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PubMed2002

Ribosome structure: revisiting the connection between translational accuracy and unconventional decoding.

The ribosome is a molecular machine that converts genetic information in the form of RNA, into protein. Recent structural studies reveal a complex set of interactions between the ribosome and its ligands, mRNA and tRNA, that indicate ways in which the ribosome could avoid costly translational errors. Ribosomes must decode each successive codon accurately, and structural data provide a clear indication of how ribosomes limit recruitment of the wrong tRNA (sense errors). In a triplet-based genetic code there are three potential forward reading frames, only one of which encodes the correct protein. Errors in which the ribosome reads a codon out of the normal reading frame (frameshift errors) occur less frequently than sense errors, although it is not clear from structural data how these errors are avoided. Some mRNA sequences, termed programmed-frameshift sites, cause the ribosome to change reading frame. Based on recent work on these sites, this article proposes that the ribosome uses the structure of the codon-anticodon complex formed by the peptidyl-tRNA, especially its wobble interaction, to constrain the incoming aminoacyl-tRNA to the correct reading frame.

Protein Biosynthesis↗
PubMed2000

Manipulating the germline: its impact on the study of carcinogenesis.

Over the past two decades, the mouse has established itself as the primary organism in which to investigate the fundamental mechanisms of carcinogenesis and to model human neoplasia. The principal reason underlying such dominance almost certainly arises out of our ever increasing ability to manipulate the murine germline. Over the past 20 years we have moved from a position where animal models arose either spontaneously or were generated through exposure to carcinogen to a position in which it is possible to create and study precise mutations of choice. The most recent advances in inducible and conditional technologies now open the possibility for both temporal and tissue-specific gene manipulation. Each of these technological breakthroughs has facilitated significant steps forward in our understanding of the genetic basis of tumorigenesis. This review will highlight some of the major advances in the production and use of murine models of neoplasia over the last two decades.

Alleles↗
PubMed1999

Global perspective of tobacco habits and lung cancer: a lesson for third world countries.

Over the past 50 years, a dominant role of tobacco smoking in lung cancer causation has been demonstrated. Almost three-quarters of the lung cancer cases can be attributed to tobacco smoking. The global variation in lung cancer incidence is thought to be directly proportional to the smoking habits prevalent in that part of the world. Lung cancer shows a greater upward trend in incidence in the USA, in central and Eastern Europe than ever before, especially in females. Japan too has recorded a 10-fold increase in incidence in both sexes since 1975. In India the problem is further compounded by absence of authentic data on time trend. The recent trend of available data suggests a more or less linear trend. At present lung cancer ranks among the top three killers in men in almost every metropolis in India. The highest incidence rate has been recorded in Bombay (14.6/ 100,000) and the lowest in Barshi (2.0/100,000). How much of these can be attributed to smoking cannot be commented on as no case-control or cohort studies have ever been undertaken in India. The situation is more alarming in other developing countries, where there is no authentic data on tobacco use or lung cancer incidences. The relationship between tobacco and cancer is both simple and complex. The majority of the cancer patients are smokers, while the cancer incidence is not proportional among smokers. To explain this, various factors such as type of smoke, duration of smoke, amount of carcinogens, presence of activation and metabolism pathways, and lately genetic environment interaction, have been put forward. It appears that the relationship is more complex than at first thought. In developing countries, it is further compounded by lack of data on usage and dependence of the economies of these countries on tobacco. The situation is alarming, with ever-increasing incidence among women and non-smokers exposed to smoke (passive smokers). Tobacco use has already become an epidemic.

Carcinogens↗
PubMed2006

Progression of regulatory gene expression states in fetal and adult pro-T-cell development.

Precursors entering the T-cell developmental pathway traverse a progression of states characterized by distinctive patterns of gene expression. Of particular interest are regulatory genes, which ultimately control the dwell time of cells in each state and establish the mechanisms that propel them forward to subsequent states. Under particular genetic and developmental circumstances, the transitions between these states occur with different timing, and environmental feedbacks may shift the steady-state accumulations of cells in each state. The fetal transit through pro-T-cell stages is faster than in the adult and subject to somewhat different genetic requirements. To explore causes of such variation, this review presents previously unpublished data on differentiation gene activation in pro-T cells of pre-T-cell receptor-deficient mutant mice and a quantitative comparison of the profiles of transcription factor gene expression in pro-T-cell subsets of fetal and adult wildtype mice. Against a background of consistent gene expression, several regulatory genes show marked differences between fetal and adult expression profiles, including those encoding two basic helix-loop-helix antagonist Id factors, the Ets family factor SpiB and the Notch target gene Deltex1. The results also reveal global differences in regulatory alterations triggered by the first T-cell receptor-dependent selection events in fetal and adult thymopoiesis.

Aging↗
PubMed2006

The view from the biochemist. Comment on "Chromatin code, local non-equilibrium dynamics, and the emergence of transcription regulatory programs" by Arndt Benecke.

The review by Arndt Benecke focuses on chromatin, a major hallmark of eukaryotic life. The dynamic of chromatin and its underlying mechanisms are discussed. In addition, theoretical properties of chromatin associated with transcriptional regulation are presented. In the present brief comment on the review by Arndt Benecke, we wish to provide additional information regarding chromatin structure and in particular on the so-called "histone code hypothesis". We will discuss about the emerging idea that chromatin structure is much more complex than previously thought. The possibility that chromatin modifications may play important roles in biology beside transcriptional regulation will also be put forward.

Chromatin↗
PubMed2004

Gene therapy for hemoglobinopathies: are we there yet?

beta-Thalassemia and sickle cell disease constitute the most common single gene defect in humans and are characterized by absent/reduced and abnormal beta-globin, respectively. Patients with these hemoglobinopathies require chronic blood transfusions and rely on bone marrow transplant for a potential cure. Gene therapy provides a viable alternative by permanent correction of the defect in hematopoietic stem cells, but it has suffered from problems of vector instability, low viral titers, and variable expression of globin genes for more than a decade. This paper reviews the field of gene therapy for hemoglobinopathies with emphasis on the complexities of the beta-globin gene and its regulation, obstacles that have impeded progress, and recent advances in vector technology that will take this field forward toward the goal of successful genetic correction of these devastating diseases.

Anemia, Sickle Cell↗
PubMedDate not supplied

Comparison of the genetic activity of 5-nitroimidazole derivatives in Escherichia coli, Neurospora crassa, Saccharomyces cerevisiae and Drosophila melanogaster.

5-nitroimidazoles, including metronidazole (compound 1) and 3 analogues (compounds 2, 3 and 4) of actual or potential chemotherapeutic use were assayed for genetic activity in test systems detecting forward and back mutations in Escherichia coli K-12/343/113, forward mutations in Neurospora crassa heterokaryon 12, mitotic gene conversion in the heteroallelic diploid yeast strain Saccharomyces cerevisiae D4 and sex-linked recessive lethals in Drosophila melanogaster. Whereas metronidazole exhibits moderate mutagenic activity in E. coli, two of the analogues, compounds 2 and 3 are strongly mutagenic even at concentrations that do not inactive the colony forming ability of the cells. The analogue compound 4 does not show any effect toward E. coli under the present experimental conditions. Similar results were obtained with N. crassa, with S. cerevisiae and with Drosophila in which compound 2 exhibits the highest effect, while compound 4 is non-mutagenic in all assays. These biological effects have been partly explained on the basis of differences in the chemical structure of the compounds.

Animals↗
PubMed1987

[Cytochemical demonstration of an endogenous inhibitor of Na-K ATPase and its relationship to familial arterial hypertension].

Acute volume expansion, an increase in sodium intake and a restraint on sodium excretion endow the plasma with the capacity to cause a natriuresis, to inhibit sodium transport and to stimulate vascular reactivity. One natriuretic substance, the atrial natriuretic peptide, has been identified. Cytochemical techniques can detect the presence of a Na-K ATPase inhibitor in the plasma of normal man and the rat, the concentration of which is controlled by salt intake. The substance responsible appears to originate in the hypothalamus. The plasma concentration of the cytochemically detectable Na-K ATPase inhibitor is substantially raised in the plasma of patients with essential hypertension, of the spontaneously hypertensive rat and of the Milan hypertensive rat. An hypothesis is put forward that links salt intake, a genetic renal lesion, the endogenous Na-K ATPase inhibitor, the atrial natriuretic peptide, and the substance responsible for vascular reactivity, with the rise in arterial pressure in hereditary forms of hypertension.

Animals↗
PubMed1998

Calibration of the single cell gel electrophoresis assay, flow cytometry analysis and forward mutation in Chinese hamster ovary cells.

The induction kinetics of genetic damage were measured in one clone of a mammalian cell line (CHO AS52) with three genotoxicity assays, the single cell gel electrophoresis (Comet) assay, laser beam flow cytometry and forward mutation. The first two assays allow for the rapid analysis of genotoxic damage in individual nuclei. The alkaline Comet assay detects DNA strand breaks, alkali-labile sites and incomplete excision repair sites. Flow cytometry measures chromosome damage that results in an unequal distribution of nuclear DNA in daughter cells. We calibrated these assays to compare acute DNA damage and longer term clastogenicity with forward mutation at the gpt locus using ethyl methanesulfonate (EMS). The EMS treatments were conducted in F12 medium for 2 h. AS52 cells carry a single functional gpt gene which provides for quantitation of gpt mutants by selecting for 6-thioguanine resistance. EMS induced a concentration-dependent response with median Comet tail moment values of 1.06 microns for the negative control and 64.6 microns with 20 mM. The coefficient of variation (CV) of the negative-control with flow cytometry was 2.33; the CV value increased to 4.87 in cells treated with 20 mM EMS, EMS (8 mM) induced a mutant frequency of 779.8 x 10(-6) at a relative survival of 64.4%. Genetic response factors were calculated and the data demonstrate that the induction kinetics of genetic damage as measured by the Comet assay (15.6) and flow cytometry (14.2) were more closely related than that determined for mutation induction (7.9). These three assays measure a wide spectrum of genetic events at the level of DNA, the gene and the chromosome and demonstrate the usefulness of the Comet assay and flow cytometry as two relatively rapid procedures to detect genotoxic damage in mammalian cells.

Animals↗
PubMed1993

Looking forward.

We are now entering the genome era of genetics, this phase being preceded by prior intellectual movements which gave the world: (1) Mendelian analysis, (2) DNA as the molecule of genetics, (3) the DNA-->RNA-->protein Central Dogma, (4) the molecular basis of gene expression and regulation, (5) the use of recombinant DNA procedures for gene isolation and manipulation, and (6) DNA sequencing and genome analysis. Soon, the human genetic information made possible by genome analysis will lead to subsequent logically following eras of predictive genetics and gene therapy.

Animals↗
PubMed2005

Insertional mutagenesis in mice: new perspectives and tools.

Insertional mutagenesis has been at the core of functional genomics in many species. In the mouse, improved vectors and methodologies allow easier genome-wide and phenotype-driven insertional mutagenesis screens. The ability to generate homozygous diploid mutations in mouse embryonic stem cells allows prescreening for specific null phenotypes prior to in vivo analysis. In addition, the discovery of active transposable elements in vertebrates, and their development as genetic tools, has led to in vivo forward insertional mutagenesis screens in the mouse. These new technologies will greatly contribute to the speed and ease with which we achieve complete functional annotation of the mouse genome.

Animals↗
PubMed2004

Translating therapies for Huntington's disease from genetic animal models to clinical trials.

Genetic animal models of inherited neurological diseases provide an opportunity to test potential treatments and explore their promise for translation to humans experiencing these diseases. Therapeutic trials conducted in mouse models of Huntington's disease have identified a growing number of potential therapies that are candidates for clinical trials. Although it is very exciting to have these candidates, there has been increasing concern about the feasibility and desirability of taking all of the compounds that may work in mice and testing them in patients with HD. There is a need to begin to prioritize leads emerging from transgenic mouse studies; however, it is difficult to compare results between compounds and laboratories, and there are also many additional factors that can affect translation to humans. Among the important issues are what constitutes an informative genetic model, what principals should be followed in designing and conducting experiments using genetic animal models, how can results from different laboratories and in different models be compared, what body of evidence is desirable to fully inform clinical decision making, and what factors contribute to the equipoise in determining whether preclinical information about a therapy makes clinical study warranted. In the context of Huntington's disease, we will review the current state of genetic models and their successes in putting forward therapeutic leads, provide a guide to assessing studies in mouse models, and discuss some of the salient issues related to translation from mice to humans.

Animals↗
PubMed1995

Molecular evolution of influenza viruses.

There are two different mechanisms by which influenza viruses might evolve: (1) Because the RNA genome of influenza viruses is segmented, new strains can suddenly be produced by reassortment, as happens, for example, during antigenic shift, creating new pandemic strains. (2) New viruses evolve relatively slowly by stepwise mutation and selection, for example, during antigenic or genetic drift. Influenza A viruses were found in various vertebrate species, where they form reservoirs that do not easily mix. While human influenza A viruses do not spread in birds and vice versa, the species barrier to pigs is relatively low, so that pigs might function as "mixing vessels" for the creation of new pandemic reassortants in Southeast Asia, where the probability is greatest for double infection of pigs by human and avian influenza viruses. Phylogenetic studies revealed that about 100 years ago, an avian influenza A virus had crossed the species barrier, presumably first to pigs, and from there to humans, forming the new stable human and classical swine lineages. In 1979, again, an avian virus showed up in the North European swine population, forming another stable swine lineage. The North European swine isolates from 1979 until about 1985 were genetically extremely unstable. A hypothesis is put forward stating that a mutator mutation is necessary to enable influenza virus to cross the species barrier by providing the new host with sufficient variants from which it can select the best fitting ones. As long as the mutator mutation is still present, such a virus should be able to cross the species barrier a second time, as happened about 100 years ago. Although the most recent swine isolates from northern Germany are again genetically stable, we nevertheless should be on the lookout to see if a North European swine virus shows up in the human population in the near future.

Animals↗
PubMed2005

Towards molecular breeding and improvement of rice in China.

China is the largest producer and consumer of rice in the world and a pioneer in applying hybrid rice technology. Although hybrid rice has contributed greatly to Chinese agriculture in the past decades, its potential to improve grain quality further is being questioned. However, to meet the challenges posed by severe crop damage by pests and diseases, the extensive use of pesticides and chemical fertilizers, and a shortage of water and energy, more elite rice cultivars are needed. In recent years, China has seen continued improvements in rice genetics, powered by functional genomics as a way forward to safeguard its rice production. Here, we briefly review the current status of rice breeding in China through strategies integrating hybrid rice technology, molecular marker-assisted breeding, functional genomics and genetically modified rice.

Breeding↗
PubMed2006

[How long the way from QTL to QTGS?].

Most of the important economic traits in higher plants are quantitative traits. Genetic basic researches for quantitative traits were strongly promoted. This article fully elaborated the complicated relationship between quantitative phenotype and its genotype, introduced the recently developed strategy of fine mapping. discussed the current difficulty and hardness among the process of dissect the genetic basis of target traits, then brought forward several research direction that remained to be improved , and finally gave a view of such prospect. Generally speaking,, however, a QTL is still a considerable DNA fragment frequently containing multiplex genes. We also provided some ways and means from QTL coarse locus research to the variation at quantitative trait gene (QTG) level and from QTG to quantitative trait nucleotides (QTN) corresponding to alleles resulted from the intragenetic polymorphism. This is a major challenge for quantitative genetics in the post-genome era.

Animals↗
PubMed2003

[Was August Weismann right?].

A new hypothesis of the genetic regulation of cell differentiation is put forward. The hypothesis is based on the assumption that the diminution and hyper-replication patterns of repetitive nucleotide sequences depend on the differentiation pathways of cells and tissues.

Animals↗
PubMed1999

The essence of SNPs.

Single nucleotide polymorphisms (SNPs) are an abundant form of genome variation, distinguished from rare variations by a requirement for the least abundant allele to have a frequency of 1% or more. A wide range of genetics disciplines stand to benefit greatly from the study and use of SNPs. The recent surge of interest in SNPs stems from, and continues to depend upon, the merging and coincident maturation of several research areas, i.e. (i) large-scale genome analysis and related technologies, (ii) bio-informatics and computing, (iii) genetic analysis of simple and complex disease states, and (iv) global human population genetics. These fields will now be propelled forward, often into uncharted territories, by ongoing discovery efforts that promise to yield hundreds of thousands of human SNPs in the next few years. Major questions are now being asked, experimentally, theoretically and ethically, about the most effective ways to unlock the full potential of the upcoming SNP revolution.

DNA↗
PubMed1984

[Nature of the phenotypic variability of somatic cells in culture: unstable phenotypic changes].

It was stated elsewhere ( Glebov , Abramyan , 1983) that the appearance of a number of phenotypic variants detected in somatic cell populations with high frequency should be provided by genetical unstable alterations. The properties of somatic cell variants that reproduce unstably a changable phenotype in the course of cell generations are analysed. These variants: (1) appear accidentally and independently on selectivity agent; (2) as a rule, the frequency of the variant arising does not increase under the action of mutagens; (3) the phenotypic reversion of unstable variants is a stochastic process; (4) such variants are characterized by intraclonal heterogeneity and by the segregation of stable alternative variants. The number of properties of phenotypically unstable variants isolated by one-step selection is similar to those for somatic cell variants isolated in the course of multistep selection. The latter are characterized by phenotypic reversion too. The appearance of unstable phenotypic variants is concluded to be associated with the genetical unstable alterations. It is argued that at least part of above alterations should be induced by the insertion of mobile genetic elements. The features of karyotypical variation in somatic cell population allow to conclude that the karyotype of cultured somatic cells is a genetically unstable attribute. The features mentioned above are: a high frequency of karyotypical alterations which is inherited by the cells with difference in the frequency of arising of karyotypical alteratons . The unstability of karyotype is restricted to the genetic unstability that is seen from non-random karyotypic variation, and interclonal difference in the chromosome stability. The site-specificity of karyotype alterations that proceed with high frequency allow to put forward a hypothesis that the process of mobile genetic element transposition is induced on the early stages of the history of constant cultured cell lines.

Animals↗