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PubMed2005

Flexibility in a gene network affecting a simple behavior in Drosophila melanogaster.

Gene interactions are emerging as central to understanding the realization of any phenotype. To probe the flexibility of interactions in a defined gene network, we isolated a set of 16 interacting genes in Drosophila, on the basis of their alteration of a quantitative behavioral phenotype-the loss of coordination in a temperature-sensitive allele of Syntaxin1A. The interactions inter se of this set of genes were then assayed in the presence and in the absence of the original Syntaxin1A mutation to ask whether the relationships among the 16 genes remain stable or differ after a change in genetic context. The pattern of epistatic interactions that occurs within this set of variants is dramatically altered in the two different genetic contexts. The results imply considerable flexibility in the network interactions of genes.

Alleles↗
PubMed2005

Commentary: Gene-environment interplay in the context of genetics, epigenetics, and gene expression.

OBJECTIVE: To comment on the article in this issue of the Journal by Professor Michael Rutter, "Environmentally Mediated Risks for Psychopathology: Research Strategies and Findings," in the context of current research findings on gene-environment interaction, epigenetics, and gene expression. METHOD: Animal and human studies are reviewed that differentiate the role of gene expression in developmental biology and psychopathology as well as studies that begin to specify the biological mechanisms involved in determining how genotype is translated into phenotype. RESULTS: Genetic instructions are not translated directly into phenotypic traits but are modified potentially at two levels: the transcription process wherein messenger RNA is produced, and translation when protein synthesis occurs. Interplay of genetic and environmental factors determines the final product of gene expression as measured by the when, where, and amount of protein synthesized. Epigenetic processes may operate at the level of messenger RNA to control gene expression. CONCLUSIONS: The field of developmental psychopathology is providing the theoretical and research framework to explore the conceptual space between the genome and the environment. Natural selection has provided mechanisms that operate within that space to facilitate adaptation to the environment. These mechanisms are more robust than genetics alone in determining the phenotype of each individual organism.

Chromosomes, Human, X↗
PubMed2006

Mapping cis-acting regulatory variation in recombinant congenic strains.

We present an integrated approach for the enriched detection of genes subject to cis-acting variation in the mouse genome. Gene expression profiling was performed with lung tissue from a panel of recombinant congenic strains (RCS) derived from A/J and C57BL/6J inbred mouse strains. A multiple-regression model measuring the association between gene expression level, donor strain of origin (DSO), and predominant strain background identified over 1,500 genes (P < 0.05) whose expression profiles differed according to the DSO. This model also identified over 1,200 genes whose expression showed dependence on background (P < 0.05), indicating the influence of background genetic context on transcription levels. Sequences obtained from 1-kb segments of 3'-untranslated regions identified single nucleotide polymorphisms in 64% of genes whose expression levels correlated with DSO status, compared with 29% of genes that displayed no association (P < 0.01, Fisher exact test). Allelic imbalance was identified in 50% of genes positive for expression-DSO association, compared with 22% of negative genes (P < 0.05, Fisher exact test). Together, these results demonstrate the utility of RCS mice for identifying the roles of proximal genetic determinants and background genetic context in determining gene expression levels. We propose the use of this integrated experimental approach in multiple tissues from this and other RCS panels as a means for genome-wide cataloging of genetic regulatory mechanisms in laboratory strains of mice.

Allelic Imbalance↗
PubMed1995

tRNAs are imported into mitochondria of Trypanosoma brucei independently of their genomic context and genetic origin.

The mitochondrial genome of Trypanosoma brucei does not encode any identifiable tRNAs. Instead, mitochondrial tRNAs are synthesized in the nucleus and subsequently imported into mitochondria. In order to analyse the signals which target the tRNAs into the mitochondria, an in vivo import system has been developed: tRNA variants were expressed episomally and their import into mitochondria assessed by purification and nuclease treatment of the mitochondrial fraction. Three tRNA genes were tested in this system: (i) a mutated version of the trypanosomal tRNA(Tyr); (ii) a cytosolic tRNA(His) of yeast; and (iii) a human cytosolic tRNA(Lys). The tRNAs were expressed in their own genomic context, or containing various lengths of the 5'-flanking sequence of the trypanosomal tRNA(Tyr) gene. In all cases efficient import of each of the tRNAs was observed. We independently confirmed the mitochondrial import of the yeast tRNA(His), since in organello [alpha-32P]ATP-labelling of the 3'-end of the tRNA was inhibited by carboxyatractyloside, a highly specific inhibitor of the mitochondrial adenine nucleotide translocator. Import of heterologous tRNAs in their own genomic contexts supports the conclusion that no specific targeting signals are necessary to import tRNAs into mitochondria of T. brucei, but rather that the tRNA structure itself is sufficient to specify import.

Animals↗
PubMed2026

ReGAIN: a bioinformatics platform for assessing probabilistic co-occurrence between resistance genes in bacterial pathogens.

MOTIVATION: Multidrug-resistant bacterial pathogens continue to rise globally, yet scalable methods are needed to infer how resistance determinants co-occur across pathogen populations and to quantify conditional dependencies underlying co-occurrence and shared genetic context. RESULTS: We present ReGAIN (Resistance Gene Association and Inference Network), an open-source platform that applies Bayesian network structure learning to infer probabilistic, conditional dependency relationships among antibiotic resistance, heavy metal tolerance, stress response, and virulence determinants in bacteria. In contrast to pairwise co-occurrence analyses, ReGAIN reports conditional probabilities, relative risks, and absolute risk differences with confidence intervals to prioritize candidate relationships for downstream prioritization. Applied across ESKAPEE pathogens, ReGAIN recapitulated established resistance gene relationships and identified additional candidate patterns consistent with co-selection and shared genetic context. Together, these results support scalable, reproducible population-wide analysis of resistance networks for surveillance, comparative genomics and epidemiology. AVAILABILITY: ReGAIN analyses are performed using Python v3.11.5 and R v4.4.1 and is available as open-source software through Bioconda at {https://anaconda.org/bioconda/regain-cli}. Source code and documentation can be found at {https://github.com/ERBringHorvath/regain_CLI}. All genomes used in this publication were downloaded from the National Center for Biotechnology Information database. Large supplementary tables and results data from the ESKAPEE pathogen example network analyses can be downloaded from https://figshare.com/articles/dataset/ReGAIN_command_line_software_and_supplemental_figures_/28959431.

Computational Biology↗
PubMed2003

Communication with close and distant relatives in the context of genetic testing for hereditary breast and ovarian cancer in cancer patients.

The psychological aspects of genetic testing for hereditary breast and ovarian cancer (HBOC) in cancer patients (diagnostic genetic testing) have so far received less attention than predictive genetic testing in unaffected persons. Our study is aimed at gaining insight into the psychological aspects of diagnostic genetic testing and at formulating practical recommendations for counseling. Cancer patients often play a key role in the communication of information to relatives because they were the first individuals to be tested in the family. The present article focuses on the communication to close and distant relatives about the hereditary cancer, the genetic test and its result. Participants previously diagnosed with breast and/or ovarian cancer, with a family history of these cancers and who requested DNA-testing, were eligible for the study. Of the 83 eligible patients who could be contacted, 63 participated (response rate = 76%). Twenty-six participants were members of a family where a BRCA1 or BRCA2 mutation was detected. The DNA-analysis in the family of 37 participants had not revealed any mutation. Data were collected by semi-structured interviews and psychological tests and questionnaires. The dissemination of information was largely focused on first-degree relatives. Communication to distant relatives about the genetic test and its result was problematic. Other than the genetic test result and age as "objective" predictors of informing distant relatives, little and/or superficial contact seemed to be the major subjective barrier to informing distant relatives. Furthermore, the knowledge about HBOC of these messengers reveals several shortcomings. Communication within the family should receive special attention during counseling.

Breast Neoplasms↗
PubMedDate not supplied

Subtle effects of herbicide use in the context of genetically modified crops: a case study with glyphosate (Roundup).

Research on the effects of glyphosate and seed germination spans 30 years. Despite several studies reporting detrimental effects of the herbicide on seedling germination and growth, glyphosate is still being registered for use as a weed killer and preharvest desiccant. Its nonselective nature and low chance of species developing resistance has lead to the development of genetically modified crops tolerant to the herbicide which also raises concerns about increased reliance on herbicide use, and subtle ecological impact. This paper presents the result of a literature review on past studies mostly, on crop species, and the results of a new experiment performed with emphasis on noncrop species. The new experimental part attempted to determine whether glyphosate (Roundup) would have an effect on the germination and growth of the F1 generation of seeds produced by plants sprayed with the herbicide. It was designed to mirror spray drift which might affect noncrop plants in nontarget drift zones. Of the 11 species tested using treatments of 0% (control), 1%, 10% or 100% of a 890 g a.i./ha label rate solution sprayed near seed maturity, seven showed a significant effect of the glyphosate treatment on germination and/or growth characteristics. Results of this experiment together with several previous studies reviewed in this paper suggest that there are significant effects to keep in mind when using herbicides such as glyphosate as severe ecological changes could occur.

Germination↗
PubMed2001

Psychiatric diagnoses in the context of genetic studies of bipolar disorder.

Precise definition of the phenotype is an issue of critical importance for the future success of genetic studies of bipolar disorders. So far, an uncertain phenotypic spectrum and genetic heterogeneity are realities that have hampered progress in genetic studies. While recognition of a broader spectrum of related illnesses is important for some applications, for genetic studies a narrow spectrum of illness closely tied to the genotype is paramount. This paper highlights current dilemmas and trends associated with phenotype specification and traces historical approaches. Finally, we explore a number of strategic directions in the diagnostic approach to bipolar disorders that may better serve genetic studies.

Bipolar Disorder↗
PubMed1980

The influence of codon context on genetic code translation.

A class of mutations that increase the deficiency of a suppressor tRNA in translating a particular amber codon has been characterized. The increased efficiency is due to a mutation resulting in a change in the mRNA that affects the nucleotide adjacent to the 3' side of the UAG triplet. Thus the interaction of tRNA with mRNA is influenced by mRNA sequences outside the triplet codon.

Base Sequence↗
PubMedDate not supplied

Patient preferences of decision-making in the context of genetic testing for breast cancer risk.

PURPOSE: We conducted a study on women's preferred physician involvement in the decision to obtain genetic testing for breast cancer risk. METHODS: Women from a primary care physician network completed a telephone survey and a written baseline questionnaire. RESULTS: The majority preferred to make up their own minds. Predictors of leaving the decision to providers were less education, less knowledge, and higher external health locus of control. Trust in one's physician mediated the effect of health locus of control on decision method. CONCLUSION: Physicians will face requests from low-risk women and will need effective communication skills to inform women about the test.

Adult↗