate that high-throughput phenotyping has the potential to replace traditional phenotyping techniques and can provide valuable gene identification information. The combination of the multifunctional phenotyping tools HRPF and GWAS provides deep insights into the genetic architecture of important traits. PMID:25295980

Have You Ever Googled a Patient or Been Friended by a Patient? Social Media Intersects the Practice of Genetic Counseling.

PubMed

Omaggio, NinaMarie F; Baker, Maria J; Conway, Laura J

2018-04-01

Patients and healthcare providers are becoming increasingly connected via social media, bringing new opportunities and challenges. Direct connection can occur between patients and providers using online tools such as Facebook and LinkedIn. In addition, providers can gather information about patients using a search engine such as Google, referred to as patient-targeted Googling (PTG). An online 54-item survey was used to gain information on (1) how and to what extent genetic counseling students and genetic counselors connect directly with patients via social media sites, and (2) gather information on providers using PTG. Four hundred genetic counseling students and genetic counselors participated in the survey. The majority of respondents (88.9%; n = 344/387) find it is never or rarely acceptable to interact with current patients via social media sites; however, 27.7% (n = 110/397) have visited a patient's social media site. Gathering information for patient care was the most commonly reported reason (76.8%; n = 43/56). Thirty-three percent (n = 130/394) have considered searching online or actually searched online for information about a patient. Curiosity was the most common reason (92.7%; n = 114/123); although, respondents also used PTG to obtain contact information and to prepare for patient sessions. Our study supports the need for development and dissemination of professional guidelines to serve as a valuable resource for practicing genetic counselors and genetic counseling training programs.

A Genetic Algorithm Approach to Motion Sensor Placement in Smart Environments.

PubMed

Thomas, Brian L; Crandall, Aaron S; Cook, Diane J

2016-04-01

Smart environments and ubiquitous computing technologies hold great promise for a wide range of real world applications. The medical community is particularly interested in high quality measurement of activities of daily living. With accurate computer modeling of older adults, decision support tools may be built to assist care providers. One aspect of effectively deploying these technologies is determining where the sensors should be placed in the home to effectively support these end goals. This work introduces and evaluates a set of approaches for generating sensor layouts in the home. These approaches range from the gold standard of human intuition-based placement to more advanced search algorithms, including Hill Climbing and Genetic Algorithms. The generated layouts are evaluated based on their ability to detect activities while minimizing the number of needed sensors. Sensor-rich environments can provide valuable insights about adults as they go about their lives. These sensors, once in place, provide information on daily behavior that can facilitate an aging-in-place approach to health care.

An Advanced Preclinical Mouse Model for Acute Myeloid Leukemia Using Patients' Cells of Various Genetic Subgroups and In Vivo Bioluminescence Imaging

PubMed Central

Vick, Binje; Rothenberg, Maja; Sandhöfer, Nadine; Carlet, Michela; Finkenzeller, Cornelia; Krupka, Christina; Grunert, Michaela; Trumpp, Andreas; Corbacioglu, Selim; Ebinger, Martin; André, Maya C.; Hiddemann, Wolfgang; Schneider, Stephanie; Subklewe, Marion; Metzeler, Klaus H.; Spiekermann, Karsten; Jeremias, Irmela

2015-01-01

Acute myeloid leukemia (AML) is a clinically and molecularly heterogeneous disease with poor outcome. Adequate model systems are required for preclinical studies to improve understanding of AML biology and to develop novel, rational treatment approaches. Xenografts in immunodeficient mice allow performing functional studies on patient-derived AML cells. We have established an improved model system that integrates serial retransplantation of patient-derived xenograft (PDX) cells in mice, genetic manipulation by lentiviral transduction, and essential quality controls by immunophenotyping and targeted resequencing of driver genes. 17/29 samples showed primary engraftment, 10/17 samples could be retransplanted and some of them allowed virtually indefinite serial transplantation. 5/6 samples were successfully transduced using lentiviruses. Neither serial transplantation nor genetic engineering markedly altered sample characteristics analyzed. Transgene expression was stable in PDX AML cells. Example given, recombinant luciferase enabled bioluminescence in vivo imaging and highly sensitive and reliable disease monitoring; imaging visualized minimal disease at 1 PDX cell in 10000 mouse bone marrow cells and facilitated quantifying leukemia initiating cells. We conclude that serial expansion, genetic engineering and imaging represent valuable tools to improve the individualized xenograft mouse model of AML. Prospectively, these advancements enable repetitive, clinically relevant studies on AML biology and preclinical treatment trials on genetically defined and heterogeneous subgroups. PMID:25793878

Commerce and genetic diagnostics.

PubMed

Silverman, Paul H

1995-01-01

The revolution in molecular biology and molecular genetics has begun to reveal the sequence of events that links genes and disease. As a result of activities such as the Human Genome Project, a parallel revolution in technology is bringing nearer to hand the possibility of readily available genetic diagnostics. Genetic testing services have begun to move out of the academic medical centers and into the private enterprise arena. Under these circumstances it is important to understand the factors affecting the availability and application of this powerful predictive tool in a for-profit mode. How does the marketplace encourage or discourage genetic testing? Will the same market influences that generate pharmaceutical sales be operating to "sell" genetic tests?

Translation and validation of a Spanish-language genetic health literacy screening tool.

PubMed

Rodríguez, Sally Ann; Roter, Debra L; Castillo-Salgado, Carlos; Hooker, Gillian W; Erby, Lori H

2015-02-01

Literacy deficits and underutilization of medical services have been linked to health disparities among minorities, and this appears especially relevant for the Latino population. Given the increasing importance of genetics, assessment of genetic health literacy may direct future efforts to better serve this vulnerable population. The current study was designed to contribute to this area by translating and validating a Spanish-language genetic health literacy measure. This was a cross-sectional study involving an interviewer-administered questionnaire. Eligible individuals were Latinos between the ages of 18 and 75 residing in Maryland, who self-reported Spanish as their primary language, recruited through convenience sampling. The genetic health literacy measure components were adapted from existing English-language measures [Erby, Roter, Larson, & Cho's (2008) Rapid Estimate of Adult Literacy in Genetics (REAL-G) and Hooker et al.'s (2014) Genetic Literacy and Comprehension]. An existing Spanish-language general health literacy measure was used to establish preliminary concurrent validity [Lee, Bender, Ruiz, & Cho's (2006) SAHLSA]. 116 individuals completed the assessment. The Spanish-language REAL-G (REAL-G-Sp) was found to correlate well with the SAHLSA (Pearson's r = .77, p < .01). A cut-off score of 59 (out of 62) distinguished low versus high genetic health literacy with a sensitivity of 86% and specificity of 71%, identifying 28% of participants as having inadequate genetic health literacy. The REAL-G-Sp was found to have preliminary concurrent validity with an existing health literacy measure in the Latino population residing in Maryland. Significant proportions of this population are predicted to have limitations in genetic health literacy, even when information is provided in Spanish.

Glasgow Coma Scale and Its Components on Admission: Are They Valuable Prognostic Tools in Acute Mixed Drug Poisoning?

PubMed Central

Eizadi Mood, N.; Sabzghabaee, A. M.; Yadegarfar, Gh.; Yaraghi, A.; Ramazani Chaleshtori, M.

2011-01-01

Introduction. The verbal, eye, and motor components of Glasgow coma scale (GCS) may be influenced by poisoned patients' behavior in an attempted suicide. So, the values of admission GCS and its components for outcomes prediction in mixed drugs poisoning were investigated. Materials and Methods. A followup study data was performed on patients with mixed drugs poisoning. Outcomes were recorded as without complications and with complications. Discrimination was evaluated by calculating the area under the receiver operating characteristic curves (AUC). Results. There was a significant difference between the mean value of each component of GCS as well as the total GCS between patients with and without complication. Discrimination was best for GCS (AUC: 0.933 ± 0.020) and verbal (0.932 ± 0.021), followed by motor (0.911 ± 0.025), then eye (0.89 ± 0.028). Conclusions. Admission GCS and its components seem to be valuable in outcome prediction of patients with mixed drug poisoning. PMID:21559299

Desktop Genetics.

PubMed

Hough, Soren H; Ajetunmobi, Ayokunmi; Brody, Leigh; Humphryes-Kirilov, Neil; Perello, Edward

2016-11-01

Desktop Genetics is a bioinformatics company building a gene-editing platform for personalized medicine. The company works with scientists around the world to design and execute state-of-the-art clustered regularly interspaced short palindromic repeats (CRISPR) experiments. Desktop Genetics feeds the lessons learned about experimental intent, single-guide RNA design and data from international genomics projects into a novel CRISPR artificial intelligence system. We believe that machine learning techniques can transform this information into a cognitive therapeutic development tool that will revolutionize medicine.

Genetic recombinational and physical linkage analyses on slash pine

Treesearch

Rob Doudrick

1996-01-01

Slash pine is native to the southeastern USA, but is commercially valuable world-wide as a timber-,fiber- and resin-producing species. Breeding objectives emphasize selection for fusiform rust disease resistance. Identification of markers linked to genetic factors conditioning specificity should expand our knowledge of disease development. Towards this end, random...

OPTIMIZING USABILITY OF AN ECONOMIC DECISION SUPPORT TOOL: PROTOTYPE OF THE EQUIPT TOOL.

PubMed

Cheung, Kei Long; Hiligsmann, Mickaël; Präger, Maximilian; Jones, Teresa; Józwiak-Hagymásy, Judit; Muñoz, Celia; Lester-George, Adam; Pokhrel, Subhash; López-Nicolás, Ángel; Trapero-Bertran, Marta; Evers, Silvia M A A; de Vries, Hein

2018-01-01

Economic decision-support tools can provide valuable information for tobacco control stakeholders, but their usability may impact the adoption of such tools. This study aims to illustrate a mixed-method usability evaluation of an economic decision-support tool for tobacco control, using the EQUIPT ROI tool prototype as a case study. A cross-sectional mixed methods design was used, including a heuristic evaluation, a thinking aloud approach, and a questionnaire testing and exploring the usability of the Return of Investment tool. A total of sixty-six users evaluated the tool (thinking aloud) and completed the questionnaire. For the heuristic evaluation, four experts evaluated the interface. In total twenty-one percent of the respondents perceived good usability. A total of 118 usability problems were identified, from which twenty-six problems were categorized as most severe, indicating high priority to fix them before implementation. Combining user-based and expert-based evaluation methods is recommended as these were shown to identify unique usability problems. The evaluation provides input to optimize usability of a decision-support tool, and may serve as a vantage point for other developers to conduct usability evaluations to refine similar tools before wide-scale implementation. Such studies could reduce implementation gaps by optimizing usability, enhancing in turn the research impact of such interventions.

Quantitative genetic tools for insecticide resistance risk assessment: estimating the heritability of resistance

Treesearch

Michael J. Firko; Jane Leslie Hayes

1990-01-01

Quantitative genetic studies of resistance can provide estimates of genetic parameters not available with other types of genetic analyses. Three methods are discussed for estimating the amount of additive genetic variation in resistance to individual insecticides and subsequent estimation of heritability (h2) of resistance. Sibling analysis and...

The Mouse House: a brief history of the ORNL mouse-genetics program, 1947-2009.

PubMed

Russell, Liane B

2013-01-01

The large mouse genetics program at the Oak Ridge National Laboratory (ORNL) is often remembered chiefly for the germ-cell mutation-rate data it generated and their uses in estimating the risk of heritable radiation damage. In fact, it soon became a multi-faceted research effort that, over a period of almost 60 years, generated a wealth of information in the areas of mammalian mutagenesis, basic genetics (later enriched by molecular techniques), cytogenetics, reproductive biology, biochemistry of germ cells, and teratology. Research in the area of germ-cell mutagenesis explored the important physical and biological factors that affect the frequency and nature of induced mutations and made several unexpected discoveries, such as the major importance of the perigametic interval (the zygote stage) for the origin of spontaneous mutations and for the sensitivity to induced genetic change. Of practical value was the discovery that ethylnitrosourea was a supermutagen for point mutations, making high-efficiency mutagenesis in the mouse feasible worldwide. Teratogenesis findings resulted in recommendations still generally accepted in radiological practice. Studies supporting the mutagenesis research added whole bodies of information about mammalian germ-cell development and about molecular targets in germ cells. The early decision to not merely count but propagate genetic variants of all sorts made possible further discoveries, such as the Y-chromosome's importance in mammalian sex determination and the identification of rare X-autosome translocations, which, in turn, led to the formulation of the single-active-X hypothesis and provided tools for studies of functional mosaicism for autosomal genes, male sterility, and chromosome-pairing mechanism. Extensive genetic and then molecular analyses of large numbers of induced specific-locus mutants resulted in fine-structure physical and correlated functional mapping of significant portions of the mouse genome and constituted a

A review of genome-wide approaches to study the genetic basis for spermatogenic defects.

PubMed

Aston, Kenneth I; Conrad, Donald F

2013-01-01

Rapidly advancing tools for genetic analysis on a genome-wide scale have been instrumental in identifying the genetic bases for many complex diseases. About half of male infertility cases are of unknown etiology in spite of tremendous efforts to characterize the genetic basis for the disorder. Advancing our understanding of the genetic basis for male infertility will require the application of established and emerging genomic tools. This chapter introduces many of the tools available for genetic studies on a genome-wide scale along with principles of study design and data analysis.

Entering the second century of maize quantitative genetics

USDA-ARS?s Scientific Manuscript database

Maize is the most widely grown cereal in the world. In addition to its role in global agriculture, it has also long served as a model organism for genetic research. Maize stands at a genetic crossroads, as it has access to all the tools available for plant genetics but exhibits a genetic architectur...

Molecular Genetics of Mycobacteriophages

PubMed Central

HATFULL, GRAHAM F.

2014-01-01

Mycobacteriophages have provided numerous essential tools for mycobacterial genetics, including delivery systems for transposons, reporter genes, and allelic exchange substrates, and components for plasmid vectors and mutagenesis. Their genetically diverse genomes also reveal insights into the broader nature of the phage population and the evolutionary mechanisms that give rise to it. The substantial advances in our understanding of the biology of mycobacteriophages including a large collection of completely sequenced genomes indicates a rich potential for further contributions in tuberculosis genetics and beyond. PMID:25328854

Ralstonia eutropha H16 in progress: Applications beside PHAs and establishment as production platform by advanced genetic tools.

PubMed

Raberg, Matthias; Volodina, Elena; Lin, Kaichien; Steinbüchel, Alexander

2018-06-01

Ralstonia eutropha strain H16 is a Gram-negative non-pathogenic betaproteobacterium ubiquitously found in soils and has been the subject of intensive research for more than 50 years. Due to its remarkable metabolically versatility, it utilizes a broad range of renewable heterotrophic resources. The substrate utilization range can be further extended by metabolic engineering as genetic tools are available. It has become the best studied "Knallgas" bacterium capable of chemolithoautotrophic growth with hydrogen as the electron donor and carbon dioxide as the carbon source. It also serves as a model organism to study the metabolism of poly(β-hydroxybutyrate), a polyester which is accumulated within the cells for storage of both carbon and energy. Thermoplastic and biodegradable properties of this polyhydroxyalkanoate (PHA) have attracted much biotechnical interest as a replacement for fossil resource-based plastics. The first applications of R. eutropha aimed at chemolithoautotrophic production of single cell protein (SCP) for food and feed and the synthesis of various PHAs. The complete annotated genome is available allowing systematic biology approaches together with data provided by available omics studies. Besides PHAs, novel biopolymers of 2-hydroxyalkanoates and polythioesters or cyanophycin as well as chemicals such as alcohols, alkanes, alkenes, and further interesting value added chemicals significantly recently extended the range of products synthesized by R. eutropha. High cell density cultivations can be performed without too much effort and the available repertoire of genetic tools is rapidly growing. Altogether, this qualifies R. eutropha strain H16 to become a production platform strain for a large spectrum of products.

Parasites as valuable stock markers for fisheries in Australasia, East Asia and the Pacific Islands.

PubMed

Lester, R J G; Moore, B R

2015-01-01

Over 30 studies in Australasia, East Asia and the Pacific Islands region have collected and analysed parasite data to determine the ranges of individual fish, many leading to conclusions about stock delineation. Parasites used as biological tags have included both those known to have long residence times in the fish and those thought to be relatively transient. In many cases the parasitological conclusions have been supported by other methods especially analysis of the chemical constituents of otoliths, and to a lesser extent, genetic data. In analysing parasite data, authors have applied multiple different statistical methodologies, including summary statistics, and univariate and multivariate approaches. Recently, a growing number of researchers have found non-parametric methods, such as analysis of similarities and cluster analysis, to be valuable. Future studies into the residence times, life cycles and geographical distributions of parasites together with more robust analytical methods will yield much important information to clarify stock structures in the area.

Ecogeographic Genetic Epidemiology

PubMed Central

Sloan, Chantel D.; Duell, Eric J.; Shi, Xun; Irwin, Rebecca; Andrew, Angeline S.; Williams, Scott M.; Moore, Jason H.

2009-01-01

Complex diseases such as cancer and heart disease result from interactions between an individual's genetics and environment, i.e. their human ecology. Rates of complex diseases have consistently demonstrated geographic patterns of incidence, or spatial “clusters” of increased incidence relative to the general population. Likewise, genetic subpopulations and environmental influences are not evenly distributed across space. Merging appropriate methods from genetic epidemiology, ecology and geography will provide a more complete understanding of the spatial interactions between genetics and environment that result in spatial patterning of disease rates. Geographic Information Systems (GIS), which are tools designed specifically for dealing with geographic data and performing spatial analyses to determine their relationship, are key to this kind of data integration. Here the authors introduce a new interdisciplinary paradigm, ecogeographic genetic epidemiology, which uses GIS and spatial statistical analyses to layer genetic subpopulation and environmental data with disease rates and thereby discern the complex gene-environment interactions which result in spatial patterns of incidence. PMID:19025788

Genetic Simulation Resources: a website for the registration and discovery of genetic data simulators

PubMed Central

Peng, Bo; Chen, Huann-Sheng; Mechanic, Leah E.; Racine, Ben; Clarke, John; Clarke, Lauren; Gillanders, Elizabeth; Feuer, Eric J.

2013-01-01

Summary: Many simulation methods and programs have been developed to simulate genetic data of the human genome. These data have been widely used, for example, to predict properties of populations retrospectively or prospectively according to mathematically intractable genetic models, and to assist the validation, statistical inference and power analysis of a variety of statistical models. However, owing to the differences in type of genetic data of interest, simulation methods, evolutionary features, input and output formats, terminologies and assumptions for different applications, choosing the right tool for a particular study can be a resource-intensive process that usually involves searching, downloading and testing many different simulation programs. Genetic Simulation Resources (GSR) is a website provided by the National Cancer Institute (NCI) that aims to help researchers compare and choose the appropriate simulation tools for their studies. This website allows authors of simulation software to register their applications and describe them with well-defined attributes, thus allowing site users to search and compare simulators according to specified features. Availability: http://popmodels.cancercontrol.cancer.gov/gsr. Contact: gsr@mail.nih.gov PMID:23435068

Production of Fatty Acid-Derived Valuable Chemicals in Synthetic Microbes

PubMed Central

Yu, Ai-Qun; Pratomo Juwono, Nina Kurniasih; Leong, Susanna Su Jan; Chang, Matthew Wook

2014-01-01

Fatty acid derivatives, such as hydroxy fatty acids, fatty alcohols, fatty acid methyl/ethyl esters, and fatty alka(e)nes, have a wide range of industrial applications including plastics, lubricants, and fuels. Currently, these chemicals are obtained mainly through chemical synthesis, which is complex and costly, and their availability from natural biological sources is extremely limited. Metabolic engineering of microorganisms has provided a platform for effective production of these valuable biochemicals. Notably, synthetic biology-based metabolic engineering strategies have been extensively applied to refactor microorganisms for improved biochemical production. Here, we reviewed: (i) the current status of metabolic engineering of microbes that produce fatty acid-derived valuable chemicals, and (ii) the recent progress of synthetic biology approaches that assist metabolic engineering, such as mRNA secondary structure engineering, sensor-regulator system, regulatable expression system, ultrasensitive input/output control system, and computer science-based design of complex gene circuits. Furthermore, key challenges and strategies were discussed. Finally, we concluded that synthetic biology provides useful metabolic engineering strategies for economically viable production of fatty acid-derived valuable chemicals in engineered microbes. PMID:25566540

Genetic evidence for the role of GDP-mannose in plant ascorbic acid (vitamin C) biosynthesis

PubMed Central

Conklin, Patricia L.; Norris, Susan R.; Wheeler, Glen L.; Williams, Elizabeth H.; Smirnoff, Nicholas; Last, Robert L.

1999-01-01

Vitamin C (l-ascorbic acid; AsA) acts as a potent antioxidant and cellular reductant in plants and animals. AsA has long been known to have many critical physiological roles in plants, yet its biosynthesis is only currently being defined. A pathway for AsA biosynthesis that features GDP-mannose and l-galactose has recently been proposed for plants. We have isolated a collection of AsA-deficient mutants of Arabidopsis thaliana that are valuable tools for testing of an AsA biosynthetic pathway. The best-characterized of these mutants (vtc1) contains ≈25% of wild-type AsA and is defective in AsA biosynthesis. By using a combination of biochemical, molecular, and genetic techniques, we have demonstrated that the VTC1 locus encodes a GDP-mannose pyrophosphorylase (mannose-1-P guanyltransferase). This enzyme provides GDP-mannose, which is used for cell wall carbohydrate biosynthesis and protein glycosylation as well as for AsA biosynthesis. In addition to genetically defining the first locus involved in AsA biosynthesis, this work highlights the power of using traditional mutagenesis techniques coupled with the Arabidopsis Genome Initiative to rapidly clone physiologically important genes. PMID:10097187

Designing specific chloroplast markers for black walnut from a set of universal primers

Treesearch

Erin Victory; Rodney L. Robichaud; Keith Woeste

2003-01-01

Chloroplasts are a valuable source of genetic information because their sequence is highly conserved, they undergo little or no recombination, and they are uniparentally inherited. Chloroplast polymorphisms are powerful genetic tools for identifying matrilineal family groups, studying gene flow from seed versus pollen movement, reconstructing phylogeographic...

HISTORICAL ANALYSIS OF ECOLOGICAL EFFECTS: A USEFUL EDUCATIONAL TOOL

EPA Science Inventory

An historical analysis that presents the ecological consequences of development can be a valuable educational tool for citizens, students, and environmental managers. In highly impacted areas, the cumulative impacts of multiple stressors can result in complex environmental condit...

Islands within an island: Population genetic structure of the endemic Sardinian newt, Euproctus platycephalus.

PubMed

Ball, Sarah E; Bovero, Stefano; Sotgiu, Giuseppe; Tessa, Giulia; Angelini, Claudio; Bielby, Jon; Durrant, Christopher; Favelli, Marco; Gazzaniga, Enrico; Garner, Trenton W J

2017-02-01

The identification of historic and contemporary barriers to dispersal is central to the conservation of endangered amphibians, but may be hindered by their complex life history and elusive nature. The complementary information generated by mitochondrial (mtDNA) and microsatellite markers generates a valuable tool in elucidating population structure and the impact of habitat fragmentation. We applied this approach to the study of an endangered montane newt, Euproctus platycephalus . Endemic to the Mediterranean island of Sardinia, it is threatened by anthropogenic activity, disease, and climate change. We have demonstrated a clear hierarchy of structure across genetically divergent and spatially distinct subpopulations. Divergence between three main mountain regions dominated genetic partitioning with both markers. Mitochondrial phylogeography revealed a deep division dating to ca. 1 million years ago (Mya), isolating the northern region, and further differentiation between the central and southern regions ca. 0.5 Mya, suggesting an association with Pleistocene severe glacial oscillations. Our findings are consistent with a model of southward range expansion during glacial periods, with postglacial range retraction to montane habitat and subsequent genetic isolation. Microsatellite markers revealed further strong population structure, demonstrating significant divergence within the central region, and partial differentiation within the south. The northern population showed reduced genetic diversity. Discordance between mitochondrial and microsatellite markers at this scale indicated a further complexity of population structure, in keeping with male-biased dispersal and female philopatry. Our study underscores the need to elucidate cryptic population structure in the ecology and conservation strategies for endangered island-restricted amphibians, especially in the context of disease and climate change.

Genetic and Genomic Toolbox of Zea mays

PubMed Central

Nannas, Natalie J.; Dawe, R. Kelly

2015-01-01

Maize has a long history of genetic and genomic tool development and is considered one of the most accessible higher plant systems. With a fully sequenced genome, a suite of cytogenetic tools, methods for both forward and reverse genetics, and characterized phenotype markers, maize is amenable to studying questions beyond plant biology. Major discoveries in the areas of transposons, imprinting, and chromosome biology came from work in maize. Moving forward in the post-genomic era, this classic model system will continue to be at the forefront of basic biological study. In this review, we outline the basics of working with maize and describe its rich genetic toolbox. PMID:25740912

Complete In Vitro Life Cycle of Trypanosoma congolense: Development of Genetic Tools

PubMed Central

Plazolles, Nicolas; Baltz, Théo

2010-01-01

Background Animal African trypanosomosis, a disease mainly caused by the protozoan parasite Trypanosoma congolense, is a major constraint to livestock productivity and has a significant impact in the developing countries of Africa. RNA interference (RNAi) has been used to study gene function and identify drug and vaccine targets in a variety of organisms including trypanosomes. However, trypanosome RNAi studies have mainly been conducted in T. brucei, as a model for human infection, largely ignoring livestock parasites of economical importance such as T. congolense, which displays different pathogenesis profiles. The whole T. congolense life cycle can be completed in vitro, but this attractive model displayed important limitations: (i) genetic tools were currently limited to insect forms and production of modified infectious BSF through differentiation was never achieved, (ii) in vitro differentiation techniques lasted several months, (iii) absence of long-term bloodstream forms (BSF) in vitro culture prevented genomic analyses. Methodology/Principal Findings We optimized culture conditions for each developmental stage and secured the differentiation steps. Specifically, we devised a medium adapted for the strenuous development of stable long-term BSF culture. Using Amaxa nucleofection technology, we greatly improved the transfection rate of the insect form and designed an inducible transgene expression system using the IL3000 reference strain. We tested it by expression of reporter genes and through RNAi. Subsequently, we achieved the complete in vitro life cycle with dramatically shortened time requirements for various wild type and transgenic strains. Finally, we established the use of modified strains for experimental infections and underlined a host adaptation phase requirement. Conclusions/Significance We devised an improved T. congolense model, which offers the opportunity to perform functional genomics analyses throughout the whole life cycle. It represents

Multiwavelength digital holography for polishing tool shape measurement

NASA Astrophysics Data System (ADS)

Lédl, Vít.; Psota, Pavel; Václavík, Jan; Doleček, Roman; Vojtíšek, Petr

2013-09-01

Classical mechano-chemical polishing is still a valuable technique, which gives unbeatable results for some types of optical surfaces. For example, optics for high power lasers requires minimized subsurface damage, very high cosmetic quality, and low mid spatial frequency error. One can hardly achieve this with use of subaperture polishing. The shape of the polishing tool plays a crucial role in achieving the required form of the optical surface. Often the shape of the polishing tool or pad is not known precisely enough during the manufacturing process. The tool shape is usually premachined and later is changed during the polishing procedure. An experienced worker could estimate the shape of the tool indirectly from the shape of the polished element, and that is why he can achieve the required shape in few reasonably long iterative steps. Therefore the lack of the exact tool shape knowledge is tolerated. Sometimes, this indirect method is not feasible even if small parts are considered. Moreover, if processes on machines like planetary (continuous) polishers are considered, the incorrect shape of the polishing pad could extend the polishing times extremely. Every iteration step takes hours. Even worse, polished piece could be wasted if the pad has a poor shape. The ability of the tool shape determination would be very valuable in those types of lengthy processes. It was our primary motivation to develop a contactless measurement method for large diffusive surfaces and demonstrate its usability. The proposed method is based on application of multiwavelength digital holographic interferometry with phase shift.

Teachers Talking about Writing Assessment: Valuable Professional Learning?

ERIC Educational Resources Information Center

Reid, Lesley

2007-01-01

This article argues that the engagement of teachers in collaborative discussions about assessment can provide a fruitful context for valuable professional learning. It is of interest to those who provide Continuous Professional Development (CPD) opportunities for teachers and teachers themselves. It looks particularly at the value of writing…

Applying Quantitative Genetic Methods to Primate Social Behavior

PubMed Central

Brent, Lauren J. N.

2013-01-01

Increasingly, behavioral ecologists have applied quantitative genetic methods to investigate the evolution of behaviors in wild animal populations. The promise of quantitative genetics in unmanaged populations opens the door for simultaneous analysis of inheritance, phenotypic plasticity, and patterns of selection on behavioral phenotypes all within the same study. In this article, we describe how quantitative genetic techniques provide studies of the evolution of behavior with information that is unique and valuable. We outline technical obstacles for applying quantitative genetic techniques that are of particular relevance to studies of behavior in primates, especially those living in noncaptive populations, e.g., the need for pedigree information, non-Gaussian phenotypes, and demonstrate how many of these barriers are now surmountable. We illustrate this by applying recent quantitative genetic methods to spatial proximity data, a simple and widely collected primate social behavior, from adult rhesus macaques on Cayo Santiago. Our analysis shows that proximity measures are consistent across repeated measurements on individuals (repeatable) and that kin have similar mean measurements (heritable). Quantitative genetics may hold lessons of considerable importance for studies of primate behavior, even those without a specific genetic focus. PMID:24659839

FitSKIRT: genetic algorithms to automatically fit dusty galaxies with a Monte Carlo radiative transfer code

NASA Astrophysics Data System (ADS)

De Geyter, G.; Baes, M.; Fritz, J.; Camps, P.

2013-02-01

We present FitSKIRT, a method to efficiently fit radiative transfer models to UV/optical images of dusty galaxies. These images have the advantage that they have better spatial resolution compared to FIR/submm data. FitSKIRT uses the GAlib genetic algorithm library to optimize the output of the SKIRT Monte Carlo radiative transfer code. Genetic algorithms prove to be a valuable tool in handling the multi- dimensional search space as well as the noise induced by the random nature of the Monte Carlo radiative transfer code. FitSKIRT is tested on artificial images of a simulated edge-on spiral galaxy, where we gradually increase the number of fitted parameters. We find that we can recover all model parameters, even if all 11 model parameters are left unconstrained. Finally, we apply the FitSKIRT code to a V-band image of the edge-on spiral galaxy NGC 4013. This galaxy has been modeled previously by other authors using different combinations of radiative transfer codes and optimization methods. Given the different models and techniques and the complexity and degeneracies in the parameter space, we find reasonable agreement between the different models. We conclude that the FitSKIRT method allows comparison between different models and geometries in a quantitative manner and minimizes the need of human intervention and biasing. The high level of automation makes it an ideal tool to use on larger sets of observed data.

Defining a genetic ideotype for crop improvement.

PubMed

Trethowan, Richard M

2014-01-01

While plant breeders traditionally base selection on phenotype, the development of genetic ideotypes can help focus the selection process. This chapter provides a road map for the establishment of a refined genetic ideotype. The first step is an accurate definition of the target environment including the underlying constraints, their probability of occurrence, and impact on phenotype. Once the environmental constraints are established, the wealth of information on plant physiological responses to stresses, known gene information, and knowledge of genotype ×environment and gene × environment interaction help refine the target ideotype and form a basis for cross prediction.Once a genetic ideotype is defined the challenge remains to build the ideotype in a plant breeding program. A number of strategies including marker-assisted recurrent selection and genomic selection can be used that also provide valuable information for the optimization of genetic ideotype. However, the informatics required to underpin the realization of the genetic ideotype then becomes crucial. The reduced cost of genotyping and the need to combine pedigree, phenotypic, and genetic data in a structured way for analysis and interpretation often become the rate-limiting steps, thus reducing genetic gain. Systems for managing these data and an example of ideotype construction for a defined environment type are discussed.

Human DDX3 protein is a valuable target to develop broad spectrum antiviral agents

PubMed Central

Brai, Annalaura; Fazi, Roberta; Tintori, Cristina; Zamperini, Claudio; Bugli, Francesca; Sanguinetti, Maurizio; Stigliano, Egidio; Esté, José; Badia, Roger; Franco, Sandra; Martinez, Javier P.; Meyerhans, Andreas; Saladini, Francesco; Zazzi, Maurizio; Garbelli, Anna; Botta, Maurizio

2016-01-01

Targeting a host factor essential for the replication of different viruses but not for the cells offers a higher genetic barrier to the development of resistance, may simplify therapy regimens for coinfections, and facilitates management of emerging viral diseases. DEAD-box polypeptide 3 (DDX3) is a human host factor required for the replication of several DNA and RNA viruses, including some of the most challenging human pathogens currently circulating, such as HIV-1, Hepatitis C virus, Dengue virus, and West Nile virus. Herein, we showed for the first time, to our knowledge, that the inhibition of DDX3 by a small molecule could be successfully exploited for the development of a broad spectrum antiviral agent. In addition to the multiple antiviral activities, hit compound 16d retained full activity against drug-resistant HIV-1 strains in the absence of cellular toxicity. Pharmacokinetics and toxicity studies in rats confirmed a good safety profile and bioavailability of 16d. Thus, DDX3 is here validated as a valuable therapeutic target. PMID:27118832

Movement behavior explains genetic differentiation in American black bears

Treesearch

Samuel A Cushman; Jesse S. Lewis

2010-01-01

Individual-based landscape genetic analyses provide empirically based models of gene flow. It would be valuable to verify the predictions of these models using independent data of a different type. Analyses using different data sources that produce consistent results provide strong support for the generality of the findings. Mating and dispersal movements are the...

Biodiversity Conservation and Conservation Biotechnology Tools

USDA-ARS?s Scientific Manuscript database

This special issue is dedicated to the in vitro tools and methods used to conserve the genetic diversity of rare and threatened species from around the world. Species that are on the brink of extinction, due to the rapid loss of genetic diversity and habitat, come mainly from resource poor areas the...

Genomic Tools in Groundnut Breeding Program: Status and Perspectives

PubMed Central

Janila, P.; Variath, Murali T.; Pandey, Manish K.; Desmae, Haile; Motagi, Babu N.; Okori, Patrick; Manohar, Surendra S.; Rathnakumar, A. L.; Radhakrishnan, T.; Liao, Boshou; Varshney, Rajeev K.

2016-01-01

Groundnut, a nutrient-rich food legume, is cultivated world over. It is valued for its good quality cooking oil, energy and protein rich food, and nutrient-rich fodder. Globally, groundnut improvement programs have developed varieties to meet the preferences of farmers, traders, processors, and consumers. Enhanced yield, tolerance to biotic and abiotic stresses and quality parameters have been the target traits. Spurt in genetic information of groundnut was facilitated by development of molecular markers, genetic, and physical maps, generation of expressed sequence tags (EST), discovery of genes, and identification of quantitative trait loci (QTL) for some important biotic and abiotic stresses and quality traits. The first groundnut variety developed using marker assisted breeding (MAB) was registered in 2003. Since then, USA, China, Japan, and India have begun to use genomic tools in routine groundnut improvement programs. Introgression lines that combine foliar fungal disease resistance and early maturity were developed using MAB. Establishment of marker-trait associations (MTA) paved way to integrate genomic tools in groundnut breeding for accelerated genetic gain. Genomic Selection (GS) tools are employed to improve drought tolerance and pod yield, governed by several minor effect QTLs. Draft genome sequence and low cost genotyping tools such as genotyping by sequencing (GBS) are expected to accelerate use of genomic tools to enhance genetic gains for target traits in groundnut. PMID:27014312

New Therapies Offer Valuable Options for Patients with Melanoma

Cancer.gov

Two phase III clinical trials of new therapies for patients with metastatic melanoma presented in June at the 2011 ASCO conference confirmed that vemurafenib and ipilimumab (Yervoy™) offer valuable new options for the disease.

The database management system: A topic and a tool

NASA Technical Reports Server (NTRS)

Plummer, O. R.

1984-01-01

Data structures and data base management systems are common tools employed to deal with the administrative information of a university. An understanding of these topics is needed by a much wider audience, ranging from those interested in computer aided design and manufacturing to those using microcomputers. These tools are becoming increasingly valuable to academic programs as they develop comprehensive computer support systems. The wide use of these tools relies upon the relational data model as a foundation. Experience with the use of the IPAD RIM5.0 program is described.

visPIG--a web tool for producing multi-region, multi-track, multi-scale plots of genetic data.

PubMed

Scales, Matthew; Jäger, Roland; Migliorini, Gabriele; Houlston, Richard S; Henrion, Marc Y R

2014-01-01

We present VISual Plotting Interface for Genetics (visPIG; http://vispig.icr.ac.uk), a web application to produce multi-track, multi-scale, multi-region plots of genetic data. visPIG has been designed to allow users not well versed with mathematical software packages and/or programming languages such as R, Matlab®, Python, etc., to integrate data from multiple sources for interpretation and to easily create publication-ready figures. While web tools such as the UCSC Genome Browser or the WashU Epigenome Browser allow custom data uploads, such tools are primarily designed for data exploration. This is also true for the desktop-run Integrative Genomics Viewer (IGV). Other locally run data visualisation software such as Circos require significant computer skills of the user. The visPIG web application is a menu-based interface that allows users to upload custom data tracks and set track-specific parameters. Figures can be downloaded as PDF or PNG files. For sensitive data, the underlying R code can also be downloaded and run locally. visPIG is multi-track: it can display many different data types (e.g association, functional annotation, intensity, interaction, heat map data,…). It also allows annotation of genes and other custom features in the plotted region(s). Data tracks can be plotted individually or on a single figure. visPIG is multi-region: it supports plotting multiple regions, be they kilo- or megabases apart or even on different chromosomes. Finally, visPIG is multi-scale: a sub-region of particular interest can be 'zoomed' in. We describe the various features of visPIG and illustrate its utility with examples. visPIG is freely available through http://vispig.icr.ac.uk under a GNU General Public License (GPLv3).

Feasibility of an Assessment Tool for Children's Competence to Consent to Predictive Genetic Testing: a Pilot Study.

PubMed

Hein, Irma M; Troost, Pieter W; Lindeboom, Robert; Christiaans, Imke; Grisso, Thomas; van Goudoever, Johannes B; Lindauer, Ramón J L

2015-12-01

Knowledge on children's capacities to consent to medical treatment is limited. Also, age limits for asking children's consent vary considerably between countries. Decision-making on predictive genetic testing (PGT) is especially complicated, considering the ongoing ethical debate. In order to examine just age limits for alleged competence to consent in children, we evaluated feasibility of a standardized assessment tool, and investigated cutoff ages for children's competence to consent to PGT. We performed a pilot study, including 17 pediatric outpatients between 6 and 18 years at risk for an autosomal dominantly inherited cardiac disease, eligible for predictive genetic testing. The reference standard for competence was established by experts trained in the relevant criteria for competent decision-making. The MacArthur Competence Assessment Tool for Treatment (MacCAT-T) served as index test. Data analysis included raw agreement between competence classifications, difference in mean ages between children judged competent and judged incompetent, and estimation of cutoff ages for judgments of competence. Twelve (71 %) children were considered competent by the reference standard, and 16 (94 %) by the MacCAT-T, with an overall agreement of 76 %. The expert judgments disagreed in most cases, while the MacCAT-T judgments agreed in 65 %. Mean age of children judged incompetent was 9.3 years and of children judged competent 12.1 years (p = .035). With 90 % sensitivity, children younger than 10.0 years were judged incompetent, with 90 % specificity children older than 11.8 years were judged competent. Feasibility of the MacCAT-T in children is confirmed. Initial findings on age cutoffs are indicative for children between the age of 12 and 18 to be judged competent for involvement in the informed consent process. Future research on appropriate age-limits for children's alleged competence to consent is needed.

The Mouse House: A brief history of the ORNL mouse-genetics program, 1947–2009

DOE Office of Scientific and Technical Information (OSTI.GOV)

Russell, Liane B.

The large mouse genetics program at the Oak Ridge National Lab is often re-membered chiefly for the germ-cell mutation-rate data it generated and their uses in estimating the risk of heritable radiation damage. In fact, it soon became a multi-faceted research effort that, over a period of almost 60 years, generated a wealth of information in the areas of mammalian mutagenesis, basic genetics (later enriched by molecular techniques), cytogenetics, reproductive biology, biochemistry of germ cells, and teratology. Research in the area of germ-cell mutagenesis explored the important physical and biological factors that affect the frequency and nature of induced mutationsmore » and made several unexpected discoveries, such as the major importance of the perigametic interval (the zygote stage) for the origin of spontaneous mutations and for the sensitivity to induced genetic change. Of practical value was the discovery that ethylnitrosourea was a supermutagen for point mutations, making high-efficiency mutagenesis in the mouse feasible worldwide. Teratogenesis findings resulted in recommendations still generally accepted in radiological practice. Studies supporting the mutagenesis research added whole bodies of information about mammalian germ-cell development and about molecular targets in germ cells. The early decision to not merely count but propagate genetic variants of all sorts made possible further discoveries, such as the Y-Chromosome s importance in mammalian sex determination and the identification of rare X-autosome translocations, which, in turn, led to the formulation of the single-active-X hypothesis and provided tools for studies of functional mosaicism for autosomal genes, male sterility, and chromosome-pairing mechanism. Extensive genetic and then molecular analyses of large numbers of induced specific-locus mutants resulted in fine-structure physical and correlated functional mapping of significant portions of the mouse genome and constituted a

New trends in bioanalytical tools for the detection of genetically modified organisms: an update.

PubMed

Michelini, Elisa; Simoni, Patrizia; Cevenini, Luca; Mezzanotte, Laura; Roda, Aldo

2008-10-01

Despite the controversies surrounding genetically modified organisms (GMOs), the production of GM crops is increasing, especially in developing countries. Thanks to new technologies involving genetic engineering and unprecedented access to genomic resources, the next decade will certainly see exponential growth in GMO production. Indeed, EU regulations based on the precautionary principle require any food containing more than 0.9% GM content to be labeled as such. The implementation of these regulations necessitates sampling protocols, the availability of certified reference materials and analytical methodologies that allow the accurate determination of the content of GMOs. In order to qualify for the validation process, a method should fulfil some criteria, defined as "acceptance criteria" by the European Network of GMO Laboratories (ENGL). Several methods have recently been developed for GMO detection and quantitation, mostly based on polymerase chain reaction (PCR) technology. PCR (including its different formats, e.g., double competitive PCR and real-time PCR) remains the technique of choice, thanks to its ability to detect even small amounts of transgenes in raw materials and processed foods. Other approaches relying on DNA detection are based on quartz crystal microbalance piezoelectric biosensors, dry reagent dipstick-type sensors and surface plasmon resonance sensors. The application of visible/near-infrared (vis/NIR) spectroscopy or mass spectrometry combined with chemometrics techniques has also been envisaged as a powerful GMO detection tool. Furthermore, in order to cope with the multiplicity of GMOs released onto the market, the new challenge is the development of routine detection systems for the simultaneous detection of numerous GMOs, including unknown GMOs.

Sign Language Legislation as a Tool for Sustainability

ERIC Educational Resources Information Center

Pabsch, Annika

2017-01-01

This article explores three models of sustainability (environmental, economic, and social) and identifies characteristics of a sustainable community necessary to sustain the Deaf community as a whole. It is argued that sign language legislation is a valuable tool for achieving sustainability for the generations to come.

Distribution and population genetics of walleye and sauger

USGS Publications Warehouse

Haponski, Amanda E.; Sloss, Brian L.

2014-01-01

Conserving genetic diversity and local adaptations are management priorities for wild populations of exploited species, which increasingly are subject to climate change, habitat loss, and pollution. These constitute growing concerns for the walleye Sander vitreus, an ecologically and economically valuable North American temperate fish with large Laurentian Great Lakes' fisheries. This study compares genetic diversity and divergence patterns across its widespread native range using mitochondrial (mt) DNA control region sequences and nine nuclear DNA microsatellite (μsat) loci, examining historic and contemporary influences. We analyze the genetic and morphological characters of a putative endemic variant– “blue pike” S. v. “glaucus” –described from Lakes Erie and Ontario, which became extinct. Walleye with turquoise-colored mucus also are evaluated, since some have questioned whether these are related to the “blue pike”.

Genetic diversity analysis of Leuconostoc mesenteroides from Korean vegetables and food products by multilocus sequence typing.

PubMed

Sharma, Anshul; Kaur, Jasmine; Lee, Sulhee; Park, Young-Seo

2018-06-01

In the present study, 35 Leuconostoc mesenteroides strains isolated from vegetables and food products from South Korea were studied by multilocus sequence typing (MLST) of seven housekeeping genes (atpA, groEL, gyrB, pheS, pyrG, rpoA, and uvrC). The fragment sizes of the seven amplified housekeeping genes ranged in length from 366 to 1414 bp. Sequence analysis indicated 27 different sequence types (STs) with 25 of them being represented by a single strain indicating high genetic diversity, whereas the remaining 2 were characterized by five strains each. In total, 220 polymorphic nucleotide sites were detected among seven housekeeping genes. The phylogenetic analysis based on the STs of the seven loci indicated that the 35 strains belonged to two major groups, A (28 strains) and B (7 strains). Split decomposition analysis showed that intraspecies recombination played a role in generating diversity among strains. The minimum spanning tree showed that the evolution of the STs was not correlated with food source. This study signifies that the multilocus sequence typing is a valuable tool to access the genetic diversity among L. mesenteroides strains from South Korea and can be used further to monitor the evolutionary changes.

Learning Genetics with Paper Pets

ERIC Educational Resources Information Center

Finnerty, Valerie Raunig

2006-01-01

By the end of the eighth grade, students are expected to have a basic understanding of the mechanism of basic genetic inheritance. However, these concepts can be difficult to teach. In this article, the author introduces a new learning tool that will help facilitate student learning and enthusiasm to the basic concepts of genetic inheritance. This…

[Research progress on molecular genetics of forest musk deer].

PubMed

Jie, Hang; Zheng, Cheng-li; Wang, Jian-ming; Feng, Xiao-lan; Zeng, De-jun; Zhao, Gui-jun

2015-11-01

Forest musk deer is one of the large-scale farming musk deer animals with the largest population at the same time. The male musk deer can secrete valuable medicines, which has high medicinal and economic value. Due to the loss of habitat and indiscriminate hunting, the numbers of wild population specie and the distribution have been drastically reduced. Therefore, in-depth understanding of the molecular genetics progress of forest musk deer will pave a way for musk deer protection and breeding. In this review, the progress associated with the molecular marker, genetic classification, artificial breeding, musk secretion and disease in past decades were reviewed, in order to provide a theoretical basis for subsequent molecular genetic researches in forest musk deer.

Genetic diversity of an Azorean endemic and endangered plant species inferred from inter-simple sequence repeat markers.

PubMed

Lopes, Maria S; Mendonça, Duarte; Bettencourt, Sílvia X; Borba, Ana R; Melo, Catarina; Baptista, Cláudio; da Câmara Machado, Artur

2014-06-26

Knowledge of the levels and distribution of genetic diversity is important for designing conservation strategies for threatened and endangered species so as to guarantee sustainable survival of populations and to preserve their evolutionary potential. Picconia azorica is a valuable Azorean endemic species recently classified as endangered. To contribute with information useful for the establishment of conservation programmes, the genetic variability and differentiation among 230 samples from 11 populations collected in three Azorean islands was accessed with eight inter-simple sequence repeat markers. A total of 64 polymorphic loci were detected. The majority of genetic variability was found within populations and no genetic structure was detected between populations and between islands. Also the coefficient of genetic differentiation and the level of gene flow indicate that geographical distances do not act as barriers for gene flow. In order to ensure the survival of populations in situ and ex situ management practices should be considered, including artificial propagation through the use of plant tissue culture techniques, not only for the restoration of habitat but also for the sustainable use of its valuable wood. Published by Oxford University Press on behalf of the Annals of Botany Company.

Gene therapy in dentistry: tool of genetic engineering. Revisited.

PubMed

Gupta, Khushboo; Singh, Saurabh; Garg, Kavita Nitish

2015-03-01

Advances in biotechnology have brought gene therapy to the forefront of medical research. The concept of transferring genes to tissues for clinical applications has been discussed nearly half a century, but the ability to manipulate genetic material via recombinant DNA technology has brought this goal to reality. The feasibility of gene transfer was first demonstrated using tumour viruses. This led to development of viral and nonviral methods for the genetic modification of somatic cells. Applications of gene therapy to dental and oral problems illustrate the potential impact of this technology on dentistry. Preclinical trial results regarding the same have been very promising. In this review we will discuss methods, vectors involved, clinical implication in dentistry and scientific issues associated with gene therapy. Copyright © 2014 Elsevier Ltd. All rights reserved.

Looking forward to genetically edited fruit crops.

PubMed

Nagamangala Kanchiswamy, Chidananda; Sargent, Daniel James; Velasco, Riccardo; Maffei, Massimo E; Malnoy, Mickael

2015-02-01

The availability of genome sequences for many fruit crops has redefined the boundaries of genetic engineering and genetically modified (GM) crop plants. However commercialization of GM crops is hindered by numerous regulatory and social hurdles. Here, we focus on recently developed genome-editing tools for fruit crop improvement and their importance from the consumer perspective. Challenges and opportunities for the deployment of new genome-editing tools for fruit plants are also discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

What makes a sustainability tool valuable, practical and useful in real-world healthcare practice? A mixed-methods study on the development of the Long Term Success Tool in Northwest London

PubMed Central

Lennox, Laura; Doyle, Cathal; Reed, Julie E

2017-01-01

Objectives Although improvement initiatives show benefits to patient care, they often fail to sustain. Models and frameworks exist to address this challenge, but issues with design, clarity and usability have been barriers to use in healthcare settings. This work aimed to collaborate with stakeholders to develop a sustainability tool relevant to people in healthcare settings and practical for use in improvement initiatives. Design Tool development was conducted in six stages. A scoping literature review, group discussions and a stakeholder engagement event explored literature findings and their resonance with stakeholders in healthcare settings. Interviews, small-scale trialling and piloting explored the design and tested the practicality of the tool in improvement initiatives. Setting National Institute for Health Research Collaboration for Leadership in Applied Health Research and Care for Northwest London (CLAHRC NWL). Participants CLAHRC NWL improvement initiative teams and staff. Results The iterative design process and engagement of stakeholders informed the articulation of the sustainability factors identified from the literature and guided tool design for practical application. Key iterations of factors and tool design are discussed. From the development process, the Long Term Success Tool (LTST) has been designed. The Tool supports those implementing improvements to reflect on 12 sustainability factors to identify risks to increase chances of achieving sustainability over time. The Tool is designed to provide a platform for improvement teams to share their own views on sustainability as well as learn about the different views held within their team to prompt discussion and actions. Conclusion The development of the LTST has reinforced the importance of working with stakeholders to design strategies which respond to their needs and preferences and can practically be implemented in real-world settings. Further research is required to study the use and

Sinbase: an integrated database to study genomics, genetics and comparative genomics in Sesamum indicum.

PubMed

Wang, Linhai; Yu, Jingyin; Li, Donghua; Zhang, Xiurong

2015-01-01

Sesame (Sesamum indicum L.) is an ancient and important oilseed crop grown widely in tropical and subtropical areas. It belongs to the gigantic order Lamiales, which includes many well-known or economically important species, such as olive (Olea europaea), leonurus (Leonurus japonicus) and lavender (Lavandula spica), many of which have important pharmacological properties. Despite their importance, genetic and genomic analyses on these species have been insufficient due to a lack of reference genome information. The now available S. indicum genome will provide an unprecedented opportunity for studying both S. indicum genetic traits and comparative genomics. To deliver S. indicum genomic information to the worldwide research community, we designed Sinbase, a web-based database with comprehensive sesame genomic, genetic and comparative genomic information. Sinbase includes sequences of assembled sesame pseudomolecular chromosomes, protein-coding genes (27,148), transposable elements (372,167) and non-coding RNAs (1,748). In particular, Sinbase provides unique and valuable information on colinear regions with various plant genomes, including Arabidopsis thaliana, Glycine max, Vitis vinifera and Solanum lycopersicum. Sinbase also provides a useful search function and data mining tools, including a keyword search and local BLAST service. Sinbase will be updated regularly with new features, improvements to genome annotation and new genomic sequences, and is freely accessible at http://ocri-genomics.org/Sinbase/. © 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.

Building a Genetic Manipulation Tool Box for Orchid Biology: Identification of Constitutive Promoters and Application of CRISPR/Cas9 in the Orchid, Dendrobium officinale

PubMed Central

Kui, Ling; Chen, Haitao; Zhang, Weixiong; He, Simei; Xiong, Zijun; Zhang, Yesheng; Yan, Liang; Zhong, Chaofang; He, Fengmei; Chen, Junwen; Zeng, Peng; Zhang, Guanghui; Yang, Shengchao; Dong, Yang; Wang, Wen; Cai, Jing

2017-01-01

Orchidaceae is the second largest family of flowering plants, which is highly valued for its ornamental purposes and medicinal uses. Dendrobium officinale is a special orchid species that can grow without seed vernalization. Because the whole-genome sequence of D. officinale is publicly available, this species is poised to become a convenient research model for the evolutionary, developmental, and genetic studies of Orchidaceae. Despite these advantages, the methods of genetic manipulation are poorly developed in D. officinale. In this study, based on the previously developed Agrobacterium-mediated gene transformation system, we identified several highly efficient promoters for exogenous gene expression and successfully applied the CRISPR/Cas9 system for editing endogenous genes in the genome of D. officinale. These two basic techniques contribute to the genetic manipulation toolbox of Orchidaceae. The pCambia-1301-35SN vector containing the CaMV 35S promoter and the β-glucuronidase (GUS) and Superfolder green fluorescence protein (SG) as reporter genes were introduced into the plant tissues by the Agrobacterium-mediated transformation system. Fluorescence emission from the transformed plants confirmed the successful transcription and translation of SG genes into functional proteins. We compared the GUS activity under different promoters including four commonly used promoters (MtHP, CVMV, MMV and PCISV) with CaMV 35S promoter and found that MMV, CVMV, and PCISV were as effective as the 35S promoter. Furthermore, we applied the CRISPR/Cas9-mediated genome editing system successfully in D. officinale. By selecting five target genes (C3H, C4H, 4CL, CCR, and IRX) in the lignocellulose biosynthesis pathway, we showed that, for a given target, this system can generate edits (insertions, deletions, or substitutions) at a rate of 10 to 100%. These results showed that our two genetic manipulation tools can efficiently express exogenous genes and edit endogenous genes in D

Building a Genetic Manipulation Tool Box for Orchid Biology: Identification of Constitutive Promoters and Application of CRISPR/Cas9 in the Orchid, Dendrobium officinale.

PubMed

Kui, Ling; Chen, Haitao; Zhang, Weixiong; He, Simei; Xiong, Zijun; Zhang, Yesheng; Yan, Liang; Zhong, Chaofang; He, Fengmei; Chen, Junwen; Zeng, Peng; Zhang, Guanghui; Yang, Shengchao; Dong, Yang; Wang, Wen; Cai, Jing

2016-01-01

Orchidaceae is the second largest family of flowering plants, which is highly valued for its ornamental purposes and medicinal uses. Dendrobium officinale is a special orchid species that can grow without seed vernalization. Because the whole-genome sequence of D. officinale is publicly available, this species is poised to become a convenient research model for the evolutionary, developmental, and genetic studies of Orchidaceae. Despite these advantages, the methods of genetic manipulation are poorly developed in D. officinale . In this study, based on the previously developed Agrobacterium -mediated gene transformation system, we identified several highly efficient promoters for exogenous gene expression and successfully applied the CRISPR/Cas9 system for editing endogenous genes in the genome of D. officinale . These two basic techniques contribute to the genetic manipulation toolbox of Orchidaceae. The pCambia-1301-35SN vector containing the CaMV 35S promoter and the β-glucuronidase ( GUS ) and Superfolder green fluorescence protein (SG) as reporter genes were introduced into the plant tissues by the Agrobacterium -mediated transformation system. Fluorescence emission from the transformed plants confirmed the successful transcription and translation of SG genes into functional proteins. We compared the GUS activity under different promoters including four commonly used promoters (MtHP, CVMV, MMV and PCISV) with CaMV 35S promoter and found that MMV, CVMV, and PCISV were as effective as the 35S promoter. Furthermore, we applied the CRISPR/Cas9-mediated genome editing system successfully in D. officinale . By selecting five target genes ( C3H, C4H, 4CL, CCR, and IRX ) in the lignocellulose biosynthesis pathway, we showed that, for a given target, this system can generate edits (insertions, deletions, or substitutions) at a rate of 10 to 100%. These results showed that our two genetic manipulation tools can efficiently express exogenous genes and edit endogenous

Common genetic risk factors for coronary artery disease: new opportunities for prevention?

PubMed

Hamrefors, Viktor

2017-05-01

Atherosclerotic cardiovascular disease (CVD) is a leading cause of mortality and morbidity worldwide, with coronary artery disease (CAD) being the single leading cause of death. Better control of risk factors, enhanced diagnostic techniques and improved medical therapies have all substantially decreased the mortality of CAD in developed countries. However, CAD and other forms of atherosclerotic CVD are projected to remain the leading cause of death by 2030 and we face a number of challenges if the outcomes of CAD are to be further improved. The fact that a substantial fraction of high-risk subjects do not reach treatment goals for important risk factors is one of these challenges. At the same time, there is also a non-negotiable fraction of 'concealed' high-risk subjects who are not detected by current risk algorithms and diagnostic modalities. In recent years, we have started to rapidly increase our knowledge of the framework of common genetics underlying CAD and atherosclerotic CVD in the population. In conjunction with modern diagnostic and therapeutic options, this new genetic knowledge may provide a valuable tool for further improvements in prevention. This review summarizes the recent findings from the search for common genetic risk factors for CAD. Furthermore, the author discusses how such recent findings could potentially be used in a number of clinical applications within CAD prevention, including in clinical risk stratification, in prediction of drug treatment response and in the search for targets for novel preventive therapies. © 2015 Scandinavian Society of Clinical Physiology and Nuclear Medicine. Published by John Wiley & Sons Ltd.

Integration of epidemiology into the genetic analysis of mastitis in Swedish Holstein.

PubMed

Windig, Jack J; Urioste, Jorge I; Strandberg, Erling

2013-04-01

Heritability of mastitis (and diseases in general) tends to be low. One possible cause is that no clear distinction can be made between resistant and nonresistant animals, because healthy animals include animals that have not been exposed to pathogens and resistant animals. To account for this, we quantified the prevalence of clinical mastitis (CM) and subclinical mastitis (SCM) in 2,069 Swedish Holstein herds as a measure of exposure. Herd prevalence averaged 26.5% for SCM and 6.4% for CM; 61% of the first lactations of 177,309 cows were classified as having at least one case of SCM and 10% as having CM. In a reaction norm approach, heritability of (S)CM was quantified as a function of herd prevalence of (S)CM. The best-fitting model was a second-order polynomial of first-lactation cow SCM as a function of herd prevalence SCM, and a first-order (linear) polynomial of first-lactation cow CM as a function of CM herd prevalence. Heritability for SCM ranged from 0.069 to 0.105 and for CM from 0.016 to 0.032. For both, we found no clear effect of herd prevalence on their heritability. Genetic correlations within traits across herd prevalences were all greater than 0.92. Whether relationships among prevalence, exposure, disease, and genetics were as expected is a matter of discussion, but reaction norm analyses may be a valuable tool for epidemiological genetics. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Genetic service delivery: infrastructure, assessment and information.

PubMed

Kaye, C I

2012-01-01

Identification of genomic determinants of complex disorders such as cancer, diabetes and cardiovascular disease has prompted public health systems to focus on genetic service delivery for prevention of these disorders, adding to their previous efforts in birth defects prevention and newborn screening. This focus is consistent with previously identified obligations of the public health system as well as the core functions of public health identified by the Institute of Medicine. Models of service delivery include provision of services by the primary care provider in conjunction with subspecialists, provision of services through the medical home with co-management by genetics providers, provision of services in conjunction with disorder-specific treatment centers, and provision of services through a network of genetics clinics linked to medical homes. Whatever the model for provision of genetic services, tools to assist providers include facilities for outreach and telemedicine, information technology, just-in-time management plans, and emergency management tools. Assessment tools to determine which care is best are critical for quality improvement and development of best practices. Because the workforce of genetics providers is not keeping pace with the need for services, an understanding of the factors contributing to this lag is important, as is the development of an improved knowledge base in genomics for primary care providers. Copyright © 2012 S. Karger AG, Basel.

Potential genetic polymorphisms predicting polycystic ovary syndrome.

PubMed

Chen, Yao; Fang, Shu-Ying

2018-05-01

Polycystic ovary syndrome (PCOS) is a heterogenous endocrine disorder with typical symptoms of oligomenorrhoea, hyperandrogenism, hirsutism, obesity, insulin resistance and increased risk of type 2 diabetes mellitus. Extensive evidence indicates that PCOS is a genetic disease and numerous biochemical pathways have been linked with its pathogenesis. A number of genes from these pathways have been investigated, which include those involved with steroid hormone biosynthesis and metabolism, action of gonadotropin and gonadal hormones, folliculogenesis, obesity and energy regulation, insulin secretion and action and many others. In this review, we summarize the historical and recent findings in genetic polymorphisms of PCOS from the relevant publications and outline some genetic polymorphisms that are potentially associated with the risk of PCOS. This information could uncover candidate genes associating with PCOS, which will be valuable for the development of novel diagnostic and treatment platforms for PCOS patients. © 2018 The authors.

Can genetics help psychometrics? Improving dimensionality assessment through genetic factor modeling.

PubMed

Franić, Sanja; Dolan, Conor V; Borsboom, Denny; Hudziak, James J; van Beijsterveldt, Catherina E M; Boomsma, Dorret I

2013-09-01

In the present article, we discuss the role that quantitative genetic methodology may play in assessing and understanding the dimensionality of psychological (psychometric) instruments. Specifically, we study the relationship between the observed covariance structures, on the one hand, and the underlying genetic and environmental influences giving rise to such structures, on the other. We note that this relationship may be such that it hampers obtaining a clear estimate of dimensionality using standard tools for dimensionality assessment alone. One situation in which dimensionality assessment may be impeded is that in which genetic and environmental influences, of which the observed covariance structure is a function, differ from each other in structure and dimensionality. We demonstrate that in such situations settling dimensionality issues may be problematic, and propose using quantitative genetic modeling to uncover the (possibly different) dimensionalities of the underlying genetic and environmental structures. We illustrate using simulations and an empirical example on childhood internalizing problems.

Hordeum chilense genome, a useful tool to investigate the endosperm yellow pigment content in the Triticeae

PubMed Central

2012-01-01

Background The wild barley Hordeum chilense fulfills some requirements for being a useful tool to investigate the endosperm yellow pigment content (YPC) in the Triticeae including its diploid constitution, the availability of genetic resources (addition and deletion stocks and a high density genetic map) and, especially, its high seed YPC not silenced in tritordeums (amphiploids derived from H. chilense and wheat). Thus, the aim of this work was to test the utility of the H. chilense genome for investigating the YPC in the Triticeae. Results Twelve genes related to endosperm carotenoid content and/or YPC in grasses (Dxr, Hdr [synonym ispH], Ggpps1, Psy2, Psy3, Pds, Zds, e-Lcy, b-Lcy, Hyd3, Ccd1 and Ppo1) were identified, and mapped in H. chilense using rice genes to identify orthologs from barley, wheat, sorghum and maize. Macrocolinearity studies revealed that gene positions were in agreement in H. vulgare and H. chilense. Additionally, three main regions associated with YPC were identified in chromosomes 2Hch, 3Hch and 7Hch in H. chilense, the former being the most significant one. Conclusions The results obtained are consistent with previous findings in wheat and suggest that Ggpps1, Zds and Hyd3 on chromosome 2Hch may be considered candidate genes in wheat for further studies in YPC improvement. Considering the syntenic location of carotenoid genes in H. chilense, we have concluded that the Hch genome may constitute a valuable tool for YPC studies in the Triticeae. PMID:23122232

Advances in genetic modification of pluripotent stem cells.

PubMed

Fontes, Andrew; Lakshmipathy, Uma

2013-11-15

Genetically engineered stem cells aid in dissecting basic cell function and are valuable tools for drug discovery, in vivo cell tracking, and gene therapy. Gene transfer into pluripotent stem cells has been a challenge due to their intrinsic feature of growing in clusters and hence not amenable to common gene delivery methods. Several advances have been made in the rapid assembly of DNA elements, optimization of culture conditions, and DNA delivery methods. This has lead to the development of viral and non-viral methods for transient or stable modification of cells, albeit with varying efficiencies. Most methods require selection and clonal expansion that demand prolonged culture and are not suited for cells with limited proliferative potential. Choosing the right platform based on preferred length, strength, and context of transgene expression is a critical step. Random integration of the transgene into the genome can be complicated due to silencing or altered regulation of expression due to genomic effects. An alternative to this are site-specific methods that target transgenes followed by screening to identify the genomic loci that support long-term expression with stem cell proliferation and differentiation. A highly precise and accurate editing of the genome driven by homology can be achieved using traditional methods as well as the newer technologies such as zinc finger nuclease, TAL effector nucleases and CRISPR. In this review, we summarize the different genetic engineering methods that have been successfully used to create modified embryonic and induced pluripotent stem cells. © 2013. Published by Elsevier Inc. All rights reserved.

Perceived Utility of Pharmacy Licensure Examination Preparation Tools

PubMed Central

Peak, Amy Sutton; Sheehan, Amy Heck; Arnett, Stephanie

2006-01-01

Objectives To identify board examination preparation tools most commonly used by recent pharmacy graduates and determine which tools are perceived as most valuable and representative of the actual content of licensure examinations. Methods An electronic survey was sent to all 2004 graduates of colleges of pharmacy in Indiana. Participants identified which specific preparation tools were used and rated tools based on usefulness, representativeness of licensure examination, and monetary value, and provided overall recommendations to future graduates. Results The most commonly used preparation tools were the Pharmacy Law Review Session offered by Dr. Thomas Wilson at Purdue University, the Complete Review for Pharmacy, Pre-NAPLEX, PharmPrep, and the Kaplan NAPLEX Review. Tools receiving high ratings in all categories included Dr. Wilson's Pharmacy Law Review Session, Pre-NAPLEX, Comprehensive Pharmacy Review, Kaplan NAPLEX Review, and Review of Pharmacy. Conclusions Although no preparation tool was associated with a higher examination pass rate, certain tools were clearly rated higher than others by test takers. PMID:17149406

Adaptive genetic potential of coniferous forest tree species under climate change: implications for sustainable forest management

NASA Astrophysics Data System (ADS)

Mihai, Georgeta; Birsan, Marius-Victor; Teodosiu, Maria; Dumitrescu, Alexandru; Daia, Mihai; Mirancea, Ionel; Ivanov, Paula; Alin, Alexandru

2017-04-01

Mountain ecosystems are extremely vulnerable to climate change. The real potential for adaptation depends upon the existence of a wide genetic diversity in trees populations, upon the adaptive genetic variation, respectively. Genetic diversity offers the guarantee that forest species can survive, adapt and evolve under the influence of changing environmental conditions. The aim of this study is to evaluate the genetic diversity and adaptive genetic potential of two local species - Norway spruce and European silver fir - in the context of regional climate change. Based on data from a long-term provenance experiments network and climate variables spanning over more than 50 years, we have investigated the impact of climatic factors on growth performance and adaptation of tree species. Our results indicate that climatic and geographic factors significantly affect forest site productivity. Mean annual temperature and annual precipitation amount were found to be statistically significant explanatory variables. Combining the additive genetic model with the analysis of nuclear markers we obtained different images of the genetic structure of tree populations. As genetic indicators we used: gene frequencies, genetic diversity, genetic differentiation, genetic variance, plasticity. Spatial genetic analyses have allowed identifying the genetic centers holding high genetic diversity which will be valuable sources of gene able to buffer the negative effects of future climate change. Correlations between the marginal populations and in the optimal vegetation, between the level of genetic diversity and ecosystem stability, will allow the assessment of future risks arising from current genetic structure. Therefore, the strategies for sustainable forest management have to rely on the adaptive genetic variation and local adaptation of the valuable genetic resources. This work was realized within the framework of the project GENCLIM (Evaluating the adaptive potential of the main

The European Classical Swine Fever Virus Database: Blueprint for a Pathogen-Specific Sequence Database with Integrated Sequence Analysis Tools

PubMed Central

Postel, Alexander; Schmeiser, Stefanie; Zimmermann, Bernd; Becher, Paul

2016-01-01

Molecular epidemiology has become an indispensable tool in the diagnosis of diseases and in tracing the infection routes of pathogens. Due to advances in conventional sequencing and the development of high throughput technologies, the field of sequence determination is in the process of being revolutionized. Platforms for sharing sequence information and providing standardized tools for phylogenetic analyses are becoming increasingly important. The database (DB) of the European Union (EU) and World Organisation for Animal Health (OIE) Reference Laboratory for classical swine fever offers one of the world’s largest semi-public virus-specific sequence collections combined with a module for phylogenetic analysis. The classical swine fever (CSF) DB (CSF-DB) became a valuable tool for supporting diagnosis and epidemiological investigations of this highly contagious disease in pigs with high socio-economic impacts worldwide. The DB has been re-designed and now allows for the storage and analysis of traditionally used, well established genomic regions and of larger genomic regions including complete viral genomes. We present an application example for the analysis of highly similar viral sequences obtained in an endemic disease situation and introduce the new geographic “CSF Maps” tool. The concept of this standardized and easy-to-use DB with an integrated genetic typing module is suited to serve as a blueprint for similar platforms for other human or animal viruses. PMID:27827988

What makes a sustainability tool valuable, practical and useful in real-world healthcare practice? A mixed-methods study on the development of the Long Term Success Tool in Northwest London.

PubMed

Lennox, Laura; Doyle, Cathal; Reed, Julie E; Bell, Derek

2017-09-24

Although improvement initiatives show benefits to patient care, they often fail to sustain. Models and frameworks exist to address this challenge, but issues with design, clarity and usability have been barriers to use in healthcare settings. This work aimed to collaborate with stakeholders to develop a sustainability tool relevant to people in healthcare settings and practical for use in improvement initiatives. Tool development was conducted in six stages. A scoping literature review, group discussions and a stakeholder engagement event explored literature findings and their resonance with stakeholders in healthcare settings. Interviews, small-scale trialling and piloting explored the design and tested the practicality of the tool in improvement initiatives. National Institute for Health Research Collaboration for Leadership in Applied Health Research and Care for Northwest London (CLAHRC NWL). CLAHRC NWL improvement initiative teams and staff. The iterative design process and engagement of stakeholders informed the articulation of the sustainability factors identified from the literature and guided tool design for practical application. Key iterations of factors and tool design are discussed. From the development process, the Long Term Success Tool (LTST) has been designed. The Tool supports those implementing improvements to reflect on 12 sustainability factors to identify risks to increase chances of achieving sustainability over time. The Tool is designed to provide a platform for improvement teams to share their own views on sustainability as well as learn about the different views held within their team to prompt discussion and actions. The development of the LTST has reinforced the importance of working with stakeholders to design strategies which respond to their needs and preferences and can practically be implemented in real-world settings. Further research is required to study the use and effectiveness of the tool in practice and assess engagement with

Tools for Using Citizen Science in Environmental, Agricultural, and Natural Resources Extension Programs

ERIC Educational Resources Information Center

Stofer, Kathryn A.

2017-01-01

Citizen science is quickly becoming a valuable tool in the Extension professional's tool kit. This is the case whether you are a 4-H agent looking to involve youth in agriscience and agriculture-related science, technology, engineering, and math experiential learning activities or an agriculture and natural resources agent seeking to help…

Comparative genetics: synergizing human and NOD mouse studies for identifying genetic causation of type 1 diabetes.

PubMed

Driver, John P; Chen, Yi-Guang; Mathews, Clayton E

2012-01-01

Although once widely anticipated to unlock how human type 1 diabetes (T1D) develops, extensive study of the nonobese diabetic (NOD) mouse has failed to yield effective treatments for patients with the disease. This has led many to question the usefulness of this animal model. While criticism about the differences between NOD and human T1D is legitimate, in many cases disease in both species results from perturbations modulated by the same genes or different genes that function within the same biological pathways. Like in humans, unusual polymorphisms within an MHC class II molecule contributes the most T1D risk in NOD mice. This insight supports the validity of this model and suggests the NOD has been improperly utilized to study how to cure or prevent disease in patients. Indeed, clinical trials are far from administering T1D therapeutics to humans at the same concentration ranges and pathological states that inhibit disease in NOD mice. Until these obstacles are overcome it is premature to label the NOD mouse a poor surrogate to test agents that cure or prevent T1D. An additional criticism of the NOD mouse is the past difficulty in identifying genes underlying T1D using conventional mapping studies. However, most of the few diabetogenic alleles identified to date appear relevant to the human disorder. This suggests that rather than abandoning genetic studies in NOD mice, future efforts should focus on improving the efficiency with which diabetes susceptibility genes are detected. The current review highlights why the NOD mouse remains a relevant and valuable tool to understand the genes and their interactions that promote autoimmune diabetes and therapeutics that inhibit this disease. It also describes a new range of technologies that will likely transform how the NOD mouse is used to uncover the genetic causes of T1D for years to come.

Genetics of behavior in the silver fox.

PubMed

Kukekova, Anna V; Temnykh, Svetlana V; Johnson, Jennifer L; Trut, Lyudmila N; Acland, Gregory M

2012-02-01

The silver fox provides a rich resource for investigating the genetics of behavior, with strains developed by intensely selective breeding that display markedly different behavioral phenotypes. Until recently, however, the tools for conducting molecular genetic investigations in this species were very limited. In this review, the history of development of this resource and the tools to exploit it are described. Although the focus is on the genetics of domestication in the silver fox, there is a broader context. In particular, one expectation of the silver fox research is that it will be synergistic with studies in other species, including humans, to yield a more comprehensive understanding of the molecular mechanisms and evolution of a wider range of social cognitive behaviors.

Genetically attenuated Trypanosoma cruzi parasites as a potential vaccination tool

PubMed Central

Brandan, Cecilia Pérez; Basombrío, Miguel Ángel

2012-01-01

Chagas disease is the clinical manifestation of the infection produced by the parasite Trypanosoma cruzi. Currently there is no vaccine to prevent this disease and the protection attained with vaccines containing non-replicating parasites is limited. Genetically attenuated trypanosomatid parasites can be obtained by deletion of selected genes. Gene deletion takes advantage of the fact that this parasite can undergo homologous recombination between endogenous and foreign DNA sequences artificially introduced in the cells. This approach facilitated the discovery of several unknown gene functions, as well as allowing us to speculate about the potential for genetically attenuated live organisms as experimental immunogens. Vaccination with live attenuated parasites has been used effectively in mice to reduce parasitemia and histological damage, and in dogs, to prevent vector-delivered infection in the field. However, the use of live parasites as immunogens is controversial due to the risk of reversion to a virulent phenotype. Herein, we present our results from experiments on genetic manipulation of two T. cruzi strains to produce parasites with impaired replication and infectivity, and using the mutation of the dhfr-ts gene as a safety device against reversion to virulence. PMID:22705838

SieveSifter: a web-based tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials.

PubMed

Fiore-Gartland, Andrew; Kullman, Nicholas; deCamp, Allan C; Clenaghan, Graham; Yang, Wayne; Magaret, Craig A; Edlefsen, Paul T; Gilbert, Peter B

2017-08-01

Analysis of HIV-1 virions from participants infected in a randomized controlled preventive HIV-1 vaccine efficacy trial can help elucidate mechanisms of partial protection. By comparing the genetic sequence of viruses from vaccine and placebo recipients to the sequence of the vaccine itself, a technique called 'sieve analysis', one can identify functional specificities of vaccine-induced immune responses. We have created an interactive web-based visualization and data access tool for exploring the results of sieve analyses performed on four major preventive HIV-1 vaccine efficacy trials: (i) the HIV Vaccine Trial Network (HVTN) 502/Step trial, (ii) the RV144/Thai trial, (iii) the HVTN 503/Phambili trial and (iv) the HVTN 505 trial. The tool acts simultaneously as a platform for rapid reinterpretation of sieve effects and as a portal for organizing and sharing the viral sequence data. Access to these valuable datasets also enables the development of novel methodology for future sieve analyses. Visualization: http://sieve.fredhutch.org/viz . Source code: https://github.com/nkullman/SIEVE . Data API: http://sieve.fredhutch.org/data . agartlan@fredhutch.org. © The Author(s) 2017. Published by Oxford University Press.

Powerful tools for genetic modification: Advances in gene editing.

PubMed

Roesch, Erica A; Drumm, Mitchell L

2017-11-01

Recent discoveries and technical advances in genetic engineering, methods called gene or genome editing, provide hope for repairing genes that cause diseases like cystic fibrosis (CF) or otherwise altering a gene for therapeutic benefit. There are both hopes and hurdles with these technologies, with new ideas emerging almost daily. Initial studies using intestinal organoid cultures carrying the common, F508del mutation have shown that gene editing by CRISPR/Cas9 can convert cells lacking CFTR function to cells with normal channel function, providing a precedent that this technology can be harnessed for CF. While this is an important precedent, the challenges that remain are not trivial. A logistical issue for this and many other genetic diseases is genetic heterogeneity. Approximately, 2000 mutations associated with CF have been found in CFTR, the gene responsible for CF, and thus a feasible strategy that would encompass all individuals affected by the disease is particularly difficult to envision. However, single strategies that would be applicable to all subjects affected by CF have been conceived and are being investigated. With all of these approaches, efficiency (the proportion of cells edited), accuracy (how often other sites in the genome are affected), and delivery of the gene editing components to the desired cells are perhaps the most significant, impending hurdles. Our understanding of each of these areas is increasing rapidly, and while it is impossible to predict when a successful strategy will reach the clinic, there is every reason to believe it is a question of "when" and not "if." © 2017 Wiley Periodicals, Inc.

Wildlife as valuable natural resources vs. intolerable pests: A suburban wildlife management model

USGS Publications Warehouse

DeStefano, S.; Deblinger, R.D.

2005-01-01

Management of wildlife in suburban environments involves a complex set of interactions between both human and wildlife populations. Managers need additional tools, such as models, that can help them assess the status of wildlife populations, devise and apply management programs, and convey this information to other professionals and the public. We present a model that conceptualizes how some wildlife populations can fluctuate between extremely low (rare, threatened, or endangered status) and extremely high (overabundant) numbers over time. Changes in wildlife abundance can induce changes in human perceptions, which continually redefine species as a valuable resource to be protected versus a pest to be controlled. Management programs thatincorporate a number of approaches and promote more stable populations of wildlife avoid the problems of the resource versus pest transformation, are less costly to society, and encourage more positive and less negative interactions between humans and wildlife. We presenta case example of the beaver Castor canadensis in Massachusetts to illustrate how this model functions and can be applied. ?? 2005 Springer Science + Business Media, Inc.

Genetic Selection to Enhance Animal Welfare Using Meat Inspection Data from Slaughter Plants

PubMed Central

Mathur, Pramod K.; Vogelzang, Roos; Mulder, Herman A.; Knol, Egbert F.

2018-01-01

Simple Summary Analysis of a large volume of meat inspection data suggests availability of genetic variation for most common indicators of poor animal welfare. This genetic variation can be used to select pigs that have the potential to resist common infections and other unfavorable welfare conditions. Genetic selection can be a tool in addition to farm management in reducing the risk of diseases, thereby reducing pain and suffering of animals. In general, the slaughter remarks have small but favorable genetic relationships with finishing and carcass quality traits. Therefore, it is possible to enhance animal welfare along with the genetic selection for economically important production traits. Abstract Animal health and welfare are monitored during meat inspection in many slaughter plants around the world. Carcasses are examined by meat inspectors and remarks are made with respect to different diseases, injuries, and other abnormalities. This is a valuable data resource for disease prevention and enhancing animal welfare, but it is rarely used for this purpose. Records on carcass remarks on 140,375 finisher pigs were analyzed to investigate the possibility of genetic selection to reduce the risk of the most prevalent diseases and indicators of suboptimal animal welfare. As part of this, effects of some non-genetic factors such as differences between farms, sexes, and growth rates were also examined. The most frequent remarks were pneumonia (15.4%), joint disorders (9.8%), pleuritis (4.7%), pericarditis (2.3%), and liver lesions (2.2%). Joint disorders were more frequent in boars than in gilts. There were also significant differences between farms. Pedigree records were available for 142,324 pigs from 14 farms and were used for genetic analysis. Heritability estimates for pneumonia, pleuritis, pericarditis, liver lesions, and joint disorders were 0.10, 0.09, 0.14, 0.24, and 0.17 on the liability scale, respectively, suggesting the existence of substantial genetic

[Genetic predisposition and Pediatric Acute Respiratory Distress Syndrome: New tools for genetic study].

PubMed

Erranz, M Benjamín; Wilhelm, B Jan; Riquelme, V Raquel; Cruces, R Pablo

2015-01-01

Acute respiratory distress syndrome (ARDS) is the most severe form of respiratory failure. Theoretically, any acute lung condition can lead to ARDS, but only a small percentage of individuals actually develop the disease. On this basis, genetic factors have been implicated in the risk of developing ARDS. Based on the pathophysiology of this disease, many candidate genes have been evaluated as potential modifiers in patient, as well as in animal models, of ARDS. Recent experimental data and clinical studies suggest that variations of genes involved in key processes of tissue, cellular and molecular lung damage may influence susceptibility and prognosis of ARDS. However, the pathogenesis of pediatric ARDS is complex, and therefore, it can be expected that many genes might contribute. Genetic variations such as single nucleotide polymorphisms and copy-number variations are likely associated with susceptibility to ARDS in children with primary lung injury. Genome-wide association (GWA) studies can objectively examine these variations, and help identify important new genes and pathogenetic pathways for future analysis. This approach might also have diagnostic and therapeutic implications, such as predicting patient risk or developing a personalized therapeutic approach to this serious syndrome. Copyright © 2015. Publicado por Elsevier España, S.L.U.

Gifting of timberland as an estate planning tool

Treesearch

William C. Siegel

2004-01-01

Estate planning and associated tax considerations frequently focus on the transfer of property at death. Lifetime gifts, however, are also a valuable planning tool. The "ability to afford the gift" should be the first consideration in a giving program. Timberland and other property that someday might be needed should not be given away.

Genetic evidence for an East Asian origin of Chinese Muslim populations Dongxiang and Hui

PubMed Central

Yao, Hong-Bing; Wang, Chuan-Chao; Tao, Xiaolan; Shang, Lei; Wen, Shao-Qing; Zhu, Bofeng; Kang, Longli; Jin, Li; Li, Hui

2016-01-01

There is a long-going debate on the genetic origin of Chinese Muslim populations, such as Uygur, Dongxiang, and Hui. However, genetic information for those Muslim populations except Uygur is extremely limited. In this study, we investigated the genetic structure and ancestry of Chinese Muslims by analyzing 15 autosomal short tandem repeats in 652 individuals from Dongxiang, Hui, and Han Chinese populations in Gansu province. Both genetic distance and Bayesian-clustering methods showed significant genetic homogeneity between the two Muslim populations and East Asian populations, suggesting a common genetic ancestry. Our analysis found no evidence of substantial gene flow from Middle East or Europe into Dongxiang and Hui people during their Islamization. The dataset generated in present study are also valuable for forensic identification and paternity tests in China. PMID:27924949

Combining Simulation Tools for End-to-End Trajectory Optimization

NASA Technical Reports Server (NTRS)

Whitley, Ryan; Gutkowski, Jeffrey; Craig, Scott; Dawn, Tim; Williams, Jacobs; Stein, William B.; Litton, Daniel; Lugo, Rafael; Qu, Min

2015-01-01

Trajectory simulations with advanced optimization algorithms are invaluable tools in the process of designing spacecraft. Due to the need for complex models, simulations are often highly tailored to the needs of the particular program or mission. NASA's Orion and SLS programs are no exception. While independent analyses are valuable to assess individual spacecraft capabilities, a complete end-to-end trajectory from launch to splashdown maximizes potential performance and ensures a continuous solution. In order to obtain end-to-end capability, Orion's in-space tool (Copernicus) was made to interface directly with the SLS's ascent tool (POST2) and a new tool to optimize the full problem by operating both simulations simultaneously was born.

A comprehensive global genotype-phenotype database for rare diseases.

PubMed

Trujillano, Daniel; Oprea, Gabriela-Elena; Schmitz, Yvonne; Bertoli-Avella, Aida M; Abou Jamra, Rami; Rolfs, Arndt

2017-01-01

The ability to discover genetic variants in a patient runs far ahead of the ability to interpret them. Databases with accurate descriptions of the causal relationship between the variants and the phenotype are valuable since these are critical tools in clinical genetic diagnostics. Here, we introduce a comprehensive and global genotype-phenotype database focusing on rare diseases. This database (CentoMD ® ) is a browser-based tool that enables access to a comprehensive, independently curated system utilizing stringent high-quality criteria and a quickly growing repository of genetic and human phenotype ontology (HPO)-based clinical information. Its main goals are to aid the evaluation of genetic variants, to enhance the validity of the genetic analytical workflow, to increase the quality of genetic diagnoses, and to improve evaluation of treatment options for patients with hereditary diseases. The database software correlates clinical information from consented patients and probands of different geographical backgrounds with a large dataset of genetic variants and, when available, biomarker information. An automated follow-up tool is incorporated that informs all users whenever a variant classification has changed. These unique features fully embedded in a CLIA/CAP-accredited quality management system allow appropriate data quality and enhanced patient safety. More than 100,000 genetically screened individuals are documented in the database, resulting in more than 470 million variant detections. Approximately, 57% of the clinically relevant and uncertain variants in the database are novel. Notably, 3% of the genetic variants identified and previously reported in the literature as being associated with a particular rare disease were reclassified, based on internal evidence, as clinically irrelevant. The database offers a comprehensive summary of the clinical validity and causality of detected gene variants with their associated phenotypes, and is a valuable tool

A Genetic Algorithm Approach to Motion Sensor Placement in Smart Environments

PubMed Central

Thomas, Brian L.; Crandall, Aaron S.; Cook, Diane J.

2016-01-01

Smart environments and ubiquitous computing technologies hold great promise for a wide range of real world applications. The medical community is particularly interested in high quality measurement of activities of daily living. With accurate computer modeling of older adults, decision support tools may be built to assist care providers. One aspect of effectively deploying these technologies is determining where the sensors should be placed in the home to effectively support these end goals. This work introduces and evaluates a set of approaches for generating sensor layouts in the home. These approaches range from the gold standard of human intuition-based placement to more advanced search algorithms, including Hill Climbing and Genetic Algorithms. The generated layouts are evaluated based on their ability to detect activities while minimizing the number of needed sensors. Sensor-rich environments can provide valuable insights about adults as they go about their lives. These sensors, once in place, provide information on daily behavior that can facilitate an aging-in-place approach to health care. PMID:27453810

SimHap GUI: An intuitive graphical user interface for genetic association analysis

PubMed Central

Carter, Kim W; McCaskie, Pamela A; Palmer, Lyle J

2008-01-01

Background Researchers wishing to conduct genetic association analysis involving single nucleotide polymorphisms (SNPs) or haplotypes are often confronted with the lack of user-friendly graphical analysis tools, requiring sophisticated statistical and informatics expertise to perform relatively straightforward tasks. Tools, such as the SimHap package for the R statistics language, provide the necessary statistical operations to conduct sophisticated genetic analysis, but lacks a graphical user interface that allows anyone but a professional statistician to effectively utilise the tool. Results We have developed SimHap GUI, a cross-platform integrated graphical analysis tool for conducting epidemiological, single SNP and haplotype-based association analysis. SimHap GUI features a novel workflow interface that guides the user through each logical step of the analysis process, making it accessible to both novice and advanced users. This tool provides a seamless interface to the SimHap R package, while providing enhanced functionality such as sophisticated data checking, automated data conversion, and real-time estimations of haplotype simulation progress. Conclusion SimHap GUI provides a novel, easy-to-use, cross-platform solution for conducting a range of genetic and non-genetic association analyses. This provides a free alternative to commercial statistics packages that is specifically designed for genetic association analysis. PMID:19109877

SimHap GUI: an intuitive graphical user interface for genetic association analysis.

PubMed

Carter, Kim W; McCaskie, Pamela A; Palmer, Lyle J

2008-12-25

Researchers wishing to conduct genetic association analysis involving single nucleotide polymorphisms (SNPs) or haplotypes are often confronted with the lack of user-friendly graphical analysis tools, requiring sophisticated statistical and informatics expertise to perform relatively straightforward tasks. Tools, such as the SimHap package for the R statistics language, provide the necessary statistical operations to conduct sophisticated genetic analysis, but lacks a graphical user interface that allows anyone but a professional statistician to effectively utilise the tool. We have developed SimHap GUI, a cross-platform integrated graphical analysis tool for conducting epidemiological, single SNP and haplotype-based association analysis. SimHap GUI features a novel workflow interface that guides the user through each logical step of the analysis process, making it accessible to both novice and advanced users. This tool provides a seamless interface to the SimHap R package, while providing enhanced functionality such as sophisticated data checking, automated data conversion, and real-time estimations of haplotype simulation progress. SimHap GUI provides a novel, easy-to-use, cross-platform solution for conducting a range of genetic and non-genetic association analyses. This provides a free alternative to commercial statistics packages that is specifically designed for genetic association analysis.

FastGCN: A GPU Accelerated Tool for Fast Gene Co-Expression Networks

PubMed Central

Liang, Meimei; Zhang, Futao; Jin, Gulei; Zhu, Jun

2015-01-01

Gene co-expression networks comprise one type of valuable biological networks. Many methods and tools have been published to construct gene co-expression networks; however, most of these tools and methods are inconvenient and time consuming for large datasets. We have developed a user-friendly, accelerated and optimized tool for constructing gene co-expression networks that can fully harness the parallel nature of GPU (Graphic Processing Unit) architectures. Genetic entropies were exploited to filter out genes with no or small expression changes in the raw data preprocessing step. Pearson correlation coefficients were then calculated. After that, we normalized these coefficients and employed the False Discovery Rate to control the multiple tests. At last, modules identification was conducted to construct the co-expression networks. All of these calculations were implemented on a GPU. We also compressed the coefficient matrix to save space. We compared the performance of the GPU implementation with those of multi-core CPU implementations with 16 CPU threads, single-thread C/C++ implementation and single-thread R implementation. Our results show that GPU implementation largely outperforms single-thread C/C++ implementation and single-thread R implementation, and GPU implementation outperforms multi-core CPU implementation when the number of genes increases. With the test dataset containing 16,000 genes and 590 individuals, we can achieve greater than 63 times the speed using a GPU implementation compared with a single-thread R implementation when 50 percent of genes were filtered out and about 80 times the speed when no genes were filtered out. PMID:25602758

FastGCN: a GPU accelerated tool for fast gene co-expression networks.

PubMed

Liang, Meimei; Zhang, Futao; Jin, Gulei; Zhu, Jun

2015-01-01

Gene co-expression networks comprise one type of valuable biological networks. Many methods and tools have been published to construct gene co-expression networks; however, most of these tools and methods are inconvenient and time consuming for large datasets. We have developed a user-friendly, accelerated and optimized tool for constructing gene co-expression networks that can fully harness the parallel nature of GPU (Graphic Processing Unit) architectures. Genetic entropies were exploited to filter out genes with no or small expression changes in the raw data preprocessing step. Pearson correlation coefficients were then calculated. After that, we normalized these coefficients and employed the False Discovery Rate to control the multiple tests. At last, modules identification was conducted to construct the co-expression networks. All of these calculations were implemented on a GPU. We also compressed the coefficient matrix to save space. We compared the performance of the GPU implementation with those of multi-core CPU implementations with 16 CPU threads, single-thread C/C++ implementation and single-thread R implementation. Our results show that GPU implementation largely outperforms single-thread C/C++ implementation and single-thread R implementation, and GPU implementation outperforms multi-core CPU implementation when the number of genes increases. With the test dataset containing 16,000 genes and 590 individuals, we can achieve greater than 63 times the speed using a GPU implementation compared with a single-thread R implementation when 50 percent of genes were filtered out and about 80 times the speed when no genes were filtered out.

SNP_tools: A compact tool package for analysis and conversion of genotype data for MS-Excel

PubMed Central

Chen, Bowang; Wilkening, Stefan; Drechsel, Marion; Hemminki, Kari

2009-01-01

Background Single nucleotide polymorphism (SNP) genotyping is a major activity in biomedical research. Scientists prefer to have a facile access to the results which may require conversions between data formats. First hand SNP data is often entered in or saved in the MS-Excel format, but this software lacks genetic and epidemiological related functions. A general tool to do basic genetic and epidemiological analysis and data conversion for MS-Excel is needed. Findings The SNP_tools package is prepared as an add-in for MS-Excel. The code is written in Visual Basic for Application, embedded in the Microsoft Office package. This add-in is an easy to use tool for users with basic computer knowledge (and requirements for basic statistical analysis). Conclusion Our implementation for Microsoft Excel 2000-2007 in Microsoft Windows 2000, XP, Vista and Windows 7 beta can handle files in different formats and converts them into other formats. It is a free software. PMID:19852806

SNP_tools: A compact tool package for analysis and conversion of genotype data for MS-Excel.

PubMed

Chen, Bowang; Wilkening, Stefan; Drechsel, Marion; Hemminki, Kari

2009-10-23

Single nucleotide polymorphism (SNP) genotyping is a major activity in biomedical research. Scientists prefer to have a facile access to the results which may require conversions between data formats. First hand SNP data is often entered in or saved in the MS-Excel format, but this software lacks genetic and epidemiological related functions. A general tool to do basic genetic and epidemiological analysis and data conversion for MS-Excel is needed. The SNP_tools package is prepared as an add-in for MS-Excel. The code is written in Visual Basic for Application, embedded in the Microsoft Office package. This add-in is an easy to use tool for users with basic computer knowledge (and requirements for basic statistical analysis). Our implementation for Microsoft Excel 2000-2007 in Microsoft Windows 2000, XP, Vista and Windows 7 beta can handle files in different formats and converts them into other formats. It is a free software.

The alien replicon: Artificial genetic constructs to direct the synthesis of transmissible self-replicating RNAs: In vivo synthesised heterologous (alien) RNA constructs are capable of initiating self-replication following transmission to the host organism.

PubMed

Kochetov, Alex V

2014-12-01

Artificial genetic constructs that direct the synthesis of self-replicating RNA molecules are used widely to induce gene silencing, for bioproduction, and for vaccination. Interestingly, one variant of the self-replicon has not been discussed in the literature: namely, transgenic organisms that synthesise alien replicons. For example, plant cells may be easily genetically modified to produce bacteriophages or insect viruses. Alien replicon-producing organisms (ARPOs) may serve as a unique tool for biocontrol or to selectively influence the characteristics of a target organism. The ARPO approach would have to meet strict biosafety criteria, and its practical applications are problematic. However, a discussion on ARPO applicability would be valuable to outline the full set of options available in the bioengineering toolbox. In this paper, RNA replicons for bioengineering are reviewed briefly, and the ARPO approach is discussed. © 2014 WILEY Periodicals, Inc.

Kidney Paired Donation and the "Valuable Consideration" Problem: The Experiences of Australia, Canada, and the United States.

PubMed

Toews, Maeghan; Giancaspro, Mark; Richards, Bernadette; Ferrari, Paolo

2017-09-01

As organ donation rates remain unable to meet the needs of individuals waiting for transplants, it is necessary to identify reasons for this shortage and develop solutions to address it. The introduction of kidney paired donation (KPD) programs represents one such innovation that has become a valuable tool in donation systems around the world. Although KPD has been successful in increasing kidney donation and transplantation, there are lingering questions about its legality. Donation through KPD is done in exchange for-and with the expectation of-a reciprocal kidney donation and transplantation. It is this reciprocity that has caused concern about whether KPD complies with existing law. Organ donation systems around the world are almost universally structured to legally prohibit the commercial exchange of organs. Australia, Canada, and the United States have accomplished this goal by prohibiting the exchange of an organ for "valuable consideration," which is a legal term that has not historically been limited to monetary exchange. Whether or not KPD programs violate this legislative prohibition will depend on the specific legislative provision being considered, and the legal system and case law of the particular jurisdiction in question. This article compares the experiences of Australia, Canada, and the United States in determining the legality of KPD and highlights the need for legal clarity and flexibility as donation and transplantation systems continue to evolve.

Genetic Map of Mango: A Tool for Mango Breeding

PubMed Central

Kuhn, David N.; Bally, Ian S. E.; Dillon, Natalie L.; Innes, David; Groh, Amy M.; Rahaman, Jordon; Ophir, Ron; Cohen, Yuval; Sherman, Amir

2017-01-01

Mango (Mangifera indica) is an economically and nutritionally important tropical/subtropical tree fruit crop. Most of the current commercial cultivars are selections rather than the products of breeding programs. To improve the efficiency of mango breeding, molecular markers have been used to create a consensus genetic map that identifies all 20 linkage groups in seven mapping populations. Polyembryony is an important mango trait, used for clonal propagation of cultivars and rootstocks. In polyembryonic mango cultivars, in addition to a zygotic embryo, several apomictic embryos develop from maternal tissue surrounding the fertilized egg cell. This trait has been associated with linkage group 8 in our consensus genetic map and has been validated in two of the seven mapping populations. In addition, we have observed a significant association between trait and single nucleotide polymorphism (SNP) markers for the vegetative trait of branch habit and the fruit traits of bloom, ground skin color, blush intensity, beak shape, and pulp color. PMID:28473837

Levulinic acid: a valuable platform chemical for fermentative syntheses

USDA-ARS?s Scientific Manuscript database

In 2004 the DOE included levulinic acid (LA) as a top platform molecule because of its production from renewable resources in large yields and its broad application potential as a precursor for many valuable chemical derivatives. While LA and its chemical derivatives have high application potential,...

Genetic and environmental melanoma models in fish

PubMed Central

Patton, E Elizabeth; Mitchell, David L; Nairn, Rodney S

2010-01-01

Experimental animal models are extremely valuable for the study of human diseases, especially those with underlying genetic components. The exploitation of various animal models, from fruitflies to mice, has led to major advances in our understanding of the etiologies of many diseases, including cancer. Cutaneous malignant melanoma is a form of cancer for which both environmental insult (i.e., UV) and hereditary predisposition are major causative factors. Fish melanoma models have been used in studies of both spontaneous and induced melanoma formation. Genetic hybrids between platyfish and swordtails, different species of the genus Xiphophorus, have been studied since the 1920s to identify genetic determinants of pigmentation and melanoma formation. Recently, transgenesis has been used to develop zebrafish and medaka models for melanoma research. This review will provide a historical perspective on the use of fish models in melanoma research, and an updated summary of current and prospective studies using these unique experimental systems. PMID:20230482

Custom oligonucleotide array-based CGH: a reliable diagnostic tool for detection of exonic copy-number changes in multiple targeted genes

PubMed Central

Vasson, Aurélie; Leroux, Céline; Orhant, Lucie; Boimard, Mathieu; Toussaint, Aurélie; Leroy, Chrystel; Commere, Virginie; Ghiotti, Tiffany; Deburgrave, Nathalie; Saillour, Yoann; Atlan, Isabelle; Fouveaut, Corinne; Beldjord, Cherif; Valleix, Sophie; Leturcq, France; Dodé, Catherine; Bienvenu, Thierry; Chelly, Jamel; Cossée, Mireille

2013-01-01

The frequency of disease-related large rearrangements (referred to as copy-number mutations, CNMs) varies among genes, and search for these mutations has an important place in diagnostic strategies. In recent years, CGH method using custom-designed high-density oligonucleotide-based arrays allowed the development of a powerful tool for detection of alterations at the level of exons and made it possible to provide flexibility through the possibility of modeling chips. The aim of our study was to test custom-designed oligonucleotide CGH array in a diagnostic laboratory setting that analyses several genes involved in various genetic diseases, and to compare it with conventional strategies. To this end, we designed a 12-plex CGH array (135k; 135 000 probes/subarray) (Roche Nimblegen) with exonic and intronic oligonucleotide probes covering 26 genes routinely analyzed in the laboratory. We tested control samples with known CNMs and patients for whom genetic causes underlying their disorders were unknown. The contribution of this technique is undeniable. Indeed, it appeared reproducible, reliable and sensitive enough to detect heterozygous single-exon deletions or duplications, complex rearrangements and somatic mosaicism. In addition, it improves reliability of CNM detection and allows determination of boundaries precisely enough to direct targeted sequencing of breakpoints. All of these points, associated with the possibility of a simultaneous analysis of several genes and scalability ‘homemade' make it a valuable tool as a new diagnostic approach of CNMs. PMID:23340513

Actor-network theory: a tool to support ethical analysis of commercial genetic testing.

PubMed

Williams-Jones, Bryn; Graham, Janice E

2003-12-01

Social, ethical and policy analysis of the issues arising from gene patenting and commercial genetic testing is enhanced by the application of science and technology studies, and Actor-Network Theory (ANT) in particular. We suggest the potential for transferring ANT's flexible nature to an applied heuristic methodology for gathering empirical information and for analysing the complex networks involved in the development of genetic technologies. Three concepts are explored in this paper--actor-networks, translation, and drift--and applied to the case of Myriad Genetics and their commercial BRACAnalysis genetic susceptibility test for hereditary breast cancer. Treating this test as an active participant in socio-technical networks clarifies the extent to which it interacts with, shapes and is shaped by people, other technologies, and institutions. Such an understanding enables more sophisticated and nuanced technology assessment, academic analysis, as well as public debate about the social, ethical and policy implications of the commercialization of new genetic technologies.

"Genetically Engineered" Nanoelectronics

NASA Technical Reports Server (NTRS)

Klimeck, Gerhard; Salazar-Lazaro, Carlos H.; Stoica, Adrian; Cwik, Thomas

2000-01-01

The quantum mechanical functionality of nanoelectronic devices such as resonant tunneling diodes (RTDs), quantum well infrared-photodetectors (QWIPs), quantum well lasers, and heterostructure field effect transistors (HFETs) is enabled by material variations on an atomic scale. The design and optimization of such devices requires a fundamental understanding of electron transport in such dimensions. The Nanoelectronic Modeling Tool (NEMO) is a general-purpose quantum device design and analysis tool based on a fundamental non-equilibrium electron transport theory. NEW was combined with a parallelized genetic algorithm package (PGAPACK) to evolve structural and material parameters to match a desired set of experimental data. A numerical experiment that evolves structural variations such as layer widths and doping concentrations is performed to analyze an experimental current voltage characteristic. The genetic algorithm is found to drive the NEMO simulation parameters close to the experimentally prescribed layer thicknesses and doping profiles. With such a quantitative agreement between theory and experiment design synthesis can be performed.

TRANSGENE ESCAPE MONITORING, POPULATION GENETICS, AND THE LAW

EPA Science Inventory

There has been little discussion about how to apply population genetics methods to monitor the spread of transgenes that are detected outside the agricultural populations where they are deployed. Population geneticists have developed tools for analyzing the genetic makeup of indi...

Travel fosters tool use in wild chimpanzees

PubMed Central

Gruber, Thibaud; Zuberbühler, Klaus; Neumann, Christof

2016-01-01

Ecological variation influences the appearance and maintenance of tool use in animals, either due to necessity or opportunity, but little is known about the relative importance of these two factors. Here, we combined long-term behavioural data on feeding and travelling with six years of field experiments in a wild chimpanzee community. In the experiments, subjects engaged with natural logs, which contained energetically valuable honey that was only accessible through tool use. Engagement with the experiment was highest after periods of low fruit availability involving more travel between food patches, while instances of actual tool-using were significantly influenced by prior travel effort only. Additionally, combining data from the main chimpanzee study communities across Africa supported this result, insofar as groups with larger travel efforts had larger tool repertoires. Travel thus appears to foster tool use in wild chimpanzees and may also have been a driving force in early hominin technological evolution. DOI: http://dx.doi.org/10.7554/eLife.16371.001 PMID:27431611

Travel fosters tool use in wild chimpanzees.

PubMed

Gruber, Thibaud; Zuberbühler, Klaus; Neumann, Christof

2016-07-19

Ecological variation influences the appearance and maintenance of tool use in animals, either due to necessity or opportunity, but little is known about the relative importance of these two factors. Here, we combined long-term behavioural data on feeding and travelling with six years of field experiments in a wild chimpanzee community. In the experiments, subjects engaged with natural logs, which contained energetically valuable honey that was only accessible through tool use. Engagement with the experiment was highest after periods of low fruit availability involving more travel between food patches, while instances of actual tool-using were significantly influenced by prior travel effort only. Additionally, combining data from the main chimpanzee study communities across Africa supported this result, insofar as groups with larger travel efforts had larger tool repertoires. Travel thus appears to foster tool use in wild chimpanzees and may also have been a driving force in early hominin technological evolution.

Advances in Genetical Genomics of Plants

PubMed Central

Joosen, R.V.L.; Ligterink, W.; Hilhorst, H.W.M.; Keurentjes, J.J.B.

2009-01-01

Natural variation provides a valuable resource to study the genetic regulation of quantitative traits. In quantitative trait locus (QTL) analyses this variation, captured in segregating mapping populations, is used to identify the genomic regions affecting these traits. The identification of the causal genes underlying QTLs is a major challenge for which the detection of gene expression differences is of major importance. By combining genetics with large scale expression profiling (i.e. genetical genomics), resulting in expression QTLs (eQTLs), great progress can be made in connecting phenotypic variation to genotypic diversity. In this review we discuss examples from human, mouse, Drosophila, yeast and plant research to illustrate the advances in genetical genomics, with a focus on understanding the regulatory mechanisms underlying natural variation. With their tolerance to inbreeding, short generation time and ease to generate large families, plants are ideal subjects to test new concepts in genetics. The comprehensive resources which are available for Arabidopsis make it a favorite model plant but genetical genomics also found its way to important crop species like rice, barley and wheat. We discuss eQTL profiling with respect to cis and trans regulation and show how combined studies with other ‘omics’ technologies, such as metabolomics and proteomics may further augment current information on transcriptional, translational and metabolomic signaling pathways and enable reconstruction of detailed regulatory networks. The fast developments in the ‘omics’ area will offer great potential for genetical genomics to elucidate the genotype-phenotype relationships for both fundamental and applied research. PMID:20514216

Colorectal Cancer Risk Assessment Tool

MedlinePlus

... 11/12/2014 Risk Calculator About the Tool Colorectal Cancer Risk Factors Download SAS and Gauss Code Page ... Rectal Cancer: Prevention, Genetics, Causes Tests to Detect Colorectal Cancer and Polyps Cancer Risk Prediction Resources Update November ...

Applied genetic conservation of Hawaiian Acacia koa: an eco-regional approach

Treesearch

Nick Dudley; Tyler Jones; Robert James; Richard Sniezko; Jessica Wright; Christina Liang; Paul F. Gugger; Phil Cannon

2017-01-01

Koa (Acacia koa) is a valuable tree species economically, ecologically, and culturally in Hawaii. A vascular wilt disease of koa, caused by the fungal pathogen Fusarium oxysporum f. sp. koae (FOXY), causes high rates of mortality in field plantings and threatens native koa forests in Hawaii. Producing seeds with genetic resistance to FOXY is vital...

Promoting Utilization of Saccharum spp. Genetic Resources through Genetic Diversity Analysis and Core Collection Construction

PubMed Central

Pathak, Bhuvan; Ayala-Silva, Tomas; Yang, Xiping; Todd, James; Glynn, Neil C.; Kuhn, David N.; Glaz, Barry; Gilbert, Robert A.; Comstock, Jack C.; Wang, Jianping

2014-01-01

Sugarcane (Saccharum spp.) and other members of Saccharum spp. are attractive biofuel feedstocks. One of the two World Collections of Sugarcane and Related Grasses (WCSRG) is in Miami, FL. This WCSRG has 1002 accessions, presumably with valuable alleles for biomass, other important agronomic traits, and stress resistance. However, the WCSRG has not been fully exploited by breeders due to its lack of characterization and unmanageable population. In order to optimize the use of this genetic resource, we aim to 1) genotypically evaluate all the 1002 accessions to understand its genetic diversity and population structure and 2) form a core collection, which captures most of the genetic diversity in the WCSRG. We screened 36 microsatellite markers on 1002 genotypes and recorded 209 alleles. Genetic diversity of the WCSRG ranged from 0 to 0.5 with an average of 0.304. The population structure analysis and principal coordinate analysis revealed three clusters with all S. spontaneum in one cluster, S. officinarum and S. hybrids in the second cluster and mostly non-Saccharum spp. in the third cluster. A core collection of 300 accessions was identified which captured the maximum genetic diversity of the entire WCSRG which can be further exploited for sugarcane and energy cane breeding. Sugarcane and energy cane breeders can effectively utilize this core collection for cultivar improvement. Further, the core collection can provide resources for forming an association panel to evaluate the traits of agronomic and commercial importance. PMID:25333358

43 CFR 2568.94 - Can I receive an allotment of land that is valuable for minerals?

Code of Federal Regulations, 2012 CFR

2012-10-01

... valuable for minerals? 2568.94 Section 2568.94 Public Lands: Interior Regulations Relating to Public Lands... be or believed to be valuable for coal, oil, or gas, but the ownership of these minerals remains with the Federal government. BLM cannot convey to you land valuable for other kinds of minerals such as...

43 CFR 2568.94 - Can I receive an allotment of land that is valuable for minerals?

Code of Federal Regulations, 2014 CFR

2014-10-01

... valuable for minerals? 2568.94 Section 2568.94 Public Lands: Interior Regulations Relating to Public Lands... be or believed to be valuable for coal, oil, or gas, but the ownership of these minerals remains with the Federal government. BLM cannot convey to you land valuable for other kinds of minerals such as...

43 CFR 2568.94 - Can I receive an allotment of land that is valuable for minerals?

Code of Federal Regulations, 2011 CFR

2011-10-01

... valuable for minerals? 2568.94 Section 2568.94 Public Lands: Interior Regulations Relating to Public Lands... be or believed to be valuable for coal, oil, or gas, but the ownership of these minerals remains with the Federal government. BLM cannot convey to you land valuable for other kinds of minerals such as...

Genetically engineering milk.

PubMed

Whitelaw, C Bruce A; Joshi, Akshay; Kumar, Satish; Lillico, Simon G; Proudfoot, Chris

2016-02-01

It has been thirty years since the first genetically engineered animal with altered milk composition was reported. During the intervening years, the world population has increased from 5bn to 7bn people. An increasing demand for protein in the human diet has followed this population expansion, putting huge stress on the food supply chain. Many solutions to the grand challenge of food security for all have been proposed and are currently under investigation and study. Amongst these, genetics still has an important role to play, aiming to continually enable the selection of livestock with enhanced traits. Part of the geneticist's tool box is the technology of genetic engineering. In this Invited Review, we indicate that this technology has come a long way, we focus on the genetic engineering of dairy animals and we argue that the new strategies for precision breeding demand proper evaluation as to how they could contribute to the essential increases in agricultural productivity our society must achieve.

Recent Developments on Genetic Engineering of Microalgae for Biofuels and Bio-Based Chemicals.

PubMed

Ng, I-Son; Tan, Shih-I; Kao, Pei-Hsun; Chang, Yu-Kaung; Chang, Jo-Shu

2017-10-01

Microalgae serve as a promising source for the production of biofuels and bio-based chemicals. They are superior to terrestrial plants as feedstock in many aspects and their biomass is naturally rich in lipids, carbohydrates, proteins, pigments, and other valuable compounds. Due to the relatively slow growth rate and high cultivation cost of microalgae, to screen efficient and robust microalgal strains as well as genetic modifications of the available strains for further improvement are of urgent demand in the development of microalgae-based biorefinery. In genetic engineering of microalgae, transformation and selection methods are the key steps to accomplish the target gene modification. However, determination of the preferable type and dosage of antibiotics used for transformant selection is usually time-consuming and microalgal-strain-dependent. Therefore, more powerful and efficient techniques should be developed to meet this need. In this review, the conventional and emerging genome-editing tools (e.g., CRISPR-Cas9, TALEN, and ZFN) used in editing the genomes of nuclear, mitochondria, and chloroplast of microalgae are thoroughly surveyed. Although all the techniques mentioned above demonstrate their abilities to perform gene editing and desired phenotype screening, there still need to overcome higher production cost and lower biomass productivity, to achieve efficient production of the desired products in microalgal biorefineries. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genetic identification of Iberian rodent species using both mitochondrial and nuclear loci: application to noninvasive sampling.

PubMed

Barbosa, S; Pauperio, J; Searle, J B; Alves, P C

2013-01-01

Species identification through noninvasive sampling is increasingly used in animal conservation genetics, given that it obviates the need to handle free-living individuals. Noninvasive sampling is particularly valuable for elusive and small species such as rodents. Although rodents are not usually assumed to be the most obvious target for conservation, of the 21 species or near-species present in Iberia, three are considered endangered and declining, while several others are poorly studied. Here, we develop a genetic tool for identifying all rodent species in Iberia by noninvasive genetic sampling. To achieve this purpose, we selected one mitochondrial gene [cytochrome b (cyt-b)] and one nuclear gene [interphotoreceptor retinoid-binding protein (IRBP)], which we first sequenced using tissue samples. Both genes allow for the phylogenetic distinction of all species except the sibling species Microtus lusitanicus and Microtus duodecimcostatus. Overall, cyt-b showed higher resolution than IRBP, revealing a clear barcoding gap. To allow these markers to be applied to noninvasive samples, we selected a short highly diagnostic fragment from each gene, which we used to obtain sequences from faeces and bones from owl pellets. Amplification success for the cyt-b and IRBP fragment was 85% and 43% in faecal and 88% and 64% in owl-pellet DNA extractions, respectively. The method allows the unambiguous identification of the great majority of Iberian rodent species from noninvasive samples, with application in studies of distribution, spatial ecology and population dynamics, and for conservation. © 2012 Blackwell Publishing Ltd.

A kidney-disease gene panel allows a comprehensive genetic diagnosis of cystic and glomerular inherited kidney diseases.

PubMed

Bullich, Gemma; Domingo-Gallego, Andrea; Vargas, Iván; Ruiz, Patricia; Lorente-Grandoso, Laura; Furlano, Mónica; Fraga, Gloria; Madrid, Álvaro; Ariceta, Gema; Borregán, Mar; Piñero-Fernández, Juan Alberto; Rodríguez-Peña, Lidia; Ballesta-Martínez, Maria Juliana; Llano-Rivas, Isabel; Meñica, Mireia Aguirre; Ballarín, José; Torrents, David; Torra, Roser; Ars, Elisabet

2018-05-22

Molecular diagnosis of inherited kidney diseases remains a challenge due to their expanding phenotypic spectra as well as the constantly growing list of disease-causing genes. Here we develop a comprehensive approach for genetic diagnosis of inherited cystic and glomerular nephropathies. Targeted next generation sequencing of 140 genes causative of or associated with cystic or glomerular nephropathies was performed in 421 patients, a validation cohort of 116 patients with previously known mutations, and a diagnostic cohort of 207 patients with suspected inherited cystic disease and 98 patients with glomerular disease. In the validation cohort, a sensitivity of 99% was achieved. In the diagnostic cohort, causative mutations were found in 78% of patients with cystic disease and 62% of patients with glomerular disease, mostly familial cases, including copy number variants. Results depict the distribution of different cystic and glomerular inherited diseases showing the most likely diagnosis according to perinatal, pediatric and adult disease onset. Of all the genetically diagnosed patients, 15% were referred with an unspecified clinical diagnosis and in 2% genetic testing changed the clinical diagnosis. Therefore, in 17% of cases our genetic analysis was crucial to establish the correct diagnosis. Complex inheritance patterns in autosomal dominant polycystic kidney disease and Alport syndrome were suspected in seven and six patients, respectively. Thus, our kidney-disease gene panel is a comprehensive, noninvasive, and cost-effective tool for genetic diagnosis of cystic and glomerular inherited kidney diseases. This allows etiologic diagnosis in three-quarters of patients and is especially valuable in patients with unspecific or atypical phenotypes. Copyright © 2018 International Society of Nephrology. Published by Elsevier Inc. All rights reserved.

The Pathway Tools software.

PubMed

Karp, Peter D; Paley, Suzanne; Romero, Pedro

2002-01-01

Bioinformatics requires reusable software tools for creating model-organism databases (MODs). The Pathway Tools is a reusable, production-quality software environment for creating a type of MOD called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc (see http://ecocyc.org) integrates our evolving understanding of the genes, proteins, metabolic network, and genetic network of an organism. This paper provides an overview of the four main components of the Pathway Tools: The PathoLogic component supports creation of new PGDBs from the annotated genome of an organism. The Pathway/Genome Navigator provides query, visualization, and Web-publishing services for PGDBs. The Pathway/Genome Editors support interactive updating of PGDBs. The Pathway Tools ontology defines the schema of PGDBs. The Pathway Tools makes use of the Ocelot object database system for data management services for PGDBs. The Pathway Tools has been used to build PGDBs for 13 organisms within SRI and by external users.

Mouse Models as Tools to Identify Genetic Pathways for Retinal Degeneration, as Exemplified by Leber's Congenital Amaurosis.

PubMed

Chang, Bo

2016-01-01

Leber's congenital amaurosis (LCA) is an inherited retinal degenerative disease characterized by severe loss of vision in the first year of life. In addition to early vision loss, a variety of other eye-related abnormalities including roving eye movements, deep-set eyes, and sensitivity to bright light also occur with this disease. Many animal models of LCA are available and the study them has led to a better understanding of the pathology of the disease, and has led to the development of therapeutic strategies aimed at curing or slowing down LCA. Mouse models, with their well-developed genetics and similarity to human physiology and anatomy, serve as powerful tools with which to investigate the etiology of human LCA. Such mice provide reproducible, experimental systems for elucidating pathways of normal development, function, designing strategies and testing compounds for translational research and gene-based therapies aimed at delaying the diseases progression. In this chapter, I describe tools used in the discovery and evaluation of mouse models of LCA including a Phoenix Image-Guided Optical Coherence Tomography (OCT) and a Diagnosys Espion Visual Electrophysiology System. Three mouse models are described, the rd3 mouse model for LCA12 and LCA1, the rd12 mouse model for LCA2, and the rd16 mouse model for LCA10.

43 CFR 2430.4 - Additional criteria for classification of lands valuable for public purposes.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 43 Public Lands: Interior 2 2011-10-01 2011-10-01 false Additional criteria for classification of... (2000) DISPOSAL CLASSIFICATIONS Criteria for Disposal Classifications § 2430.4 Additional criteria for classification of lands valuable for public purposes. (a) To be valuable for public purposes, lands must be...

Genetic Testing for Cardiomyopathies in Clinical Practice.

PubMed

Ingles, Jodie; Bagnall, Richard D; Semsarian, Christopher

2018-04-01

Cardiac genetic testing for inherited cardiomyopathies has become a routine aspect of care. Advances in genetic testing technologies have made testing more comprehensive and affordable. With this increase come greater understanding of the genetic basis of these diseases, but also shines a light on the challenges. Ability to ascertain whether a rare variant is causative of disease is problematic. A genetic diagnosis in a family can offer an invaluable tool for cascade genetic testing of at-risk relatives and avenues for reproductive testing options. A careful approach to cardiac genetic testing that recognizes where there is potential for harm ensures the best possible outcomes for families. Copyright © 2017 Elsevier Inc. All rights reserved.

Field Trips as Valuable Learning Experiences in Geography Courses

ERIC Educational Resources Information Center

Krakowka, Amy Richmond

2012-01-01

Field trips have been acknowledged as valuable learning experiences in geography. This article uses Kolb's (1984) experiential learning model to discuss how students learn and how field trips can help enhance learning. Using Kolb's experiential learning theory as a guide in the design of field trips helps ensure that field trips contribute to…

Lessons from 25 years of genetic mapping in onion: where next?

USDA-ARS?s Scientific Manuscript database

Genetic maps are useful tools for both basic research and plant improvement. Close association of genetic markers with genes controlling economically important traits allows for indirect selection, avoiding often time-consuming and expensive phenotypic evaluations. As a result, detailed genetic maps...

Decision Matrices: Tools to Enhance Middle School Engineering Instruction

ERIC Educational Resources Information Center

Gonczi, Amanda L.; Bergman, Brenda G.; Huntoon, Jackie; Allen, Robin; McIntyre, Barb; Turner, Sheri; Davis, Jen; Handler, Rob

2017-01-01

Decision matrices are valuable engineering tools. They allow engineers to objectively examine solution options. Decision matrices can be incorporated in K-12 classrooms to support authentic engineering instruction. In this article we provide examples of how decision matrices have been incorporated into 6th and 7th grade classrooms as part of an…

Genome-Based Genetic Tool Development for Bacillus methanolicus: Theta- and Rolling Circle-Replicating Plasmids for Inducible Gene Expression and Application to Methanol-Based Cadaverine Production.

PubMed

Irla, Marta; Heggeset, Tonje M B; Nærdal, Ingemar; Paul, Lidia; Haugen, Tone; Le, Simone B; Brautaset, Trygve; Wendisch, Volker F

2016-01-01

Bacillus methanolicus is a thermophilic methylotroph able to overproduce amino acids from methanol, a substrate not used for human or animal nutrition. Based on our previous RNA-seq analysis a mannitol inducible promoter and a putative mannitol activator gene mtlR were identified. The mannitol inducible promoter was applied for controlled gene expression using fluorescent reporter proteins and a flow cytometry analysis, and improved by changing the -35 promoter region and by co-expression of the mtlR regulator gene. For independent complementary gene expression control, the heterologous xylose-inducible system from B. megaterium was employed and a two-plasmid gene expression system was developed. Four different replicons for expression vectors were compared with respect to their copy number and stability. As an application example, methanol-based production of cadaverine was shown to be improved from 11.3 to 17.5 g/L when a heterologous lysine decarboxylase gene cadA was expressed from a theta-replicating rather than a rolling-circle replicating vector. The current work on inducible promoter systems and compatible theta- or rolling circle-replicating vectors is an important extension of the poorly developed B. methanolicus genetic toolbox, valuable for genetic engineering and further exploration of this bacterium.

Genome-Based Genetic Tool Development for Bacillus methanolicus: Theta- and Rolling Circle-Replicating Plasmids for Inducible Gene Expression and Application to Methanol-Based Cadaverine Production

PubMed Central

Irla, Marta; Heggeset, Tonje M. B.; Nærdal, Ingemar; Paul, Lidia; Haugen, Tone; Le, Simone B.; Brautaset, Trygve; Wendisch, Volker F.

2016-01-01

Bacillus methanolicus is a thermophilic methylotroph able to overproduce amino acids from methanol, a substrate not used for human or animal nutrition. Based on our previous RNA-seq analysis a mannitol inducible promoter and a putative mannitol activator gene mtlR were identified. The mannitol inducible promoter was applied for controlled gene expression using fluorescent reporter proteins and a flow cytometry analysis, and improved by changing the -35 promoter region and by co-expression of the mtlR regulator gene. For independent complementary gene expression control, the heterologous xylose-inducible system from B. megaterium was employed and a two-plasmid gene expression system was developed. Four different replicons for expression vectors were compared with respect to their copy number and stability. As an application example, methanol-based production of cadaverine was shown to be improved from 11.3 to 17.5 g/L when a heterologous lysine decarboxylase gene cadA was expressed from a theta-replicating rather than a rolling-circle replicating vector. The current work on inducible promoter systems and compatible theta- or rolling circle-replicating vectors is an important extension of the poorly developed B. methanolicus genetic toolbox, valuable for genetic engineering and further exploration of this bacterium. PMID:27713731

Epidemiologic and Genetic Aspects of Spina Bifida and Other Neural Tube Defects

ERIC Educational Resources Information Center

Au, Kit Sing; Ashley-Koch, Allison; Northrup, Hope

2010-01-01

The worldwide incidence of neural tube defects (NTDs) ranges from 1.0 to 10.0 per 1,000 births with almost equal frequencies between two major categories: anencephaly and spina bifida (SB). Epidemiological studies have provided valuable insight for (a) researchers to identify nongenetic and genetic factors contributing to etiology, (b) public…

Characterization and Recovery of Valuables from Waste Copper Smelting Slag

NASA Astrophysics Data System (ADS)

Prince, Sarfo; Young, Jamie; Ma, Guojun; Young, Courtney

Silicate slags produced from smelting copper concentrates contains valuables such as Cu and Fe as well as heavy metals such as Pb and As which are considered hazardous. In this paper, various slags were characterized with several techniques: SEM-MLA, XRD, TG-DTA and ICP-MS. A recovery process was developed to separate the valuables from the silicates thereby producing value-added products and simultaneously reducing environmental concerns. Results show that the major phases in air-cooled slag are fayalite and magnetite whereas the water-cooled slag is amorphous. Thermodynamic calculations and carbothermal reduction experiments indicate that most of Cu and Fe can be recovered from both types using minor amounts of lime and alumina and treating at 1350°C (1623K) or higher for 30 min. The secondary slag can be recycled to the glass and/or ceramic industries.

Software tool for data mining and its applications

NASA Astrophysics Data System (ADS)

Yang, Jie; Ye, Chenzhou; Chen, Nianyi

2002-03-01

A software tool for data mining is introduced, which integrates pattern recognition (PCA, Fisher, clustering, hyperenvelop, regression), artificial intelligence (knowledge representation, decision trees), statistical learning (rough set, support vector machine), computational intelligence (neural network, genetic algorithm, fuzzy systems). It consists of nine function models: pattern recognition, decision trees, association rule, fuzzy rule, neural network, genetic algorithm, Hyper Envelop, support vector machine, visualization. The principle and knowledge representation of some function models of data mining are described. The software tool of data mining is realized by Visual C++ under Windows 2000. Nonmonotony in data mining is dealt with by concept hierarchy and layered mining. The software tool of data mining has satisfactorily applied in the prediction of regularities of the formation of ternary intermetallic compounds in alloy systems, and diagnosis of brain glioma.

Substrate topography: A valuable in vitro tool, but a clinical red herring for in vivo tenogenesis.

PubMed

English, Andrew; Azeem, Ayesha; Spanoudes, Kyriakos; Jones, Eleanor; Tripathi, Bhawana; Basu, Nandita; McNamara, Karrina; Tofail, Syed A M; Rooney, Niall; Riley, Graham; O'Riordan, Alan; Cross, Graham; Hutmacher, Dietmar; Biggs, Manus; Pandit, Abhay; Zeugolis, Dimitrios I

2015-11-01

Controlling the cell-substrate interactions at the bio-interface is becoming an inherent element in the design of implantable devices. Modulation of cellular adhesion in vitro, through topographical cues, is a well-documented process that offers control over subsequent cellular functions. However, it is still unclear whether surface topography can be translated into a clinically functional response in vivo at the tissue/device interface. Herein, we demonstrated that anisotropic substrates with a groove depth of ∼317nm and ∼1988nm promoted human tenocyte alignment parallel to the underlying topography in vitro. However, the rigid poly(lactic-co-glycolic acid) substrates used in this study upregulated the expression of chondrogenic and osteogenic genes, indicating possible tenocyte trans-differentiation. Of significant importance is that none of the topographies assessed (∼37nm, ∼317nm and ∼1988nm groove depth) induced extracellular matrix orientation parallel to the substrate orientation in a rat patellar tendon model. These data indicate that two-dimensional imprinting technologies are useful tools for in vitro cell phenotype maintenance, rather than for organised neotissue formation in vivo, should multifactorial approaches that consider both surface topography and substrate rigidity be established. Herein, we ventured to assess the influence of parallel groves, ranging from nano- to micro-level, on tenocytes response in vitro and on host response using a tendon and a subcutaneous model. In vitro analysis indicates that anisotropically ordered micro-scale grooves, as opposed to nano-scale grooves, maintain physiological cell morphology. The rather rigid PLGA substrates appeared to induce trans-differentiation towards chondrogenic and/or steogenic lineage, as evidence by TILDA gene analysis. In vivo data in both tendon and subcutaneous models indicate that none of the substrates induced bidirectional host cell and tissue growth. Collective, these

Genetics Home Reference: prolidase deficiency

MedlinePlus

... mutations as a tool to investigate structure-function relationship. J Hum Genet. 2004;49(9):500-6. ... for Links Data Files & API Site Map Subscribe Customer Support USA.gov Copyright Privacy Accessibility FOIA Viewers & ...

Redefining the genetics of Murine Gammaherpesvirus 68 via transcriptome-based annotation

PubMed Central

Johnson, L. Steven; Willert, Erin K.; Virgin, Herbert W.

2010-01-01

Summary Viral genetic studies often focus on large open reading frames (ORFs) identified during genome annotation (ORF-based annotation). Here we provide a tool and software set for defining gene expression by murine gammaherpesvirus 68 (γHV68) nucleotide-by-nucleotide across the 119,450 basepair (bp) genome. These tools allowed us to determine that viral RNA expression was significantly more complex than predicted from ORF-based annotation, including over 73,000 nucleotides of unexpected transcription within 30 expressed genomic regions (EGRs). Approximately 90% of this RNA expression was antisense to genomic regions containing known large ORFs. We verified the existence of novel transcripts in three EGRs using standard methods to validate the approach and determined which parts of the transcriptome depend on protein or viral DNA synthesis. This redefines the genetic map of γHV68, indicates that herpesviruses contain significantly more genetic complexity than predicted from ORF-based genome annotations, and provides new tools and approaches for viral genetic studies. PMID:20542255

Application of high-resolution melting analysis for authenticity testing of valuable Dendrobium commercial products.

PubMed

Dong, Xiaoman; Jiang, Chao; Yuan, Yuan; Peng, Daiyin; Luo, Yuqin; Zhao, Yuyang; Huang, Luqi

2018-01-01

The accurate identification of botanical origin in commercial products is important to ensure food authenticity and safety for consumers. The Dendrobium species have long been commercialised as functional food supplements and herbal medicines in Asia. Three valuable Dendrobium species, namely Dendrobium officinale, D. huoshanense and D. moniliforme, are often mutually adulterated in trade products in pursuit of higher profit. In this paper, a rapid and reliable semi-quantitative method for identifying the botanical origin of Dendrobium products in terminal markets was developed using high-resolution melting (HRM) analysis with specific primer pairs to target the trnL-F region. The HRM analysis method detected amounts of D. moniliforme adulterants as low as 1% in D. huoshanense or D. officinale products. The results have demonstrated that HRM analysis is a fast and effective tool for the differentiation of these Dendrobium species both for their authenticity as well as for the semi-quantitative determination of the purity of their processed products. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Genetically engineered mouse models of melanoma.

PubMed

Pérez-Guijarro, Eva; Day, Chi-Ping; Merlino, Glenn; Zaidi, M Raza

2017-06-01

Melanoma is a complex disease that exhibits highly heterogeneous etiological, histopathological, and genetic features, as well as therapeutic responses. Genetically engineered mouse (GEM) models provide powerful tools to unravel the molecular mechanisms critical for melanoma development and drug resistance. Here, we expound briefly the basis of the mouse modeling design, the available technology for genetic engineering, and the aspects influencing the use of GEMs to model melanoma. Furthermore, we describe in detail the currently available GEM models of melanoma. Cancer 2017;123:2089-103. © 2017 American Cancer Society. © 2017 American Cancer Society.

Genetic diversity and stock identification of small abalone (Haliotis diversicolor) in Taiwan and Japan

PubMed Central

Hsu, Te-Hua; Gwo, Jin-Chywan

2017-01-01

Small abalone (Haliotis diversicolor) is a commercially valuable species for both fisheries and aquaculture. The production of annual farmed small abalone in Taiwan, once the highest in the world, has dramatically decreased in the past 15 years, and currently, the industry is close to collapse. Understanding the genetic diversity of small abalone and developing stock identification methods will be useful for genetic breeding, restoring collapsed stocks, managing stocks, and preventing illegal trade. We investigated 307 cultured and wild individuals from Taiwan, Japan, and Bali Island (Indonesia) by using the mitochondrial cytochrome c oxidase subunit I (COI) gene. Network analysis of mtDNA COI gene sequences revealed that the individuals collected from Taiwan, Japan, and Indonesia could be identified, and showed significant genetic divergence. In addition, the Indonesian population (Haliotis diversicolor squamata) was significantly different from the other populations and might need to be considered a separate species. We discovered a single nucleotide polymorphism marker in the mtDNA COI gene that can be used to distinguish the Taiwan population from the Japan population. We also developed a polymerase chain reaction-restriction fragment length polymorphism method for rapid detection. Furthermore, we could identify the cultured stocks, wild population, and hybrid stocks by using 6 microsatellites and amplified fragment length polymorphism. This study contributes useful tools for stock identification and the production of high-disease resistant small abalone strains (Japan × Taiwan or Taiwan × Japan). Efforts should be made to avoid unintentional random genetic mixing of the Taiwan population with the Japan population and subsequent breakdown of population differentiation, which impair local adaptation of the Taiwan wild population. Molecular markers revealed a split between the Taiwan and Japan populations, and the existence of a possible barrier to the free

Genetic diversity and stock identification of small abalone (Haliotis diversicolor) in Taiwan and Japan.

PubMed

Hsu, Te-Hua; Gwo, Jin-Chywan

2017-01-01

Small abalone (Haliotis diversicolor) is a commercially valuable species for both fisheries and aquaculture. The production of annual farmed small abalone in Taiwan, once the highest in the world, has dramatically decreased in the past 15 years, and currently, the industry is close to collapse. Understanding the genetic diversity of small abalone and developing stock identification methods will be useful for genetic breeding, restoring collapsed stocks, managing stocks, and preventing illegal trade. We investigated 307 cultured and wild individuals from Taiwan, Japan, and Bali Island (Indonesia) by using the mitochondrial cytochrome c oxidase subunit I (COI) gene. Network analysis of mtDNA COI gene sequences revealed that the individuals collected from Taiwan, Japan, and Indonesia could be identified, and showed significant genetic divergence. In addition, the Indonesian population (Haliotis diversicolor squamata) was significantly different from the other populations and might need to be considered a separate species. We discovered a single nucleotide polymorphism marker in the mtDNA COI gene that can be used to distinguish the Taiwan population from the Japan population. We also developed a polymerase chain reaction-restriction fragment length polymorphism method for rapid detection. Furthermore, we could identify the cultured stocks, wild population, and hybrid stocks by using 6 microsatellites and amplified fragment length polymorphism. This study contributes useful tools for stock identification and the production of high-disease resistant small abalone strains (Japan × Taiwan or Taiwan × Japan). Efforts should be made to avoid unintentional random genetic mixing of the Taiwan population with the Japan population and subsequent breakdown of population differentiation, which impair local adaptation of the Taiwan wild population. Molecular markers revealed a split between the Taiwan and Japan populations, and the existence of a possible barrier to the free

Infrared Thermal Imaging as a Tool in University Physics Education

ERIC Educational Resources Information Center

Mollmann, Klaus-Peter; Vollmer, Michael

2007-01-01

Infrared thermal imaging is a valuable tool in physics education at the university level. It can help to visualize and thereby enhance understanding of physical phenomena from mechanics, thermal physics, electromagnetism, optics and radiation physics, qualitatively as well as quantitatively. We report on its use as lecture demonstrations, student…

The Culture Audit: A Leadership Tool for Assessment and Strategic Planning in Diverse Schools and Colleges

ERIC Educational Resources Information Center

Bustamante, Rebecca M.

2006-01-01

This module is designed to introduce educational leaders to an organizational assessment tool called a "culture audit." Literature on organizational cultural competence suggests that culture audits are a valuable tool for determining how well school policies, programs, and practices respond to the needs of diverse groups and prepare…

Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

PubMed

Zong, Jian-Wei; Zhao, Tian-Tian; Ma, Qing-Hua; Liang, Li-Song; Wang, Gui-Xi

2015-01-01

Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR) markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777). According to the coefficient of genetic differentiation (Fst = 0.1215), genetic variation within the populations (87.85%) were remarkably higher than among populations (12.15%). The average gene flow (Nm = 1.8080) significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080) among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages) dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km) among populations (r = 0.419, P = 0.005), suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic distance. These

Re-evaluating causal modeling with mantel tests in landscape genetics

Treesearch

Samuel A. Cushman; Tzeidle N. Wasserman; Erin L. Landguth; Andrew J. Shirk

2013-01-01

The predominant analytical approach to associate landscape patterns with gene flow processes is based on the association of cost distances with genetic distances between individuals. Mantel and partial Mantel tests have been the dominant statistical tools used to correlate cost distances and genetic distances in landscape genetics. However, the inherent high...

How to Design a Genetic Mating Scheme: A Basic Training Package for Drosophila Genetics

PubMed Central

Roote, John; Prokop, Andreas

2013-01-01

Drosophila melanogaster is a powerful model organism for biological research. The essential and common instrument of fly research is genetics, the art of applying Mendelian rules in the specific context of Drosophila with its unique classical genetic tools and the breadth of modern genetic tools and strategies brought in by molecular biology, transgenic technologies and the use of recombinases. Training newcomers to fly genetics is a complex and time-consuming task but too important to be left to chance. Surprisingly, suitable training resources for beginners currently are not available. Here we provide a training package for basic Drosophila genetics, designed to ensure that basic knowledge on all key areas is covered while reducing the time invested by trainers. First, a manual introduces to fly history, rationale for mating schemes, fly handling, Mendelian rules in fly, markers and balancers, mating scheme design, and transgenic technologies. Its self-study is followed by a practical training session on gender and marker selection, introducing real flies under the dissecting microscope. Next, through self-study of a PowerPoint presentation, trainees are guided step-by-step through a mating scheme. Finally, to consolidate knowledge, trainees are asked to design similar mating schemes reflecting routine tasks in a fly laboratory. This exercise requires individual feedback but also provides unique opportunities for trainers to spot weaknesses and strengths of each trainee and take remedial action. This training package is being successfully applied at the Manchester fly facility and may serve as a model for further training resources covering other aspects of fly research. PMID:23390611

The genetics of dystonia: new twists in an old tale

PubMed Central

Charlesworth, Gavin; Bhatia, Kailash P.

2013-01-01

Dystonia is a common movement disorder seen by neurologists in clinic. Genetic forms of the disease are important to recognize clinically and also provide valuable information about possible pathogenic mechanisms within the wider disorder. In the past few years, with the advent of new sequencing technologies, there has been a step change in the pace of discovery in the field of dystonia genetics. In just over a year, four new genes have been shown to cause primary dystonia (CIZ1, ANO3, TUBB4A and GNAL), PRRT2 has been identified as the cause of paroxysmal kinesigenic dystonia and other genes, such as SLC30A10 and ATP1A3, have been linked to more complicated forms of dystonia or new phenotypes. In this review, we provide an overview of the current state of knowledge regarding genetic forms of dystonia—related to both new and well-known genes alike—and incorporating genetic, clinical and molecular information. We discuss the mechanistic insights provided by the study of the genetic causes of dystonia and provide a helpful clinical algorithm to aid clinicians in correctly predicting the genetic basis of various forms of dystonia. PMID:23775978

Development of Multifunctional Magnetic Nanoparticles for Genetic Engineering and Tracking of Neural Stem Cells.

PubMed

Adams, Christopher; Israel, Liron Limor; Ostrovsky, Stella; Taylor, Arthur; Poptani, Harish; Lellouche, Jean-Paul; Chari, Divya

2016-04-06

Genetic modification of cell transplant populations and cell tracking ability are key underpinnings for effective cell therapies. Current strategies to achieve these goals utilize methods which are unsuitable for clinical translation because of related safety issues, and multiple protocol steps adding to cost and complexity. Multifunctional magnetic nanoparticles (MNPs) offering dual mode gene delivery and imaging contrast capacity offer a valuable tool in this context. Despite their key benefits, there is a critical lack of neurocompatible and multifunctional particles described for use with transplant populations for neurological applications. Here, a systematic screen of MNPs (using a core shown to cause contrast in magnetic resonance imaging (MRI)) bearing various surface chemistries (polyethylenimine (PEI) and oxidized PEI and hybrids of oxidized PEI/alginic acid, PEI/chitosan and PEI/polyamidoamine) is performed to test their ability to genetically engineer neural stem cells (NSCs; a cell population of high clinical relevance for central nervous system disorders). It is demonstrated that gene delivery to NSCs can be safely achieved using two of the developed formulations (PEI and oxPEI/alginic acid) when used in conjunction with oscillating magnetofection technology. After transfection, intracellular particles can be detected by histological procedures with labeled cells displaying contrast in MRI (for real time cell tracking). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

FINDbase: a relational database recording frequencies of genetic defects leading to inherited disorders worldwide.

PubMed

van Baal, Sjozef; Kaimakis, Polynikis; Phommarinh, Manyphong; Koumbi, Daphne; Cuppens, Harry; Riccardino, Francesca; Macek, Milan; Scriver, Charles R; Patrinos, George P

2007-01-01

Frequency of INherited Disorders database (FINDbase) (http://www.findbase.org) is a relational database, derived from the ETHNOS software, recording frequencies of causative mutations leading to inherited disorders worldwide. Database records include the population and ethnic group, the disorder name and the related gene, accompanied by links to any corresponding locus-specific mutation database, to the respective Online Mendelian Inheritance in Man entries and the mutation together with its frequency in that population. The initial information is derived from the published literature, locus-specific databases and genetic disease consortia. FINDbase offers a user-friendly query interface, providing instant access to the list and frequencies of the different mutations. Query outputs can be either in a table or graphical format, accompanied by reference(s) on the data source. Registered users from three different groups, namely administrator, national coordinator and curator, are responsible for database curation and/or data entry/correction online via a password-protected interface. Databaseaccess is free of charge and there are no registration requirements for data querying. FINDbase provides a simple, web-based system for population-based mutation data collection and retrieval and can serve not only as a valuable online tool for molecular genetic testing of inherited disorders but also as a non-profit model for sustainable database funding, in the form of a 'database-journal'.

Chemical genetics-based development of small molecules targeting hepatitis C virus.

PubMed

Jin, Guanghai; Lee, Jisu; Lee, Kyeong

2017-09-01

Hepatitis C virus (HCV) infection is a major worldwide problem that has emerged as one of the most significant diseases affecting humans. There are currently no vaccines or efficient therapies without side effects, despite today's advanced medical technology. Currently, the common therapy for most patients (i.e. genotype 1) is combination of HCV-specific direct-acting antivirals (DAAs). Up to 2011, the standard of care (SOC) was a combination of peg-IFNα with ribavirin (RBV). After approval of NS3/4A protease inhibitor, SOC was peg-IFNα and RBV with either the first-generation DAAs boceprevir or telaprevir. In the past several years, various novel small molecules have been discovered and some of them (i.e., HCV polymerase, protease, helicase and entry inhibitors) have undergone clinical trials. Between 2013 and 2016, the second-generation DAA drugs simeprevir, asunaprevir, daclatasvir, dasabuvir, sofosbuvir, and elbasvir were approved, as well as the combinational drugs Harvoni ® , Zepatier ® , Technivie ® , and Epclusa ® . A number of reviews have been recently published describing the structure-activity relationship (SAR) in the development of HCV inhibitors and outlining current therapeutic approaches to hepatitis C infection. Target identification involves studying a drug's mechanism of action (MOA), and a variety of target identification methods have been developed in the past few years. Chemical biology has emerged as a powerful tool for studying biological processes using small molecules. The use of chemical genetic methods is a valuable strategy for studying the molecular mechanisms of the viral lifecycle and screening for anti-viral agents. Two general screening approaches have been employed: forward and reverse chemical genetics. This review reveals information on the small molecules in HCV drug discovery by using chemical genetics for targeting the HCV protein and describes successful examples of targets identified with these methods.

Leaf phenomics: a systematic reverse genetic screen for Arabidopsis leaf mutants.

PubMed

Wilson-Sánchez, David; Rubio-Díaz, Silvia; Muñoz-Viana, Rafael; Pérez-Pérez, José Manuel; Jover-Gil, Sara; Ponce, María Rosa; Micol, José Luis

2014-09-01

The study and eventual manipulation of leaf development in plants requires a thorough understanding of the genetic basis of leaf organogenesis. Forward genetic screens have identified hundreds of Arabidopsis mutants with altered leaf development, but the genome has not yet been saturated. To identify genes required for leaf development we are screening the Arabidopsis Salk Unimutant collection. We have identified 608 lines that exhibit a leaf phenotype with full penetrance and almost constant expressivity and 98 additional lines with segregating mutant phenotypes. To allow indexing and integration with other mutants, the mutant phenotypes were described using a custom leaf phenotype ontology. We found that the indexed mutation is present in the annotated locus for 78% of the 553 mutants genotyped, and that in half of these the annotated T-DNA is responsible for the phenotype. To quickly map non-annotated T-DNA insertions, we developed a reliable, cost-effective and easy method based on whole-genome sequencing. To enable comprehensive access to our data, we implemented a public web application named PhenoLeaf (http://genetics.umh.es/phenoleaf) that allows researchers to query the results of our screen, including text and visual phenotype information. We demonstrated how this new resource can facilitate gene function discovery by identifying and characterizing At1g77600, which we found to be required for proximal-distal cell cycle-driven leaf growth, and At3g62870, which encodes a ribosomal protein needed for cell proliferation and chloroplast function. This collection provides a valuable tool for the study of leaf development, characterization of biomass feedstocks and examination of other traits in this fundamental photosynthetic organ. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

A modeling tool to support decision making in future hydropower development in Chile

NASA Astrophysics Data System (ADS)

Vicuna, S.; Hermansen, C.; Cerda, J. P.; Olivares, M. A.; Gomez, T. I.; Toha, E.; Poblete, D.; Mao, L.; Falvey, M. J.; Pliscoff, P.; Melo, O.; Lacy, S.; Peredo, M.; Marquet, P. A.; Maturana, J.; Gironas, J. A.

2017-12-01

Modeling tools support planning by providing transparent means to assess the outcome of natural resources management alternatives within technical frameworks in the presence of conflicting objectives. Such tools, when employed to model different scenarios, complement discussion in a policy-making context. Examples of practical use of this type of tool exist, such as the Canadian public forest management, but are not common, especially in the context of developing countries. We present a tool to support the selection from a portfolio of potential future hydropower projects in Chile. This tool, developed by a large team of researchers under the guidance of the Chilean Energy Ministry, is especially relevant in the context of evident regionalism, skepticism and change in societal values in a country that has achieved a sustained growth alongside increased demands from society. The tool operates at a scale of a river reach, between 1-5 km long, on a domain that can be defined according to the scale needs of the related discussion, and its application can vary from river basins to regions or other spatial configurations that may be of interest. The tool addresses both available hydropower potential and the existence (inferred or observed) of other ecological, social, cultural and productive characteristics of the territory which are valuable to society, and provides a means to evaluate their interaction. The occurrence of each of these other valuable characteristics in the territory is measured by generating a presence-density score for each. Considering the level of constraint each characteristic imposes on hydropower development, they are weighted against each other and an aggregate score is computed. With this information, optimal trade-offs are computed between additional hydropower capacity and valuable local characteristics over the entire domain, using the classical knapsack 0-1 optimization algorithm. Various scenarios of different weightings and hydropower

Genetic diversity of high performance cultivars of upland and irrigated Brazilian rice.

PubMed

Coelho, G R C; Brondani, C; Hoffmann, L V; Valdisser, P A M R; Borba, T C O; Mendonça, J A; Rodrigues, L A; de Menezes, I P P

2017-09-21

The objective of this study was to analyze the diversity and discrimination of high-performance Brazilian rice cultivars using microsatellite markers. Twenty-nine rice cultivars belonging to EMBRAPA Arroz e Feijão germplasm bank in Brazil were genotyped by 24 SSR markers to establish their structure and genetic discrimination. It was demonstrated that the analyzed germplasm of rice presents an expressive and significant genetic diversity with low heterogeneity among the cultivars. All 29 cultivars were differentiated genetically, and were organized into two groups related to their upland and irrigated cultivation systems. These groups showed a high genetic differentiation, with greater diversity within the group that includes the cultivars for irrigated system. The genotyping data of these cultivars, with the morphological e phenotypical data, are valuable information to be used by rice breeding programs to develop new improved cultivars.

Lentiviral vectors and cardiovascular diseases: a genetic tool for manipulating cardiomyocyte differentiation and function.

PubMed

Di Pasquale, E; Latronico, M V G; Jotti, G S; Condorelli, G

2012-06-01

Engineered recombinant viral vectors are a powerful tool for vehiculating genetic information into mammalian cells. Because of their ability to infect both dividing and non-dividing cells with high efficiency, lentiviral vectors have gained particular interest for basic research and preclinical studies in the cardiovascular field. We review here the major applications for lentiviral-vector technology in the cardiovascular field: we will discuss their use in trailing gene expression during the induction of differentiation, in protocols for the isolation of cardiac cells and in the tracking of cardiac cells after transplantation in vivo; we will also describe lentivirally-mediated gene delivery uses, such as the induction of a phenotype of interest in a target cell or the treatment of cardiovascular diseases. In addition, a section of the review will be dedicated to reprogramming approaches, focusing attention on the generation of pluripotent stem cells and on transdifferentiation, two emerging strategies for the production of cardiac myocytes from human cells and for the investigation of human diseases. Finally, in order to give a perspective on their future clinical use we will critically discuss advantages and disadvantages of lentivirus-based strategies for the treatment of cardiovascular diseases.

Tools for Observation: Art and the Scientific Process

NASA Astrophysics Data System (ADS)

Pettit, E. C.; Coryell-Martin, M.; Maisch, K.

2015-12-01

Art can support the scientific process during different phases of a scientific discovery. Art can help explain and extend the scientific concepts for the general public; in this way art is a powerful tool for communication. Art can aid the scientist in processing and interpreting the data towards an understanding of the concepts and processes; in this way art is powerful - if often subconscious - tool to inform the process of discovery. Less often acknowledged, art can help engage students and inspire scientists during the initial development of ideas, observations, and questions; in this way art is a powerful tool to develop scientific questions and hypotheses. When we use art as a tool for communication of scientific discoveries, it helps break down barriers and makes science concepts less intimidating and more accessible and understandable for the learner. Scientists themselves use artistic concepts and processes - directly or indirectly - to help deepen their understanding. Teachers are following suit by using art more to stimulate students' creative thinking and problem solving. We show the value of teaching students to use the artistic "way of seeing" to develop their skills in observation, questioning, and critical thinking. In this way, art can be a powerful tool to engage students (from elementary to graduate) in the beginning phase of a scientific discovery, which is catalyzed by inquiry and curiosity. Through qualitative assessment of the Girls on Ice program, we show that many of the specific techniques taught by art teachers are valuable for science students to develop their observation skills. In particular, the concepts of contour drawing, squinting, gesture drawing, inverted drawing, and others can provide valuable training for student scientists. These art techniques encourage students to let go of preconceptions and "see" the world (the "data") in new ways they help students focus on both large-scale patterns and small-scale details.

Burkholderia thailandensis: Genetic Manipulation.

PubMed

Garcia, Erin C

2017-05-16

Burkholderia thailandensis is a Gram-negative bacterium endemic to Southeast Asian and northern Australian soils. It is non-pathogenic; therefore, it is commonly used as a model organism for the related human pathogens Burkholderia mallei and Burkholderia pseudomallei. B. thailandensis is relatively easily genetically manipulated and a variety of robust genetic tools can be used in this organism. This unit describes protocols for conjugation, natural transformation, mini-Tn7 insertion, and allelic exchange in B. thailandensis. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Per-operative vibration analysis: a valuable tool for defining correct stem insertion: preliminary report.

PubMed

Mulier, Michiel; Pastrav, Cesar; Van der Perre, Georges

2008-01-01

Defining the stem insertion end point during total hip replacement still relies on the surgeon's feeling. When a custom-made stem prosthesis with an optimal fit into the femoral canal is used, the risk of per-operative fractures is even greater than with standard prostheses. Vibration analysis is used in other clinical settings and has been tested as a means to detect optimal stem insertion in the laboratory. The first per-operative use of vibration analysis during non-cemented custom-made stem insertion in 30 patients is reported here. Thirty patients eligible for total hip replacement with uncemented stem prosthesis were included. The neck of the stem was connected with a shaker that emitted white noise as excitation signal and an impedance head that measured the frequency response. The response signal was sent to a computer that analyzed the frequency response function after each insertion phase. A technician present in the operating theatre but outside the laminated airflow provided feed-back to the surgeon. The correlation index between the frequency response function measured during the last two insertion hammering sessions was >0.99 in 86.7% of the cases. In four cases the surgeon stopped the insertion procedure because of a perceived risk of fracture. Two special cases illustrating the potential benefit of per-operative vibration analysis are described. The results of intra-operative vibration analysis indicate that this technique may be a useful tool assisting the orthopaedic surgeon in defining the insertion endpoint of the stem. The development of a more user-friendly device is therefore warranted.

λ5-Phosphorus-Containing α-Diazo Compounds: A Valuable Tool for Accessing Phosphorus-Functionalized Molecules.

PubMed

Marinozzi, Maura; Pertusati, Fabrizio; Serpi, Michaela

2016-11-23

The compounds characterized by the presence of a λ 5 -phosphorus functionality at the α-position with respect to the diazo moiety, here referred to as λ 5 -phosphorus-containing α-diazo compounds (PCDCs), represent a vast class of extremely versatile reagents in organic chemistry and are particularly useful in the preparation of phosphonate- and phosphinoxide-functionalized molecules. Indeed, thanks to the high reactivity of the diazo moiety, PCDCs can be induced to undergo a wide variety of chemical transformations. Among them are carbon-hydrogen, as well as heteroatom-hydrogen insertion reactions, cyclopropanation, ylide formation, Wolff rearrangement, and cycloaddition reactions. PCDCs can be easily prepared from readily accessible precursors by a variety of different methods, such as diazotization, Bamford-Stevens-type elimination, and diazo transfer reactions. This evidence along with their relative stability and manageability make them appealing tools in organic synthesis. This Review aims to demonstrate the ongoing utility of PCDCs in the modern preparation of different classes of phosphorus-containing compounds, phosphonates, in particular. Furthermore, to address the lack of precedent collective papers, this Review also summarizes the methods for PCDCs preparation.

Genetic Diversity Analysis of Medicinally Important Horticultural Crop Aegle marmelos by ISSR Markers.

PubMed

Mujeeb, Farina; Bajpai, Preeti; Pathak, Neelam; Verma, Smita Rastogi

2017-01-01

Inter simple sequence repeat (ISSR) markers help in identifying and determining the extent of genetic diversity in cultivars. Here, we describe their application in determining the genetic diversity of bael (Aegle marmelos Corr.). Universal ISSR primers are selected and their marker characteristics such as polymorphism information content, effective multiplex ratio and marker index have been evaluated. ISSR-PCR is then performed using universal ISSR primers to generate polymorphic bands. This information is used to determine the degree of genetic similarity among the bael varieties/accessions by cluster analysis using unweighted pair-group method with arithmetic averages (UPGMA). This technology is valuable for biodiversity conservation and for making an efficient choice of parents in breeding programs.

TSPmap, a tool making use of traveling salesperson problem solvers in the efficient and accurate construction of high-density genetic linkage maps.

PubMed

Monroe, J Grey; Allen, Zachariah A; Tanger, Paul; Mullen, Jack L; Lovell, John T; Moyers, Brook T; Whitley, Darrell; McKay, John K

2017-01-01

Recent advances in nucleic acid sequencing technologies have led to a dramatic increase in the number of markers available to generate genetic linkage maps. This increased marker density can be used to improve genome assemblies as well as add much needed resolution for loci controlling variation in ecologically and agriculturally important traits. However, traditional genetic map construction methods from these large marker datasets can be computationally prohibitive and highly error prone. We present TSPmap , a method which implements both approximate and exact Traveling Salesperson Problem solvers to generate linkage maps. We demonstrate that for datasets with large numbers of genomic markers (e.g. 10,000) and in multiple population types generated from inbred parents, TSPmap can rapidly produce high quality linkage maps with low sensitivity to missing and erroneous genotyping data compared to two other benchmark methods, JoinMap and MSTmap . TSPmap is open source and freely available as an R package. With the advancement of low cost sequencing technologies, the number of markers used in the generation of genetic maps is expected to continue to rise. TSPmap will be a useful tool to handle such large datasets into the future, quickly producing high quality maps using a large number of genomic markers.

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

PubMed Central

2010-01-01

Background Genome-scale metabolic reconstructions under the Constraint Based Reconstruction and Analysis (COBRA) framework are valuable tools for analyzing the metabolic capabilities of organisms and interpreting experimental data. As the number of such reconstructions and analysis methods increases, there is a greater need for data uniformity and ease of distribution and use. Description We describe BiGG, a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest. Conclusions BiGG addresses a need in the systems biology community to have access to high quality curated metabolic models and reconstructions. It is freely available for academic use at http://bigg.ucsd.edu. PMID:20426874

MALDI-TOF mass spectrometry following short incubation on a solid medium is a valuable tool for rapid pathogen identification from positive blood cultures.

PubMed

Kohlmann, Rebekka; Hoffmann, Alexander; Geis, Gabriele; Gatermann, Sören

2015-01-01

approach allowed an optimized treatment recommendation. MALDI-TOF MS following 4h pre-culture is a valuable tool for rapid pathogen identification from positive blood cultures, allowing easy integration in diagnostic routine and the opportunity of considerably earlier treatment adaptation. Copyright © 2015 Elsevier GmbH. All rights reserved.

Genetics on the World Wide Web.

PubMed

Trangenstein, P A; Hetteberg, C

1998-11-01

Since 1990, when the Human Genome Project was initiated, the amount of genetic information on the World Wide Web (WWW) has grown substantially. The WWW has become an important resource for current, accurate, and reliable genetic information for health care professionals and the general public. The purpose of this article is to provide a variety of genetics-related WWW sites that are useful for all levels of practitioners interested in genetics. In selecting sites to be included in this article, a number of evaluation tools were reviewed. The primary concern was that these sites be reputable and provide accurate, timely information. A table of the WWW sites is included for quick easy reference.

Genetics and Genomics

USDA-ARS?s Scientific Manuscript database

Good progress is being made on genetics and genomics of sugar beet, however it is in process and the tools are now being generated and some results are being analyzed. The GABI BeetSeq project released a first draft of the sugar beet genome of KWS2320, a dihaploid (see http://bvseq.molgen.mpg.de/Gen...

The production of audiovisual teaching tools in minimally invasive surgery.

PubMed

Tolerton, Sarah K; Hugh, Thomas J; Cosman, Peter H

2012-01-01

Audiovisual learning resources have become valuable adjuncts to formal teaching in surgical training. This report discusses the process and challenges of preparing an audiovisual teaching tool for laparoscopic cholecystectomy. The relative value in surgical education and training, for both the creator and viewer are addressed. This audiovisual teaching resource was prepared as part of the Master of Surgery program at the University of Sydney, Australia. The different methods of video production used to create operative teaching tools are discussed. Collating and editing material for an audiovisual teaching resource can be a time-consuming and technically challenging process. However, quality learning resources can now be produced even with limited prior video editing experience. With minimal cost and suitable guidance to ensure clinically relevant content, most surgeons should be able to produce short, high-quality education videos of both open and minimally invasive surgery. Despite the challenges faced during production of audiovisual teaching tools, these resources are now relatively easy to produce using readily available software. These resources are particularly attractive to surgical trainees when real time operative footage is used. They serve as valuable adjuncts to formal teaching, particularly in the setting of minimally invasive surgery. Copyright © 2012 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

Genetic therapy for the nervous system

PubMed Central

Bowers, William J.; Breakefield, Xandra O.; Sena-Esteves, Miguel

2011-01-01

Genetic therapy is undergoing a renaissance with expansion of viral and synthetic vectors, use of oligonucleotides (RNA and DNA) and sequence-targeted regulatory molecules, as well as genetically modified cells, including induced pluripotent stem cells from the patients themselves. Several clinical trials for neurologic syndromes appear quite promising. This review covers genetic strategies to ameliorate neurologic syndromes of different etiologies, including lysosomal storage diseases, Alzheimer's disease and other amyloidopathies, Parkinson's disease, spinal muscular atrophy, amyotrophic lateral sclerosis and brain tumors. This field has been propelled by genetic technologies, including identifying disease genes and disruptive mutations, design of genomic interacting elements to regulate transcription and splicing of specific precursor mRNAs and use of novel non-coding regulatory RNAs. These versatile new tools for manipulation of genetic elements provide the ability to tailor the mode of genetic intervention to specific aspects of a disease state. PMID:21429918

Genetic therapy for the nervous system.

PubMed

Bowers, William J; Breakefield, Xandra O; Sena-Esteves, Miguel

2011-04-15

Genetic therapy is undergoing a renaissance with expansion of viral and synthetic vectors, use of oligonucleotides (RNA and DNA) and sequence-targeted regulatory molecules, as well as genetically modified cells, including induced pluripotent stem cells from the patients themselves. Several clinical trials for neurologic syndromes appear quite promising. This review covers genetic strategies to ameliorate neurologic syndromes of different etiologies, including lysosomal storage diseases, Alzheimer's disease and other amyloidopathies, Parkinson's disease, spinal muscular atrophy, amyotrophic lateral sclerosis and brain tumors. This field has been propelled by genetic technologies, including identifying disease genes and disruptive mutations, design of genomic interacting elements to regulate transcription and splicing of specific precursor mRNAs and use of novel non-coding regulatory RNAs. These versatile new tools for manipulation of genetic elements provide the ability to tailor the mode of genetic intervention to specific aspects of a disease state.

Desmopressin test during petrosal sinus sampling: a valuable tool to discriminate pituitary or ectopic ACTH-dependent Cushing's syndrome.

PubMed

Castinetti, F; Morange, I; Dufour, H; Jaquet, P; Conte-Devolx, B; Girard, N; Brue, T

2007-09-01

Corticotropin-releasing hormone (CRH)-stimulated petrosal sinus sampling is currently the gold standard method for the differential diagnosis between pituitary and ectopic ACTH-dependent Cushing's syndrome. Our objective was to determine sensitivity and specificity of desmopressin test during petrosal sinus sampling. Forty-three patients had petrosal sinus sampling because of the lack of visible adenoma on magnetic resonance imaging (MRI) and/or because of discordant cortisol response to high-dose dexamethasone suppression test. ACTH sampling was performed in an antecubital vein, right and left petrosal sinuses, then at each location 5 and 10 min after injection of desmopressin. Diagnosis was based on the ACTH ratio between petrosal sinus and humeral vein ACTH after desmopressin test. Diagnosis was confirmed after surgery. A receiver operating characteristics curve was used to determine optimal sensitivity and specificity. Thirty-six patients had Cushing's disease (CD) and seven had ectopic ACTH secretion. A ratio > 2 after desmopressin was found in 35 of the 36 cases of CD (sensitivity: 95%). A ratio < or = 2 was found in the seven patients with ectopic ACTH secretion (specificity: 100%). Sinus sampling was ineffective in determining the left or right localization of the adenoma (sensitivity = 50%). No major adverse effects were observed during or after the procedure. Desmopressin test during petrosal sinus sampling is a safe and effective diagnostic procedure in ACTH-dependent Cushing's syndrome. It thus represents a valuable alternative to CRH.

Genetic architecture of sex determination in fish: applications to sex ratio control in aquaculture

PubMed Central

Martínez, Paulino; Viñas, Ana M.; Sánchez, Laura; Díaz, Noelia; Ribas, Laia; Piferrer, Francesc

2014-01-01

Controlling the sex ratio is essential in finfish farming. A balanced sex ratio is usually good for broodstock management, since it enables to develop appropriate breeding schemes. However, in some species the production of monosex populations is desirable because the existence of sexual dimorphism, primarily in growth or first time of sexual maturation, but also in color or shape, can render one sex more valuable. The knowledge of the genetic architecture of sex determination (SD) is convenient for controlling sex ratio and for the implementation of breeding programs. Unlike mammals and birds, which show highly conserved master genes that control a conserved genetic network responsible for gonad differentiation (GD), a huge diversity of SD mechanisms has been reported in fish. Despite theory predictions, more than one gene is in many cases involved in fish SD and genetic differences have been observed in the GD network. Environmental factors also play a relevant role and epigenetic mechanisms are becoming increasingly recognized for the establishment and maintenance of the GD pathways. Although major genetic factors are frequently involved in fish SD, these observations strongly suggest that SD in this group resembles a complex trait. Accordingly, the application of quantitative genetics combined with genomic tools is desirable to address its study and in fact, when applied, it has frequently demonstrated a multigene trait interacting with environmental factors in model and cultured fish species. This scenario has notable implications for aquaculture and, depending upon the species, from chromosome manipulation or environmental control techniques up to classical selection or marker assisted selection programs, are being applied. In this review, we selected four relevant species or fish groups to illustrate this diversity and hence the technologies that can be used by the industry for the control of sex ratio: turbot and European sea bass, two reference species of

Fischer 344 and Lewis Rat Strains as a Model of Genetic Vulnerability to Drug Addiction

PubMed Central

Cadoni, Cristina

2016-01-01

Today it is well acknowledged that both nature and nurture play important roles in the genesis of psychopathologies, including drug addiction. Increasing evidence suggests that genetic factors contribute for at least 40–60% of the variation in liability to drug dependence. Human genetic studies suggest that multiple genes of small effect, rather than single genes, contribute to the genesis of behavioral psychopathologies. Therefore, the use of inbred rat strains might provide a valuable tool to identify differences, linked to genotype, important in liability to addiction and related disorders. In this regard, Lewis and Fischer 344 inbred rats have been proposed as a model of genetic vulnerability to drug addiction, given their innate differences in sensitivity to the reinforcing and rewarding effects of drugs of abuse, as well their different responsiveness to stressful stimuli. This review will provide evidence in support of this model for the study of the genetic influence on addiction vulnerability, with particular emphasis on differences in mesolimbic dopamine (DA) transmission, rewarding and emotional function. It will be highlighted that Lewis and Fischer 344 rats differ not only in several indices of DA transmission and adaptive changes following repeated drug exposure, but also in hypothalamic-pituitary-adrenal (HPA) axis responsiveness, influencing not only the ability of the individual to cope with stressful events, but also interfering with rewarding and motivational processes, given the influence of corticosteroids on dopamine neuron functionality. Further differences between the two strains, as impulsivity or anxiousness, might contribute to their different proneness to addiction, and likely these features might be linked to their different DA neurotransmission plasticity. Although differences in other neurotransmitter systems might deserve further investigation, results from the reviewed studies might open new vistas in understanding aberrant

Fischer 344 and Lewis Rat Strains as a Model of Genetic Vulnerability to Drug Addiction.

PubMed

Cadoni, Cristina

2016-01-01

Today it is well acknowledged that both nature and nurture play important roles in the genesis of psychopathologies, including drug addiction. Increasing evidence suggests that genetic factors contribute for at least 40-60% of the variation in liability to drug dependence. Human genetic studies suggest that multiple genes of small effect, rather than single genes, contribute to the genesis of behavioral psychopathologies. Therefore, the use of inbred rat strains might provide a valuable tool to identify differences, linked to genotype, important in liability to addiction and related disorders. In this regard, Lewis and Fischer 344 inbred rats have been proposed as a model of genetic vulnerability to drug addiction, given their innate differences in sensitivity to the reinforcing and rewarding effects of drugs of abuse, as well their different responsiveness to stressful stimuli. This review will provide evidence in support of this model for the study of the genetic influence on addiction vulnerability, with particular emphasis on differences in mesolimbic dopamine (DA) transmission, rewarding and emotional function. It will be highlighted that Lewis and Fischer 344 rats differ not only in several indices of DA transmission and adaptive changes following repeated drug exposure, but also in hypothalamic-pituitary-adrenal (HPA) axis responsiveness, influencing not only the ability of the individual to cope with stressful events, but also interfering with rewarding and motivational processes, given the influence of corticosteroids on dopamine neuron functionality. Further differences between the two strains, as impulsivity or anxiousness, might contribute to their different proneness to addiction, and likely these features might be linked to their different DA neurotransmission plasticity. Although differences in other neurotransmitter systems might deserve further investigation, results from the reviewed studies might open new vistas in understanding aberrant

Methods for genetic transformation in Dendrobium.

PubMed

da Silva, Jaime A Teixeira; Dobránszki, Judit; Cardoso, Jean Carlos; Chandler, Stephen F; Zeng, Songjun

2016-03-01

The genetic transformation of Dendrobium orchids will allow for the introduction of novel colours, altered architecture and valuable traits such as abiotic and biotic stress tolerance. The orchid genus Dendrobium contains species that have both ornamental value and medicinal importance. There is thus interest in producing cultivars that have increased resistance to pests, novel horticultural characteristics such as novel flower colours, improved productivity, longer flower spikes, or longer post-harvest shelf-life. Tissue culture is used to establish clonal plants while in vitro flowering allows for the production of flowers or floral parts within a sterile environment, expanding the selection of explants that can be used for tissue culture or genetic transformation. The latter is potentially the most effective, rapid and practical way to introduce new agronomic traits into Dendrobium. Most (69.4 %) Dendrobium genetic transformation studies have used particle bombardment (biolistics) while 64 % have employed some form of Agrobacterium-mediated transformation. A singe study has explored ovary injection, but no studies exist on floral dip transformation. While most of these studies have involved the use of selector or reporter genes, there are now a handful of studies that have introduced genes for horticulturally important traits.

Macromedia Flash as a Tool for Mathematics Teaching and Learning

ERIC Educational Resources Information Center

Garofalo, Joe; Summers, Tim

2004-01-01

Macromedia Flash is a powerful and robust development tool. Because of its graphical, sound, and animation capabilities (and ubiquitous browser plug-in), major companies employ it in their website development (see www.nike.com or www.espn.com). These same features also make Flash a valuable environment for building multi-representational "movies"…

Development of a genetic tool for product regulation in the diverse British pig breed market.

PubMed

Wilkinson, Samantha; Archibald, Alan L; Haley, Chris S; Megens, Hendrik-Jan; Crooijmans, Richard P M A; Groenen, Martien A M; Wiener, Pamela; Ogden, Rob

2012-11-15

The application of DNA markers for the identification of biological samples from both human and non-human species is widespread and includes use in food authentication. In the food industry the financial incentive to substituting the true name of a food product with a higher value alternative is driving food fraud. This applies to British pork products where products derived from traditional pig breeds are of premium value. The objective of this study was to develop a genetic assay for regulatory authentication of traditional pig breed-labelled products in the porcine food industry in the United Kingdom. The dataset comprised of a comprehensive coverage of breed types present in Britain: 460 individuals from 7 traditional breeds, 5 commercial purebreds, 1 imported European breed and 1 imported Asian breed were genotyped using the PorcineSNP60 beadchip. Following breed-informative SNP selection, assignment power was calculated for increasing SNP panel size. A 96-plex assay created using the most informative SNPs revealed remarkably high genetic differentiation between the British pig breeds, with an average FST of 0.54 and Bayesian clustering analysis also indicated that they were distinct homogenous populations. The posterior probability of assignment of any individual of a presumed origin actually originating from that breed given an alternative breed origin was > 99.5% in 174 out of 182 contrasts, at a test value of log(LR) > 0. Validation of the 96-plex assay using independent test samples of known origin was successful; a subsequent survey of market samples revealed a high level of breed label conformity. The newly created 96-plex assay using selected markers from the PorcineSNP60 beadchip enables powerful assignment of samples to traditional breed origin and can effectively identify mislabelling, providing a highly effective tool for DNA analysis in food forensics.

Development of a genetic tool for product regulation in the diverse British pig breed market

PubMed Central

2012-01-01

Background The application of DNA markers for the identification of biological samples from both human and non-human species is widespread and includes use in food authentication. In the food industry the financial incentive to substituting the true name of a food product with a higher value alternative is driving food fraud. This applies to British pork products where products derived from traditional pig breeds are of premium value. The objective of this study was to develop a genetic assay for regulatory authentication of traditional pig breed-labelled products in the porcine food industry in the United Kingdom. Results The dataset comprised of a comprehensive coverage of breed types present in Britain: 460 individuals from 7 traditional breeds, 5 commercial purebreds, 1 imported European breed and 1 imported Asian breed were genotyped using the PorcineSNP60 beadchip. Following breed-informative SNP selection, assignment power was calculated for increasing SNP panel size. A 96-plex assay created using the most informative SNPs revealed remarkably high genetic differentiation between the British pig breeds, with an average FST of 0.54 and Bayesian clustering analysis also indicated that they were distinct homogenous populations. The posterior probability of assignment of any individual of a presumed origin actually originating from that breed given an alternative breed origin was > 99.5% in 174 out of 182 contrasts, at a test value of log(LR) > 0. Validation of the 96-plex assay using independent test samples of known origin was successful; a subsequent survey of market samples revealed a high level of breed label conformity. Conclusion The newly created 96-plex assay using selected markers from the PorcineSNP60 beadchip enables powerful assignment of samples to traditional breed origin and can effectively identify mislabelling, providing a highly effective tool for DNA analysis in food forensics. PMID:23150935

Contribution of genetics to ecological restoration.

PubMed

Mijangos, Jose Luis; Pacioni, Carlo; Spencer, Peter B S; Craig, Michael D

2015-01-01

Ecological restoration of degraded ecosystems has emerged as a critical tool in the fight to reverse and ameliorate the current loss of biodiversity and ecosystem services. Approaches derived from different genetic disciplines are extending the theoretical and applied frameworks on which ecological restoration is based. We performed a search of scientific articles and identified 160 articles that employed a genetic approach within a restoration context to shed light on the links between genetics and restoration. These articles were then classified on whether they examined association between genetics and fitness or the application of genetics in demographic studies, and on the way the studies informed restoration practice. Although genetic research in restoration is rapidly growing, we found that studies could make better use of the extensive toolbox developed by applied fields in genetics. Overall, 41% of reviewed studies used genetic information to evaluate or monitor restoration, and 59% provided genetic information to guide prerestoration decision-making processes. Reviewed studies suggest that restoration practitioners often overlook the importance of including genetic aspects within their restoration goals. Even though there is a genetic basis influencing the provision of ecosystem services, few studies explored this relationship. We provide a view of research gaps, future directions and challenges in the genetics of restoration. © 2014 John Wiley & Sons Ltd.

Estimation of the frequency of occult mutations for an autosomal recessive disease in the presence of genetic heterogeneity: application to genetic hearing loss disorders.

PubMed

Kimberling, William J

2005-11-01

The routine testing for pathologic mutation(s) in a patient's DNA has become the foundation of modern molecular genetic diagnosis. It is especially valuable when the phenotype shows genetic heterogeneity, and its importance will grow as treatments become genotype specific. However, the technology of mutation detection is imperfect and mutations are often missed. This can be especially troublesome when dealing with a recessive disorder where the combination of genetic heterogeneity and missed mutation creates an imprecision in the genotypic assessment of individuals who do not appear to have the expected complement of two pathologic mutations. This article describes a statistical approach to the estimation of the likelihood of a genetic diagnosis under these conditions. In addition to providing a means of testing for missed mutations, it also provides a method of estimating and testing for the presence of genetic heterogeneity in the absence of linkage data. Gene frequencies as well as estimates of sensitivity and specificity can be obtained as well. The test is applied to GJB2 recessive nonsyndromic deafness, Usher syndrome types Ib and IIa, and Pendred-enlarged vestibular aqueduct syndrome. Copyright 2005 Wiley-Liss, Inc.

Genetic characterization and improved genotyping of the dysferlin-deficient mouse strain Dysf (tm1Kcam).

PubMed

Wiktorowicz, Tatiana; Kinter, Jochen; Kobuke, Kazuhiro; Campbell, Kevin P; Sinnreich, Michael

2015-01-01

Mouse models of dysferlinopathies are valuable tools with which to investigate the pathomechanisms underlying these diseases and to test novel therapeutic strategies. One such mouse model is the Dysf (tm1Kcam) strain, which was generated using a targeting vector to replace a 12-kb region of the dysferlin gene and which features a progressive muscular dystrophy. A prerequisite for successful animal studies using genetic mouse models is an accurate genotyping protocol. Unfortunately, the lack of robustness of currently available genotyping protocols for the Dysf (tm1Kcam) mouse has prevented efficient colony management. Initial attempts to improve the genotyping protocol based on the published genomic structure failed. These difficulties led us to analyze the targeted locus of the dysferlin gene of the Dysf (tm1Kcam) mouse in greater detail. In this study we resequenced and analyzed the targeted locus of the Dysf (tm1Kcam) mouse and developed a novel PCR protocol for genotyping. We found that instead of a deletion, the dysferlin locus in the Dysf (tm1Kcam) mouse carries a targeted insertion. This genetic characterization enabled us to establish a reliable method for genotyping of the Dysf (tm1Kcam) mouse, and thus has made efficient colony management possible. Our work will make the Dysf (tm1Kcam) mouse model more attractive for animal studies of dysferlinopathies.

Applying Evolutionary Genetics to Developmental Toxicology and Risk Assessment

PubMed Central

Leung, Maxwell C. K.; Procter, Andrew C.; Goldstone, Jared V.; Foox, Jonathan; DeSalle, Robert; Mattingly, Carolyn J.; Siddall, Mark E.; Timme-Laragy, Alicia R.

2018-01-01

Evolutionary thinking continues to challenge our views on health and disease. Yet, there is a communication gap between evolutionary biologists and toxicologists in recognizing the connections among developmental pathways, high-throughput screening, and birth defects in humans. To increase our capability in identifying potential developmental toxicants in humans, we propose to apply evolutionary genetics to improve the experimental design and data interpretation with various in vitro and whole-organism models. We review five molecular systems of stress response and update 18 consensual cell-cell signaling pathways that are the hallmark for early development, organogenesis, and differentiation; and revisit the principles of teratology in light of recent advances in high-throughput screening, big data techniques, and systems toxicology. Multiscale systems modeling plays an integral role in the evolutionary approach to cross-species extrapolation. Phylogenetic analysis and comparative bioinformatics are both valuable tools in identifying and validating the molecular initiating events that account for adverse developmental outcomes in humans. The discordance of susceptibility between test species and humans (ontogeny) reflects their differences in evolutionary history (phylogeny). This synthesis not only can lead to novel applications in developmental toxicity and risk assessment, but also can pave the way for applying an evo-devo perspective to the study of developmental origins of health and disease. PMID:28267574

Genetic monitoring as a promising tool for conservation and management

Treesearch

Michael K. Schwartz; Gordon Luikart; Robin S. Waples

2007-01-01

In response to ever-increasing anthropogenic changes to natural ecosystems, regional, national and international organizations have established guidelines for monitoring biological diversity. Most monitoring programs, however, do not take full advantage of the potential afforded by molecular genetic markers, which can provide information relevant to both ecological and...

Predicting Gene Structure Changes Resulting from Genetic Variants via Exon Definition Features.

PubMed

Majoros, William H; Holt, Carson; Campbell, Michael S; Ware, Doreen; Yandell, Mark; Reddy, Timothy E

2018-04-25

Genetic variation that disrupts gene function by altering gene splicing between individuals can substantially influence traits and disease. In those cases, accurately predicting the effects of genetic variation on splicing can be highly valuable for investigating the mechanisms underlying those traits and diseases. While methods have been developed to generate high quality computational predictions of gene structures in reference genomes, the same methods perform poorly when used to predict the potentially deleterious effects of genetic changes that alter gene splicing between individuals. Underlying that discrepancy in predictive ability are the common assumptions by reference gene finding algorithms that genes are conserved, well-formed, and produce functional proteins. We describe a probabilistic approach for predicting recent changes to gene structure that may or may not conserve function. The model is applicable to both coding and noncoding genes, and can be trained on existing gene annotations without requiring curated examples of aberrant splicing. We apply this model to the problem of predicting altered splicing patterns in the genomes of individual humans, and we demonstrate that performing gene-structure prediction without relying on conserved coding features is feasible. The model predicts an unexpected abundance of variants that create de novo splice sites, an observation supported by both simulations and empirical data from RNA-seq experiments. While these de novo splice variants are commonly misinterpreted by other tools as coding or noncoding variants of little or no effect, we find that in some cases they can have large effects on splicing activity and protein products, and we propose that they may commonly act as cryptic factors in disease. The software is available from geneprediction.org/SGRF. bmajoros@duke.edu. Supplementary information is available at Bioinformatics online.

Clinical audit, a valuable tool to improve quality of care: General methodology and applications in nephrology.

PubMed

Esposito, Pasquale; Dal Canton, Antonio

2014-11-06

Evaluation and improvement of quality of care provided to the patients are of crucial importance in the daily clinical practice and in the health policy planning and financing. Different tools have been developed, including incident analysis, health technology assessment and clinical audit. The clinical audit consist of measuring a clinical outcome or a process, against well-defined standards set on the principles of evidence-based medicine in order to identify the changes needed to improve the quality of care. In particular, patients suffering from chronic renal diseases, present many problems that have been set as topics for clinical audit projects, such as hypertension, anaemia and mineral metabolism management. Although the results of these studies have been encouraging, demonstrating the effectiveness of audit, overall the present evidence is not clearly in favour of clinical audit. These findings call attention to the need to further studies to validate this methodology in different operating scenarios. This review examines the principle of clinical audit, focusing on experiences performed in nephrology settings.

Design of portable valuables touch alarm circuit

NASA Astrophysics Data System (ADS)

Li, Biqing; Li, Zhao

2017-03-01

In this paper, the name of the alarm is portable touch burglar alarm. It not only has the advantages of high sensitivity, small size and light weight, but it is easy on the trigger, the circuit is simple and easy to be implemented, besides, it works stably. This alarm is featured with simple design, convenient use, strong flexibility and reliable performance, thus it can be installed on the door or window and even can be carried on human's body. When the human body touches the metal valuables that need to be protected, the device will start the alarm equipment so as to make the bell keep ringing, and the alarm sound stops until the power is cut off.

Development of an Optimum Rescue Tool, Detailed Prototype Concept Design.

DTIC Science & Technology

1981-06-01

vAll Ai24 108 0VLOOKIN Of A1 OPTIU.M *t$CUI VOOL OITAILEO /D ..010 ",:N COAC IPT DES III AMETIc/01fI SANTA SAROARA CA IT A Ot SIN IT aL. -~ JUaI A...penetrate hardened metal structures of aircraft. A large number of tools are transported to the scene of a crashed air- craft. Valuable time is lost deciding...carrying system is necessary for transport of the tool to allow the operator free use of his hands. Such a system would be a shoulder sling assembly

Power Pack Your Center Brochure--Keys To Developing an Effective Marketing Tool.

ERIC Educational Resources Information Center

Wassom, Julie

2000-01-01

Suggests that a center's informational brochure can be either a valuable marketing tool or an expensive elimination incentive. Provides a list of five questions center directors should address before beginning the design and development of the center brochure. Lists seven guidelines for brochure development. (SD)

Educational Tool for Optimal Controller Tuning Using Evolutionary Strategies

ERIC Educational Resources Information Center

Carmona Morales, D.; Jimenez-Hornero, J. E.; Vazquez, F.; Morilla, F.

2012-01-01

In this paper, an optimal tuning tool is presented for control structures based on multivariable proportional-integral-derivative (PID) control, using genetic algorithms as an alternative to traditional optimization algorithms. From an educational point of view, this tool provides students with the necessary means to consolidate their knowledge on…

PATENTS IN GENOMICS AND HUMAN GENETICS

PubMed Central

Cook-Deegan, Robert; Heaney, Christopher

2010-01-01

Genomics and human genetics are scientifically fundamental and commercially valuable. These fields grew to prominence in an era of growth in government and nonprofit research funding, and of even greater growth of privately funded research and development in biotechnology and pharmaceuticals. Patents on DNA technologies are a central feature of this story, illustrating how patent law adapts---and sometimes fails to adapt---to emerging genomic technologies. In instrumentation and for therapeutic proteins, patents have largely played their traditional role of inducing investment in engineering and product development, including expensive postdiscovery clinical research to prove safety and efficacy. Patents on methods and DNA sequences relevant to clinical genetic testing show less evidence of benefits and more evidence of problems and impediments, largely attributable to university exclusive licensing practices. Whole-genome sequencing will confront uncertainty about infringing granted patents but jurisprudence trends away from upholding the broadest and potentially most troublesome patent claims. PMID:20590431

Phenome-Wide Association Studies as a Tool to Advance Precision Medicine

PubMed Central

Denny, Joshua C.; Bastarache, Lisa; Roden, Dan M.

2017-01-01

Beginning in the early 2000s, the accumulation of biospecimens linked to electronic health records (EHRs) made possible genome-phenome studies (i.e., comparative analyses of genetic variants and phenotypes) using only data collected as a by-product of typical health care. In addition to disease and trait genetics, EHRs proved a valuable resource for analyzing pharmacogenetic traits and developing reverse genetics approaches such as phenome-wide association studies (PheWASs). PheWASs are designed to survey which of many phenotypes may be associated with a given genetic variant. PheWAS methods have been validated through replication of hundreds of known genotype-phenotype associations, and their use has differentiated between true pleiotropy and clinical comorbidity, added context to genetic discoveries, and helped define disease subtypes, and may also help repurpose medications. PheWAS methods have also proven to be useful with research-collected data. Future efforts that integrate broad, robust collection of phenotype data (e.g., EHR data) with purpose-collected research data in combination with a greater understanding of EHR data will create a rich resource for increasingly more efficient and detailed genome-phenome analysis to usher in new discoveries in precision medicine. PMID:27147087

Evaluation of a novel electronic genetic screening and clinical decision support tool in prenatal clinical settings.

PubMed

Edelman, Emily A; Lin, Bruce K; Doksum, Teresa; Drohan, Brian; Edelson, Vaughn; Dolan, Siobhan M; Hughes, Kevin; O'Leary, James; Vasquez, Lisa; Copeland, Sara; Galvin, Shelley L; DeGroat, Nicole; Pardanani, Setul; Gregory Feero, W; Adams, Claire; Jones, Renee; Scott, Joan

2014-07-01

"The Pregnancy and Health Profile" (PHP) is a free prenatal genetic screening and clinical decision support (CDS) software tool for prenatal providers. PHP collects family health history (FHH) during intake and provides point-of-care risk assessment for providers and education for patients. This pilot study evaluated patient and provider responses to PHP and effects of using PHP in practice. PHP was implemented in four clinics. Surveys assessed provider confidence and knowledge and patient and provider satisfaction with PHP. Data on the implementation process were obtained through semi-structured interviews with administrators. Quantitative survey data were analyzed using Chi square test, Fisher's exact test, paired t tests, and multivariate logistic regression. Open-ended survey questions and interviews were analyzed using qualitative thematic analysis. Of the 83% (513/618) of patients that provided feedback, 97% felt PHP was easy to use and 98% easy to understand. Thirty percent (21/71) of participating physicians completed both pre- and post-implementation feedback surveys [13 obstetricians (OBs) and 8 family medicine physicians (FPs)]. Confidence in managing genetic risks significantly improved for OBs on 2/6 measures (p values ≤0.001) but not for FPs. Physician knowledge did not significantly change. Providers reported value in added patient engagement and reported mixed feedback about the CDS report. We identified key steps, resources, and staff support required to implement PHP in a clinical setting. To our knowledge, this study is the first to report on the integration of patient-completed, electronically captured and CDS-enabled FHH software into primary prenatal practice. PHP is acceptable to patients and providers. Key to successful implementation in the future will be customization options and interoperability with electronic health records.

Drugging the PI3 Kinome: From Chemical Tools to Drugs in the Clinic

PubMed Central

Workman, Paul; Clarke, Paul A; Raynaud, Florence I; van Montfort, Rob LM

2011-01-01

The phosphatidylinositide 3-kinase (PI3K) pathway is very commonly activated in a wide range of human cancers and is a major driving force in oncogenesis. One of the class I lipid kinase members of the PI3K family, p110α, is probably the most commonly mutated kinase in the human genome. Alongside genetic, molecular biological and biochemical studies, chemical inhibitors have been extremely helpful tools in understanding the role of PI3K enzymes in signal transduction and downstream physiological and pathological processes, and also in validating PI3Ks as therapeutic targets. Although they have been valuable in the past, the early and still frequently employed inhibitors, wortmannin and LY294002, have significant limitations as chemical tools. Here, we discuss the case history of the discovery and properties of an increasingly used chemical probe, the pan-class I PI3K and mTOR inhibitor PI-103 (a pyridofuropyrimidine) and its very recent evolution into the thienopyrimidine drug GDC-0941 that exhibits excellent oral anticancer activity in preclinical models and is now undergoing Phase I clinical trials in cancer patients. We also illustrate the impact of structural biology on the design of PI3K inhibitors and on the interpretation of their effects. The challenges and outlook for drugging the PI3 kinome are discussed in the more general context of the role of structural biology and chemical biology in innovative drug discovery. PMID:20179189

Primary culture of glial cells from mouse sympathetic cervical ganglion: a valuable tool for studying glial cell biology.

PubMed

de Almeida-Leite, Camila Megale; Arantes, Rosa Maria Esteves

2010-12-15

Central nervous system glial cells as astrocytes and microglia have been investigated in vitro and many intracellular pathways have been clarified upon various stimuli. Peripheral glial cells, however, are not as deeply investigated in vitro despite its importance role in inflammatory and neurodegenerative diseases. Based on our previous experience of culturing neuronal cells, our objective was to standardize and morphologically characterize a primary culture of mouse superior cervical ganglion glial cells in order to obtain a useful tool to study peripheral glial cell biology. Superior cervical ganglia from neonatal C57BL6 mice were enzymatically and mechanically dissociated and cells were plated on diluted Matrigel coated wells in a final concentration of 10,000cells/well. Five to 8 days post plating, glial cell cultures were fixed for morphological and immunocytochemical characterization. Glial cells showed a flat and irregular shape, two or three long cytoplasm processes, and round, oval or long shaped nuclei, with regular outline. Cell proliferation and mitosis were detected both qualitative and quantitatively. Glial cells were able to maintain their phenotype in our culture model including immunoreactivity against glial cell marker GFAP. This is the first description of immunocytochemical characterization of mouse sympathetic cervical ganglion glial cells in primary culture. This work discusses the uses and limitations of our model as a tool to study many aspects of peripheral glial cell biology. Copyright © 2010 Elsevier B.V. All rights reserved.

The role of genetics in improving forest health

Treesearch

Mary F. Mahalovich

1995-01-01

An often ignored tool to improve forest health is the application of genetics-Tree improvement programs in the Inland West utilize genetic principles to develop-seed transfer guidelines to avoid the problems associated with off-site plantings and to improve characteristics in conifers related to forest health. PC-based expert systems have been developed to aid in seed...

A meta-analysis reveals a positive correlation between genetic diversity metrics and environmental status in the long-lived seagrass Posidonia oceanica.

PubMed

Jahnke, Marlene; Olsen, Jeanine L; Procaccini, Gabriele

2015-05-01

The seagrass Posidonia oceanica is a key engineering species structuring coastal marine systems throughout much of the Mediterranean basin. Its decline is of concern, leading to the search for short- and long-term indicators of seagrass health. Using ArcGIS maps from a recent, high-resolution (1-4 km) modelling study of 18 disturbance factors affecting coastal marine systems across the Mediterranean (Micheli et al. 2013, http://globalmarine.nceas.ucsb.edu/mediterranean/), we tested for correlations with genetic diversity metrics (allelic diversity, genotypic/clonal diversity and heterozygosity) in a meta-analysis of 56 meadows. Contrary to initial predictions, weak but significantly positive correlations were found for commercial shipping, organic pollution (pesticides) and cumulative impact. This counterintuitive finding suggests greater resistance and resilience of individuals with higher genetic and genotypic diversity under disturbance (at least for a time) and/or increased sexual reproduction under an intermediate disturbance model. We interpret the absence of low and medium levels of genetic variation at impacted locations as probable local extinctions of individuals that already exceeded their resistance capacity. Alternatively, high diversity at high-impact sites is likely a temporal artefact, reflecting the mismatch with pre-environmental impact conditions, especially because flowering and sexual recruitment are seldom observed. While genetic diversity metrics are a valuable tool for restoration and mitigation, caution must be exercised in the interpretation of correlative patterns as found in this study, because the exceptional longevity of individuals creates a temporal mismatch that may falsely suggest good meadow health status, while gradual deterioration of allelic diversity might go unnoticed. © 2015 John Wiley & Sons Ltd.

Rendering the Intractable More Tractable: Tools from Caenorhabditis elegans Ripe for Import into Parasitic Nematodes

PubMed Central

Ward, Jordan D.

2015-01-01

Recent and rapid advances in genetic and molecular tools have brought spectacular tractability to Caenorhabditis elegans, a model that was initially prized because of its simple design and ease of imaging. C. elegans has long been a powerful model in biomedical research, and tools such as RNAi and the CRISPR/Cas9 system allow facile knockdown of genes and genome editing, respectively. These developments have created an additional opportunity to tackle one of the most debilitating burdens on global health and food security: parasitic nematodes. I review how development of nonparasitic nematodes as genetic models informs efforts to import tools into parasitic nematodes. Current tools in three commonly studied parasites (Strongyloides spp., Brugia malayi, and Ascaris suum) are described, as are tools from C. elegans that are ripe for adaptation and the benefits and barriers to doing so. These tools will enable dissection of a huge array of questions that have been all but completely impenetrable to date, allowing investigation into host–parasite and parasite–vector interactions, and the genetic basis of parasitism. PMID:26644478

The Mystery in Science: A Neglected Tool for Science Education

ERIC Educational Resources Information Center

Papacosta, Pangratios

2008-01-01

Of the many valuable tools available to science education, the mystery in science is the one that is most ignored, underused, or misunderstood. whenever it is used, it is only as mere entertainment or as an attention grabber. In this article, the author discusses how the mystery in science can improve student attitudes, generate a life-long…

High-resolution DNA melting analysis in plant research

USDA-ARS?s Scientific Manuscript database

Genetic and genomic studies provide valuable insight into the inheritance, structure, organization, and function of genes. The knowledge gained from the analysis of plant genes is beneficial to all aspects of plant research, including crop improvement. New methods and tools are continually developed...

A spontaneous eggplant (Solanum melongena L.) color mutant conditions anthocyanin-free fruit pigmentation

USDA-ARS?s Scientific Manuscript database

Induced or spontaneously occuring color mutants in plants provide valuable tools for elucidating the genetic and developmental regulation of genes that influence pigmentation. We identified a single plant of the eggplant (Solanum melongena) cultivar Black Beauty bearing green fruit. Black Beauty no...

Genetic Code Expansion as a Tool to Study Regulatory Processes of Transcription

NASA Astrophysics Data System (ADS)

Schmidt, Moritz; Summerer, Daniel

2014-02-01

The expansion of the genetic code with noncanonical amino acids (ncAA) enables the chemical and biophysical properties of proteins to be tailored, inside cells, with a previously unattainable level of precision. A wide range of ncAA with functions not found in canonical amino acids have been genetically encoded in recent years and have delivered insights into biological processes that would be difficult to access with traditional approaches of molecular biology. A major field for the development and application of novel ncAA-functions has been transcription and its regulation. This is particularly attractive, since advanced DNA sequencing- and proteomics-techniques continue to deliver vast information on these processes on a global level, but complementing methodologies to study them on a detailed, molecular level and in living cells have been comparably scarce. In a growing number of studies, genetic code expansion has now been applied to precisely control the chemical properties of transcription factors, RNA polymerases and histones, and this has enabled new insights into their interactions, conformational changes, cellular localizations and the functional roles of posttranslational modifications.

Role of Radiologic Imaging in Genetic and Acquired Neuromuscular Disorders.

PubMed

Ortolan, Paolo; Zanato, Riccardo; Coran, Alessandro; Beltrame, Valeria; Stramare, Roberto

2015-03-11

Great technologic and clinical progress have been made in the last two decades in identifying genetic defects of several neuromuscular diseases, as Spinal Muscular Atrophy, genetic muscular dystrophies and other genetic myopathies. The diagnosis is usually challenging, due to great variability in genetic abnormalities and clinical phenotypes and the poor specificity of complementary analyses, i.e., serum creatine kinase (CK) and electrophysiology. Muscle biopsy represents the gold standard for the diagnosis of genetic neuromuscular diseases, but clinical imaging of muscle tissue is an important diagnostic tool to identify and quantifyies muscle damage. Radiologic imaging is, indeed, increasingly used as a diagnostic tool to describe patterns and the extent of muscle involvement, thanks to modern techniques that enable to definethe definition of degrees of muscle atrophy and changes in connective tissue. They usually grade the severity of the disease process with greater accuracy than clinical scores. Clinical imaging is more than complementary to perform muscle biopsy, especially as ultrasound scans are often mandatory to identify the muscle to be biopsied. We will here detail and provideWe will herein provide detailed examples of the radiologic methods that can be used in genetic and acquired neuromuscular disorders, stressing pros and cons. Muscle Imaging, MRI, CT, genetic muscle disorders, myopathies, dystrophies.

Role of Radiologic Imaging in Genetic and Acquired Neuromuscular Disorders

PubMed Central

Zanato, Riccardo; Coran, Alessandro; Beltrame, Valeria; Stramare, Roberto

2015-01-01

Great technologic and clinical progress have been made in the last two decades in identifying genetic defects of several neuromuscular diseases, as Spinal Muscular Atrophy, genetic muscular dystrophies and other genetic myopathies. The diagnosis is usually challenging, due to great variability in genetic abnormalities and clinical phenotypes and the poor specificity of complementary analyses, i.e., serum creatine kinase (CK) and electrophysiology. Muscle biopsy represents the gold standard for the diagnosis of genetic neuromuscular diseases, but clinical imaging of muscle tissue is an important diagnostic tool to identify and quantifyies muscle damage. Radiologic imaging is, indeed, increasingly used as a diagnostic tool to describe patterns and the extent of muscle involvement, thanks to modern techniques that enable to definethe definition of degrees of muscle atrophy and changes in connective tissue. They usually grade the severity of the disease process with greater accuracy than clinical scores. Clinical imaging is more than complementary to perform muscle biopsy, especially as ultrasound scans are often mandatory to identify the muscle to be biopsied. We will here detail and provideWe will herein provide detailed examples of the radiologic methods that can be used in genetic and acquired neuromuscular disorders, stressing pros and cons. Key Words: Muscle Imaging, MRI, CT, genetic muscle disorders, myopathies, dystrophies PMID:26913153

Waveband specific transcriptional control of select genetic pathways in vertebrate skin (Xiphophorus maculatus).

PubMed

Walter, Ronald B; Boswell, Mikki; Chang, Jordan; Boswell, William T; Lu, Yuan; Navarro, Kaela; Walter, Sean M; Walter, Dylan J; Salinas, Raquel; Savage, Markita

2018-05-10

transcriptional suppression after exposure to the 520-530 nm waveband. Collectively, these results suggest one may manipulate transcription of specific genetic pathways in skin by exposure of the intact animal to specific wavebands of light. In addition, we identify genes transcriptionally modulated in a predictable manner by specific waveband exposures. Such genes, and their regulatory elements, may represent valuable tools for genetic engineering and gene therapy protocols.

[Human genetic data from a data protection law perspective].

PubMed

Schulte In den Bäumen, Tobias

2007-02-01

The collection and use of genetic data have caused much concern in the German population. Data protection is widely seen as the tool to address these fears. The term genetic data is not self-explanatory, as it depends on the different types of genetic diseases. The protection of genetic data as defined with regard to the different sets of diseases needs to fit into the preexisting data protection legislation. Still, the particularities of genetic data such as the multipersonal impact need to be considered. A balance between the information needs of society and the right to privacy requires a medically driven criteria. The medical term of indication which corresponds with the data protection term of purpose should serve as a tool in order to balance the rights of the patients and their relatives or between clients and third persons involved. Some countries have set up new legislative acts to address the challenges of human genetics. The current state of German data protection law leaves citizen rather unprotected as long as the data are used for medical purposes in a wider sense. A special law on the collection of genetic data has been discussed for several years, but it should be questioned whether the scope of a sector-specific law would serve citizens better. It seems to be preferable to adjust the existing Data Protection Act rather than drafting a specific law which covers the field of human genetics. This adaptation should reflect upon the different technical ways in which genetic data are collected and used.

A reconfigurable NAND/NOR genetic logic gate

PubMed Central

2012-01-01

Background Engineering genetic Boolean logic circuits is a major research theme of synthetic biology. By altering or introducing connections between genetic components, novel regulatory networks are built in order to mimic the behaviour of electronic devices such as logic gates. While electronics is a highly standardized science, genetic logic is still in its infancy, with few agreed standards. In this paper we focus on the interpretation of logical values in terms of molecular concentrations. Results We describe the results of computational investigations of a novel circuit that is able to trigger specific differential responses depending on the input standard used. The circuit can therefore be dynamically reconfigured (without modification) to serve as both a NAND/NOR logic gate. This multi-functional behaviour is achieved by a) varying the meanings of inputs, and b) using branch predictions (as in computer science) to display a constrained output. A thorough computational study is performed, which provides valuable insights for the future laboratory validation. The simulations focus on both single-cell and population behaviours. The latter give particular insights into the spatial behaviour of our engineered cells on a surface with a non-homogeneous distribution of inputs. Conclusions We present a dynamically-reconfigurable NAND/NOR genetic logic circuit that can be switched between modes of operation via a simple shift in input signal concentration. The circuit addresses important issues in genetic logic that will have significance for more complex synthetic biology applications. PMID:22989145

A reconfigurable NAND/NOR genetic logic gate.

PubMed

Goñi-Moreno, Angel; Amos, Martyn

2012-09-18

Engineering genetic Boolean logic circuits is a major research theme of synthetic biology. By altering or introducing connections between genetic components, novel regulatory networks are built in order to mimic the behaviour of electronic devices such as logic gates. While electronics is a highly standardized science, genetic logic is still in its infancy, with few agreed standards. In this paper we focus on the interpretation of logical values in terms of molecular concentrations. We describe the results of computational investigations of a novel circuit that is able to trigger specific differential responses depending on the input standard used. The circuit can therefore be dynamically reconfigured (without modification) to serve as both a NAND/NOR logic gate. This multi-functional behaviour is achieved by a) varying the meanings of inputs, and b) using branch predictions (as in computer science) to display a constrained output. A thorough computational study is performed, which provides valuable insights for the future laboratory validation. The simulations focus on both single-cell and population behaviours. The latter give particular insights into the spatial behaviour of our engineered cells on a surface with a non-homogeneous distribution of inputs. We present a dynamically-reconfigurable NAND/NOR genetic logic circuit that can be switched between modes of operation via a simple shift in input signal concentration. The circuit addresses important issues in genetic logic that will have significance for more complex synthetic biology applications.

Metabolomics of Genetically Modified Crops

PubMed Central

Simó, Carolina; Ibáñez, Clara; Valdés, Alberto; Cifuentes, Alejandro; García-Cañas, Virginia

2014-01-01

Metabolomic-based approaches are increasingly applied to analyse genetically modified organisms (GMOs) making it possible to obtain broader and deeper information on the composition of GMOs compared to that obtained from traditional analytical approaches. The combination in metabolomics of advanced analytical methods and bioinformatics tools provides wide chemical compositional data that contributes to corroborate (or not) the substantial equivalence and occurrence of unintended changes resulting from genetic transformation. This review provides insight into recent progress in metabolomics studies on transgenic crops focusing mainly in papers published in the last decade. PMID:25334064

Clinical audit, a valuable tool to improve quality of care: General methodology and applications in nephrology

PubMed Central

Esposito, Pasquale; Dal Canton, Antonio

2014-01-01

Evaluation and improvement of quality of care provided to the patients are of crucial importance in the daily clinical practice and in the health policy planning and financing. Different tools have been developed, including incident analysis, health technology assessment and clinical audit. The clinical audit consist of measuring a clinical outcome or a process, against well-defined standards set on the principles of evidence-based medicine in order to identify the changes needed to improve the quality of care. In particular, patients suffering from chronic renal diseases, present many problems that have been set as topics for clinical audit projects, such as hypertension, anaemia and mineral metabolism management. Although the results of these studies have been encouraging, demonstrating the effectiveness of audit, overall the present evidence is not clearly in favour of clinical audit. These findings call attention to the need to further studies to validate this methodology in different operating scenarios. This review examines the principle of clinical audit, focusing on experiences performed in nephrology settings. PMID:25374819

Genetic diversity and structure of an endangered desert shrub and the implications for conservation

Treesearch

Zhihao Su; Bryce A. Richardson; Li Zhuo; Xiaolong Jiang; Wenjun Li; Xiaoshan Kang

2017-01-01

Population genetic information can provide valuable insight for the conservation and management of threatened and endangered plant species. Tamarix taklamakanensis is an endangered shrub endemic to arid basins of northwestern China. This species serves to stabilize soils in this region, but has seen substantial loss in its abundance due to depletion of ground water....

EvoSNP-DB: A database of genetic diversity in East Asian populations.

PubMed

Kim, Young Uk; Kim, Young Jin; Lee, Jong-Young; Park, Kiejung

2013-08-01

Genome-wide association studies (GWAS) have become popular as an approach for the identification of large numbers of phenotype-associated variants. However, differences in genetic architecture and environmental factors mean that the effect of variants can vary across populations. Understanding population genetic diversity is valuable for the investigation of possible population specific and independent effects of variants. EvoSNP-DB aims to provide information regarding genetic diversity among East Asian populations, including Chinese, Japanese, and Korean. Non-redundant SNPs (1.6 million) were genotyped in 54 Korean trios (162 samples) and were compared with 4 million SNPs from HapMap phase II populations. EvoSNP-DB provides two user interfaces for data query and visualization, and integrates scores of genetic diversity (Fst and VarLD) at the level of SNPs, genes, and chromosome regions. EvoSNP-DB is a web-based application that allows users to navigate and visualize measurements of population genetic differences in an interactive manner, and is available online at [http://biomi.cdc.go.kr/EvoSNP/].

Restricted gene flow and fine-scale population structuring in tool using New Caledonian crows

NASA Astrophysics Data System (ADS)

Rutz, C.; Ryder, T. B.; Fleischer, R. C.

2012-04-01

New Caledonian crows Corvus moneduloides are the most prolific avian tool users. It has been suggested that some aspects of their complex tool use behaviour are under the influence of cultural processes, involving the social transmission—and perhaps even progressive refinement—of tool designs. Using microsatellite and mt-haplotype profiling of crows from three distinct habitats (dry forest, farmland and beachside habitat), we show that New Caledonian crow populations can exhibit significant fine-scale genetic structuring. Our finding that some sites of <10 km apart were highly differentiated demonstrates considerable potential for genetic and/or cultural isolation of crow groups. Restricted movement of birds between local populations at such small spatial scales, especially across habitat boundaries, illustrates how specific tool designs could be preserved over time, and how tool technologies of different crow groups could diverge due to drift and local selection pressures. Young New Caledonian crows have an unusually long juvenile dependency period, during which they acquire complex tool-related foraging skills. We suggest that the resulting delayed natal dispersal drives population-divergence patterns in this species. Our work provides essential context for future studies that examine the genetic makeup of crow populations across larger geographic areas, including localities with suspected cultural differences in crow tool technologies.

Project delivery acceleration tool box : improvements to the Department of Transportation's project delivery process.

DOT National Transportation Integrated Search

2004-05-01

The purpose of this document is to provide to Caltrans' employees, as well as external partners, some valuable tools that can be used to help accelerate project delivery. This document contains a compilation of all the Department's recent acceleratio...

Investigating the population structure and genetic differentiation of livestock guard dog breeds.

PubMed

Bigi, D; Marelli, S P; Liotta, L; Frattini, S; Talenti, A; Pagnacco, G; Polli, M; Crepaldi, P

2018-01-14

Livestock guarding dogs are a valuable adjunct to the pastoral community. Having been traditionally selected for their working ability, they fulfil their function with minimal interaction or command from their human owners. In this study, the population structure and the genetic differentiation of three Italian livestock guardian breeds (Sila's Dog, Maremma and Abruzzese Sheepdog and Mannara's Dog) and three functionally and physically similar breeds (Cane Corso, Central Asian Shepherd Dog and Caucasian Shepherd Dog), totalling 179 dogs unrelated at the second generation, were investigated with 18 autosomal microsatellite markers. Values for the number of alleles per locus, observed and expected heterozygosity, Hardy-Weinberg Equilibrium, F stats, Nei's and Reynold's genetic distances, clustering and sub-population formation abilities and individual genetic structures were calculated. Our results show clear breed differentiation, whereby all the considered breeds show reasonable genetic variability despite small population sizes and variable selection schemes. These results provide meaningful data to stakeholders in specific breed and environmental conservation programmes.

Tool-use: An open window into body representation and its plasticity

PubMed Central

Martel, Marie; Cardinali, Lucilla; Roy, Alice C.; Farnè, Alessandro

2016-01-01

ABSTRACT Over the last decades, scientists have questioned the origin of the exquisite human mastery of tools. Seminal studies in monkeys, healthy participants and brain-damaged patients have primarily focused on the plastic changes that tool-use induces on spatial representations. More recently, we focused on the modifications tool-use must exert on the sensorimotor system and highlighted plastic changes at the level of the body representation used by the brain to control our movements, i.e., the Body Schema. Evidence is emerging for tool-use to affect also more visually and conceptually based representations of the body, such as the Body Image. Here we offer a critical review of the way different tool-use paradigms have been, and should be, used to try disentangling the critical features that are responsible for tool incorporation into different body representations. We will conclude that tool-use may offer a very valuable means to investigate high-order body representations and their plasticity. PMID:27315277

Tool-use: An open window into body representation and its plasticity.

PubMed

Martel, Marie; Cardinali, Lucilla; Roy, Alice C; Farnè, Alessandro

2016-01-01

Over the last decades, scientists have questioned the origin of the exquisite human mastery of tools. Seminal studies in monkeys, healthy participants and brain-damaged patients have primarily focused on the plastic changes that tool-use induces on spatial representations. More recently, we focused on the modifications tool-use must exert on the sensorimotor system and highlighted plastic changes at the level of the body representation used by the brain to control our movements, i.e., the Body Schema. Evidence is emerging for tool-use to affect also more visually and conceptually based representations of the body, such as the Body Image. Here we offer a critical review of the way different tool-use paradigms have been, and should be, used to try disentangling the critical features that are responsible for tool incorporation into different body representations. We will conclude that tool-use may offer a very valuable means to investigate high-order body representations and their plasticity.

The future is now: Technology's impact on the practice of genetic counseling.

PubMed

Gordon, Erynn S; Babu, Deepti; Laney, Dawn A

2018-03-01

Smartphones, artificial intelligence, automation, digital communication, and other types of technology are playing an increasingly important role in our daily lives. It is no surprise that technology is also shaping the practice of medicine, and more specifically the practice of genetic counseling. While digital tools have been part of the practice of medical genetics for decades, such as internet- or CD-ROM-based tools like Online Mendelian Inheritance in Man and Pictures of Standard Syndromes and Undiagnosed Malformations in the 1980s, the potential for emerging tools to change how we practice and the way patients consume information is startling. Technology has the potential to aid in at-risk patient identification, assist in generating a differential diagnosis, improve efficiency in medical history collection and risk assessment, provide educational support for patients, and streamline follow-up. Here we review the historic and current uses of technology in genetic counseling, identify challenges to integration, and propose future applications of technology that can shape the practice of genetic counseling. © 2018 Wiley Periodicals, Inc.

Journal Writing as an Adult Learning Tool. Practice Application Brief No. 22.

ERIC Educational Resources Information Center

Kerka, Sandra

Journals can be valuable tools for fostering adult learning and experience. Research has supported the following assumptions about learning from journals: (1) articulating connections between new and existing knowledge improves learning; (2) writing about learning is a way of demonstrating what has been learned; (3) journal writing accentuates…

'RetinoGenetics': a comprehensive mutation database for genes related to inherited retinal degeneration.

PubMed

Ran, Xia; Cai, Wei-Jun; Huang, Xiu-Feng; Liu, Qi; Lu, Fan; Qu, Jia; Wu, Jinyu; Jin, Zi-Bing

2014-01-01

Inherited retinal degeneration (IRD), a leading cause of human blindness worldwide, is exceptionally heterogeneous with clinical heterogeneity and genetic variety. During the past decades, tremendous efforts have been made to explore the complex heterogeneity, and massive mutations have been identified in different genes underlying IRD with the significant advancement of sequencing technology. In this study, we developed a comprehensive database, 'RetinoGenetics', which contains informative knowledge about all known IRD-related genes and mutations for IRD. 'RetinoGenetics' currently contains 4270 mutations in 186 genes, with detailed information associated with 164 phenotypes from 934 publications and various types of functional annotations. Then extensive annotations were performed to each gene using various resources, including Gene Ontology, KEGG pathways, protein-protein interaction, mutational annotations and gene-disease network. Furthermore, by using the search functions, convenient browsing ways and intuitive graphical displays, 'RetinoGenetics' could serve as a valuable resource for unveiling the genetic basis of IRD. Taken together, 'RetinoGenetics' is an integrative, informative and updatable resource for IRD-related genetic predispositions. Database URL: http://www.retinogenetics.org/. © The Author(s) 2014. Published by Oxford University Press.

Genetic Testing as a Tool to Identify Horses with or at Risk for Ocular Disorders.

PubMed

Bellone, Rebecca R

2017-12-01

Advances in equine genetics and genomics resources have enabled the understanding of some inherited ocular disorders and ocular manifestations. These ocular disorders include congenital stationary night blindness, equine recurrent uveitis, multiple congenital ocular anomalies, and squamous cell carcinoma. Genetic testing can identify horses with or at risk for disease and thus can assist in clinical management. In addition, genetic testing can identify horses that are carriers and thus can inform breeding decisions. Use of genetic tests in management and breeding decisions should aid in reducing the incidence of these disorders and improving the outcomes for horses at highest risk. Copyright © 2017 Elsevier Inc. All rights reserved.

Population genetics analysis of Phlebotomus papatasi sand flies from Egypt and Jordan based on mitochondrial cytochrome b haplotypes.

PubMed

Flanley, Catherine M; Ramalho-Ortigao, Marcelo; Coutinho-Abreu, Iliano V; Mukbel, Rami; Hanafi, Hanafi A; El-Hossary, Shabaan S; Fawaz, Emad El-Din Y; Hoel, David F; Bray, Alexander W; Stayback, Gwen; Shoue, Douglas A; Kamhawi, Shaden; Karakuş, Mehmet; Jaouadi, Kaouther; Yaghoobie-Ershadi, Mohammad Reza; Krüger, Andreas; Amro, Ahmad; Kenawy, Mohamed Amin; Dokhan, Mostafa Ramadhan; Warburg, Alon; Hamarsheh, Omar; McDowell, Mary Ann

2018-03-27

Phlebotomus papatasi sand flies are major vectors of Leishmania major and phlebovirus infection in North Africa and across the Middle East to the Indian subcontinent. Population genetics is a valuable tool in understanding the level of genetic variability present in vector populations, vector competence, and the development of novel control strategies. This study investigated the genetic differentiation between P. papatasi populations in Egypt and Jordan that inhabit distinct ecotopes and compared this structure to P. papatasi populations from a broader geographical range. A 461 base pair (bp) fragment from the mtDNA cytochrome b (cyt b) gene was PCR amplified and sequenced from 116 individual female sand flies from Aswan and North Sinai, Egypt, as well as Swaimeh and Malka, Jordan. Haplotypes were identified and used to generate a median-joining network, F ST values and isolation-by-distance were also evaluated. Additional sand fly individuals from Afghanistan, Iran, Israel, Jordan, Libya, Tunisia and Turkey were included as well as previously published haplotypes to provide a geographically broad genetic variation analysis. Thirteen haplotypes displaying nine variant sites were identified from P. papatasi collected in Egypt and Jordan. No private haplotypes were identified from samples in North Sinai, Egypt, two were observed in Aswan, Egypt, four from Swaimeh, Jordan and two in Malka, Jordan. The Jordan populations clustered separately from the Egypt populations and produced more private haplotypes than those from Egypt. Pairwise F ST values fall in the range 0.024-0.648. The clustering patterns and pairwise F ST values indicate a strong differentiation between Egyptian and Jordanian populations, although this population structure is not due to isolation-by-distance. Other factors, such as environmental influences and the genetic variability in the circulating Le. major parasites, could possibly contribute to this heterogeneity. The present study aligns with

Genetic basis of arrhythmogenic cardiomyopathy.

PubMed

Karmouch, Jennifer; Protonotarios, Alexandros; Syrris, Petros

2018-05-01

To date 16 genes have been associated with arrhythmogenic cardiomyopathy (ACM). Mutations in these genes can lead to a broad spectrum of phenotypic expression ranging from disease affecting predominantly the right or left ventricle, to biventricular subtypes. Understanding the genetic causes of ACM is important in diagnosis and management of the disorder. This review summarizes recent advances in molecular genetics and discusses the application of next-generation sequencing technology in genetic testing in ACM. Use of next-generation sequencing methods has resulted in the identification of novel causative variants and genes for ACM. The involvement of filamin C in ACM demonstrates the genetic overlap between ACM and other types of cardiomyopathy. Putative pathogenic variants have been detected in cadherin 2 gene, a protein involved in cell adhesion. Large genomic rearrangements in desmosome genes have been systematically investigated in a cohort of ACM patients. Recent studies have identified novel causes of ACM providing new insights into the genetic spectrum of the disease and highlighting an overlapping phenotype between ACM and dilated cardiomyopathy. Next-generation sequencing is a useful tool for research and genetic diagnostic screening but interpretation of identified sequence variants requires caution and should be performed in specialized centres.

DEVELOPMENT OF A DNA ARCHIVE FOR GENETIC MONITORING OF FISH POPULATIONS

EPA Science Inventory

Analysis of intraspecific genetic diversity provides a potentially powerful tool to estimate the impacts of environmental stressors on populations. Genetic responses of populations to novel stressors include dramatic shifts in genotype frequencies at loci under selection (i.e. ad...

Assessing Sustainability of Coral Reef Ecosystem Services using a Spatially-Explicit Decision Support Tool

EPA Science Inventory

Forecasting and communicating the potential outcomes of decision options requires support tools that aid in evaluating alternative scenarios in a user-friendly context and that highlight variables relevant to the decision options and valuable stakeholders. Envision is a GIS-base...

Cathodoluminescence Petrography: A Valuable Tool for Teaching and Research.

ERIC Educational Resources Information Center

Kopp, Otto C.

1981-01-01

Cathodoluminescence is visible light emitted from a specimen when it is bombarded with electrons. A technique known as cathodoluminescence petrography can provide information especially useful in studies or courses related to mineralogy and petrology. The technique is briefly presented, along with examples to illustrate typical results. (Author/WB)

History of health, a valuable tool in public health

PubMed Central

Perdiguero, E; Bernabeu, J; Huertas, R; Rodriguez-Ocana, E

2001-01-01

The aim of this article is to highlight the importance of the history of public health for public health research and practice itself. After summarily reviewing the current great vitality of the history of collective health oriented initiatives, we explain three particular features of the historical vantage point in public health, namely the importance of the context, the relevance of a diachronic attitude and the critical perspective. In order to illustrate those three topics, we bring up examples taken from three centuries of fight against malaria, the so called "re-emerging diseases" and the 1918 influenza epidemic. The historical approach enriches our critical perception of the social effects of initiatives undertaken in the name of public health, shows the shortcomings of public health interventions based on single factors and asks for a wider time scope in the assessment of current problems. The use of a historical perspective to examine the plurality of determinants in any particular health condition will help to solve the longlasting debate on the primacy of individual versus population factors, which has been particularly intense in recent times.


Keywords: history PMID:11511647

History of health, a valuable tool in public health.

PubMed

Perdiguero, E; Bernabeu, J; Huertas, R; Rodríguez-Ocaña, E

2001-09-01

The aim of this article is to highlight the importance of the history of public health for public health research and practice itself. After summarily reviewing the current great vitality of the history of collective health oriented initiatives, we explain three particular features of the historical vantage point in public health, namely the importance of the context, the relevance of a diachronic attitude and the critical perspective. In order to illustrate those three topics, we bring up examples taken from three centuries of fight against malaria, the so called "re-emerging diseases" and the 1918 influenza epidemic. The historical approach enriches our critical perception of the social effects of initiatives undertaken in the name of public health, shows the shortcomings of public health interventions based on single factors and asks for a wider time scope in the assessment of current problems. The use of a historical perspective to examine the plurality of determinants in any particular health condition will help to solve the longlasting debate on the primacy of individual versus population factors, which has been particularly intense in recent times.

Reduced Genetic Diversity and Increased Structure in American Mink on the Swedish Coast following Invasive Species Control.

PubMed

Zalewski, Andrzej; Zalewska, Hanna; Lunneryd, Sven-Gunnar; André, Carl; Mikusiński, Grzegorz

2016-01-01

Eradication and population reductions are often used to mitigate the negative impacts of non-native invasive species on native biodiversity. However, monitoring the effectiveness of non-native species control programmes is necessary to evaluate the efficacy of these measures. Genetic monitoring could provide valuable insights into temporal changes in demographic, ecological, and evolutionary processes in invasive populations being subject to control programmes. Such programmes should cause a decrease in effective population size and/or in genetic diversity of the targeted non-native species and an increase in population genetic structuring over time. We used microsatellite DNA data from American mink (Neovison vison) to determine whether the removal of this predator on the Koster Islands archipelago and the nearby Swedish mainland affected genetic variation over six consecutive years of mink culling by trappers as part of a population control programme. We found that on Koster Islands allelic richness decreased (from on average 4.53 to 3.55), genetic structuring increased, and effective population size did not change. In contrast, the mink population from the Swedish coast showed no changes in genetic diversity or structure, suggesting the stability of this population over 6 years of culling. Effective population size did not change over time but was higher on the coast than on the islands across all years. Migration rates from the islands to the coast were almost two times higher than from the coast to the islands. Most migrants leaving the coast were localised on the southern edge of the archipelago, as expected from the direction of the sea current between the two sites. Genetic monitoring provided valuable information on temporal changes in the population of American mink suggesting that this approach can be used to evaluate and improve control programmes of invasive vertebrates.

Genetic variation and structure in remnant population of critically endangered Melicope zahlbruckneri

USGS Publications Warehouse

Raji, J. A.; Atkinson, Carter T.

2016-01-01

The distribution and amount of genetic variation within and between populations of plant species are important for their adaptability to future habitat changes and also critical for their restoration and overall management. This study was initiated to assess the genetic status of the remnant population of Melicope zahlbruckneri–a critically endangered species in Hawaii, and determine the extent of genetic variation and diversity in order to propose valuable conservation approaches. Estimated genetic structure of individuals based on molecular marker allele frequencies identified genetic groups with low overall differentiation but identified the most genetically diverse individuals within the population. Analysis of Amplified Fragment Length Polymorphic (AFLP) marker loci in the population based on Bayesian model and multivariate statistics classified the population into four subgroups. We inferred a mixed species population structure based on Bayesian clustering and frequency of unique alleles. The percentage of Polymorphic Fragment (PPF) ranged from 18.8 to 64.6% for all marker loci with an average of 54.9% within the population. Inclusion of all surviving M. zahlbruckneri trees in future restorative planting at new sites are suggested, and approaches for longer term maintenance of genetic variability are discussed. To our knowledge, this study represents the first report of molecular genetic analysis of the remaining population of M. zahlbruckneri and also illustrates the importance of genetic variability for conservation of a small endangered population.

Horizontal integration of OMIM across the medical school preclinical curriculum for early reinforcement of clinical genetics principles.

PubMed

Diehl, Adam C; Reader, Lauren; Hamosh, Ada; Bodurtha, Joann N

2015-02-01

With the relentless expansion of genetics into every field of medicine, stronger preclinical and clinical medical student education in genetics is needed. The explosion of genetic information cannot be addressed by simply adding content hours. We proposed that students be provided a tool to access accurate clinical information on genetic conditions and, through this tool, build life-long learning habits to carry them through their medical careers. Surveys conducted at the Johns Hopkins University School of Medicine revealed that medical students in all years lacked confidence when approaching genetic conditions and lacked a reliable resource for accurate genetic information. In response, the school created a horizontal thread that stretches across the first-year curriculum and is devoted to teaching students how to use Online Mendelian Inheritance in Man (OMIM) (http://omim.org) and the databases to which it links as a starting point for approaching genetic conditions. The thread improved the first-year students' confidence in clinical genetics concepts and encouraged use of OMIM as a primary source for genetic information. Most students showed confidence in OMIM as a learning tool and wanted to see the thread repeated in subsequent years. Incorporating OMIM into the preclinical curriculum improved students' confidence in clinical genetics concepts.

Genetic testing for hearing impairment.

PubMed

Topsakal, V; Van Camp, G; Van de Heyning, P

2005-01-01

For some patients, genetic testing can reveal the etiology of their hearing impairment, and can provide evidence for a medical diagnosis. However, a gap between fundamental genetic research on hereditary deafness and clinical otology emerges because of the steadily increasing number of discovered genes for hereditary hearing impairment (HHI) and the comparably low clinical differentiation of the HHIs. In an attempt to keep up with the scientific progress, this article enumerates the indications of genetic testing for HHI from a clinical point of view and describes the most frequently encountered HHIs in Belgium. Domains of recent scientific interest, molecular biological aspects, and some pitfalls with HHIs are highlighted. The overview comprises bilateral congenital hearing loss, late-onset progressive high frequency hearing loss, progressive bilateral cochleo-vestibular deficit, and progressive low frequency hearing loss. Also, several syndromal forms of HHI are summarized, and the availability of genetic tests mentioned. Finally, the requirements for successful linkage analysis, an important genetic research tool for localizing the potential genes of a trait on a chromosome, are briefly described.

Self-Monitoring Symptoms in Glaucoma: A Feasibility Study of a Web-Based Diary Tool

PubMed Central

McDonald, Leanne; Glen, Fiona C.; Taylor, Deanna J.

2017-01-01

Purpose. Glaucoma patients annually spend only a few hours in an eye clinic but spend more than 5000 waking hours engaged in everything else. We propose that patients could self-monitor changes in visual symptoms providing valuable between clinic information; we test the hypothesis that this is feasible using a web-based diary tool. Methods. Ten glaucoma patients with a range of visual field loss took part in an eight-week pilot study. After completing a series of baseline tests, volunteers were prompted to monitor symptoms every three days and complete a diary about their vision during daily life using a bespoke web-based diary tool. Response to an end of a study questionnaire about the usefulness of the exercise was a main outcome measure. Results. Eight of the 10 patients rated the monitoring scheme to be “valuable” or “very valuable.” Completion rate to items was excellent (96%). Themes from a qualitative synthesis of the diary entries related to behavioural aspects of glaucoma. One patient concluded that a constant focus on monitoring symptoms led to negative feelings. Conclusions. A web-based diary tool for monitoring self-reported glaucoma symptoms is practically feasible. The tool must be carefully designed to ensure participants are benefitting, and it is not increasing anxiety. PMID:28546876

QUALITY ASSURANCE PROJECT PLANS: A USELESS PAPER EXERCISE OR VALUABLE AID?

EPA Science Inventory

Two perspectives on the fundamental question "Are quality assurance project plans (QAPPS) a useless paper exercise or a valuable aid?" will be explored. These perspectives include those of a Branch Chief (i.e., the supervisor/manager) and an active researcher. As a Branch Chief, ...

Genetic risks and healthy choices: creating citizen-consumers of genetic services through empowerment and facilitation.

PubMed

Harvey, Alison

2010-03-01

Genetic testing to identify susceptibility to a variety of common complex diseases is increasingly becoming available. In this article, focusing on the development of genetic susceptibility testing for diet-related disease, I examine the emergence of direct-to-the-consumer genetic testing services and the (re)configuration of healthcare provision, both within and outside the specialist genetics service, in the UK. I identify two key techniques within these practices: empowerment and facilitation. Using Foucauldian social theory, I show that empowerment and facilitation are being positioned as tools for the creation of citizen-consumers who will make appropriate dietary choices, based on the results of their genetic analysis. Through these techniques, individuals are transformed into properly entrepreneurial citizens who will, through judicious choices, act to maximise their 'vital capital' (their health) and the capital of the social body. I argue that the user of these services is not purely an economic figure, making rational choices as a consumer, but that her configuration as a citizen-consumer who avails herself of genetic information and services in a proper manner ensures that she is fit to contribute to the economic life of our present.

Emancipating Chlamydia: Advances in the Genetic Manipulation of a Recalcitrant Intracellular Pathogen