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Heterologous expression of excitability proteins: route to more specific drugs?

Many clinically important drugs act on the intrinsic membrane proteins (ion channels, receptors, and ion pumps) that control cell excitability. A major goal of pharmacology has been to develop drugs that are more specific for a particular subtype of excitability molecule. DNA cloning has revealed that many excitability proteins are encoded by multigene families and that the diversity of previously recognized pharmacological subtypes is matched, and probably surpassed, by the diversity of messenger RNAs that encode excitability molecules. In general, the diverse subtypes retain their properties when the excitability proteins are expressed in foreign cells such as oocytes and mammalian cell lines. Such heterologous expression may therefore become a tool for testing drugs against specific subtypes. In a systematic research program to exploit this possibility, major considerations include alternative processing of messenger RNA for excitability proteins, coupling to second-messenger systems, and expression of enough protein to provide material for structural studies.

Animals↗

Improvement of alignment accuracy utilizing sequentially conserved motifs.

BACKGROUND: Multiple sequence alignment algorithms are very important tools in molecular biology today. Accurate alignment of proteins is central to several areas such as homology modelling, docking studies, understanding evolutionary trends and study of structure-function relationships. In recent times, improvement of existing progressing programs and implementation of new iterative algorithms have made a significant change in this field. RESULTS: We report an alignment algorithm that combines progressive dynamic algorithm, local substructure alignment and iterative refinement to achieve an improved, user-interactive tool. Large-scale benchmarking studies show that this FMALIGN server produces alignments that, aside from preservation of functional and structural conservation, have accuracy comparable to other popular multiple alignment programs. CONCLUSIONS: The FMALIGN server allows the user to fix conserved regions in equivalent position in the alignment thereby reducing the chance of global misalignment to a great extent. FMALIGN is available at http://caps.ncbs.res.in/FMALIGN/Home.html.

Algorithms↗

Genetic aspects of methicillin resistance in Staphylococcus aureus and methods used for its detection in clinical laboratories in the United States.

The mecA gene in methicillin-resistant Staphylococcus aureus (MRSA) directs production of a novel penicillin-binding protein (PBP 2A), an enzyme active in cell wall synthesis. MecA, alone, however, does not determine the degree of resistance expressed by strains of MRSA. Differential resistance or variations in other genes that participate in cell wall synthesis, such as laboratory mutant fem genes, may account, in part, for the heterogeneity of methicillin resistance expression in MRSA. The exact mechanisms of methicillin resistance expression in clinical isolates remain to be elucidated. Laboratories use selective agars containing oxacillin and turbidity pattern recognition programs in automated instruments to identify MRSA, although not all mecA-containing strains are detected. Until a rapid and inexpensive DNA probe assay is widely available, newer test methods such as the E test (AB Biodisk), oxidation-reduction indicators in MIC trays (Alamar), and the rapid fluorescent BBl. Crystal system seem promising.

Anti-Bacterial Agents↗

Quantitative trait loci for component physiological traits determining salt tolerance in rice.

Rice (Oryza sativa) is sensitive to salinity, which affects one-fifth of irrigated land worldwide. Reducing sodium and chloride uptake into rice while maintaining potassium uptake are characteristics that would aid growth under saline conditions. We describe genetic determinants of the net quantity of ions transported to the shoot, clearly distinguishing between quantitative trait loci (QTL) for the quantity of ions in a shoot and for those that affect the concentration of an ion in the shoot. The latter coincide with QTL for vegetative growth (vigor) and their interpretation is therefore ambiguous. We distinguished those QTL that are independent of vigor and thus directly indicate quantitative variation in the underlying mechanisms of ion uptake. These QTL independently govern sodium uptake, potassium uptake, and sodium:potassium selectivity. The QTL for sodium and potassium uptake are on different linkage groups (chromosomes). This is consistent with the independent inheritance of sodium and potassium uptake in the mapping population and with the mechanistically different uptake pathways for sodium and potassium in rice under saline conditions (apoplastic leakage and membrane transport, respectively). We report the chromosomal location of ion transport and selectivity traits that are compatible with agronomic needs and we indicate markers to assist selection in a breeding program. Based upon knowledge of the underlying mechanisms of ion uptake in rice, we argue that QTL for sodium transport are likely to act through the control of root development, whereas QTL for potassium uptake are likely to act through the structure or regulation of membrane-sited transport components.

Analysis of Variance↗

A review of hereditary malignant melanoma including biomarkers in familial atypical multiple mole melanoma syndrome.

This review provides a comprehensive coverage of hereditary malignant melanoma with emphasis upon its heterogeneity as well as newly developed biomarker investigations. The recently described familial atypical multiple mole melanoma (FAMMM) syndrome is featured. Particular attention has been given to findings of increased hyperdiploidy observed as an in vitro phenomenon in cultured skin fibroblasts from high-risk and FAMMM-affected subjects. The FAMMM genotype is complex in that it predisposes a patient not only to melanoma (cutaneous and intraocular malignant melanoma) but also to other histologic varieties of cancer, including cancer of the lung, pancreas, and breast. Attention is given to cancer surveillance and management programs for patients at increased risk for the several forms of hereditary malignant melanoma. This approach capitalizes advantageously upon employment of a knowledge of genetics and hereditary cancer syndrome identification, with particular attention to tumor associations.

Diseases in Twins↗

[Comparative genetics and evolutionary morphology of symbiosis formed by plants with nitrogen-fixing microbes and endomycorrhizal fungi].

Results of comparative morphological and genetic analyses are described for two major plant-microbe endosymbioses: N2-fixing nodules (with rhizobia or actinomycetes Frankia) and arbuscular mycorrhiza (with Glomales fungi). Development from the primordia formed de novo in root tissues is common for all known types of N2-fixing nodules. However, their structure varies greatly with respect to: (i) tissue topology (location of vascular bundles is peripheral in legumes but central in non-legumes); (ii) position of nodule primordium (inner or outer cortex in legumes, whereas pericycle in non-legumes); (iii) stability of apical meristem (persistent in the indeterminate nodules, transient in the determinate ones). In addition, legumes vary in ability to form compartments harboring endosymbiotic rhizobia that can be located intercellularly (infection threads) and intracellularly (symbiosomes). Using pea (Pisum sativum) symbiotic mutants, the nodule developmental program is dissected into a range of spatially and temporarily differentiated steps composing four sub-programs (development of endosymbiotic compartments; nodule histogenesis; autoregulation of nodulation; bacteroid differentiation). The developmental mutations are suggested in some cases to reverse the endosymbiotic system into the morphologically simpler forms some of which may correspond to the ancestral stages of nodule evolution. Origination of legume-rhizobial and actinorhizal symbioses is suggested to be based on a set of preadaptations many of which had been evolved in angiosperms during coevolution with arbuscular mycorrhizal fungi (e.g. inter- and intracellular maintenance of symbionts, their control via defence-like reactions and recognition of chitin-like molecules). Analysis of parallel morphological variation in symbiotic mutants and wild-growing legume species enables us to reconstruct the major stages of evolution for N2-fixing symbioses. This evolution proceeded to a sufficient degree independently from the basic physiological function of nodules (symbiotic N2-fixation) and possibly a recruiting of plant genes that initially fulfilled various "non-symbiotic" functions into the genetic networks monitoring plant-microbe interactions.

Bacterial Physiological Phenomena↗

[HIV-1 diversity: a tool for studying the pandemic].

HIV-1 is remarkable for the diversity of strains comprising the HIV/AIDS pandemic. In the last decade, classification of viral variants as groups, subtypes, and circulating recombinant forms (CRF) and the observation of specific mutational patterns have become powerful tools for studying viral molecular dynamics. Monitoring the worldwide distribution of HIV-1 diversity has been used in both epidemiological surveillance programs and in reconstructing the history of regional epidemics. Specific patterns of virus spatial distribution also suggest differences in pathogenicity and transmissibility among the various subtypes. Molecular analyses of viral sequences allow estimating the rate of divergence among variants and the dynamic forces shaping the phylogenetic trees.

Acquired Immunodeficiency Syndrome↗

Evaluation of candidate gene effects for beef backfat via Bayesian model selection.

Candidate gene approaches provide tools for exploring and localizing causative genes affecting quantitative traits and the underlying variation may be better understood by determining the relative magnitudes of effects of their polymorphisms. Diacyglycerol O-acyltransferase 1 (DGAT1), fatty acid binding protein (heart) 3 (FABP3), growth hormone 1 (GH1), leptin (LEP) and thyroglobulin (TG) have been previously identified as genes contributing to genetic control of subcutaneous fat thickness (SFT) in beef cattle. In the present research, Bayesian model selection was used to evaluate effects of these five candidate genes by comparing competing non-nested models and treating candidate gene effects as either random or fixed. The analyses were implemented in SAS to simplify the programming and computation. Phenotypic data were gathered from a F(2) population of Wagyu x Limousin cattle. The five candidate genes had significant but varied effects on SFT in this population. Bayesian model selection identified the DGAT1 model as the one with the greatest model probability, whether candidate gene effects were considered random or fixed, and DGAT1 had the greatest additive effect on SFT. The SAS codes developed in the study are freely available and can be downloaded at: http://www.ansci.wsu.edu/programs/.

Adiposity↗

A constraint logic programming framework for constructing DNA restriction maps.

Restriction mapping is an important computational problem in molecular biology, particularly in genetic engineering and DNA sequencing. It is different in that it is not only a purely computational problem but involves an interaction between experimental data collection procedures and the mapping algorithms. Consequently, the problem is loosely defined and in practice requires a flexible and versatile algorithm. We describe a framework for solving many restriction mapping problems in the constraint logic programming language CLP (R) which takes advantage of the declarative and powerful features of constraint logic programming. A CLP (R) algorithm is developed for solving a simple restriction mapping problem. The algorithm is the extended to handle more complex variations of restriction mapping such as fragments with errors, circular maps, multiple enzymes and partial digests. The mapping variants are integrated within the same framework and differ in the constraints required to define the kind of map consistency. Various search heuristics and control strategies to improve the search process are also incorporated as constraints.

Algorithms↗

Correlated response in feed efficiency accompanying selection for milk yield in Jerseys.

Gross feed efficiency (milk energy output divided by energy consumed) was measured in 232 Jersey cows resulting from direct selection for milk yield and a control line of 121 daughters of 20 Jersey bulls taken randomly from commercial artificial insemination sampling programs in 1967. Data were collected between 1971 and 1982 from primiparous cows in middle to late lactation in 21 feeding trials of 28 d. Cows were fed hay and silage ad libitum plus grain according to production at the rate of 1 kg grain/3 kg milk. Models for least squares analyses included trial, line, days in milk, and either body weight change (model 1) or energy balance (model 2), estimated as the difference between energy requirements and actual energy intake. Body weight change was an insignificant source of variation, and gross feed efficiency did not differ between genetic lines using model 1. Significant line differences in gross efficiency were obtained after adjusting for energy balance; however, problems of multicollinearity invalidates meaningful inference. Results indicate genetic lines of Jerseys did not differ in gross feed efficiency when fed according to yield and suggest selection has not affected efficiency of direct conversion of nutrients into milk.

Animal Feed↗

Genetic influences on reproductive performance.

The potential for genetic improvement of reproductive performance in pigs is great. Improvement can be achieved by increased commercial use of F1 hybrid females produced by crossing lines with excellent reproductive performance and by selection within nucleus populations of these lines for improved reproduction as well a for growth and carcass characteristics. The value of incorporating reproductive traits in selection programs is critically dependent on the relative economic values of fat (or lean) and of extra pigs produced. There is widespread agreement that litter size is the first choice as both the selection objective and the criterion to improve reproductive performance, on economic, genetic, and ease of measurement grounds. Although there are few examples of successful response to selection for increased litter size in pigs (exceptions being the University of Nebraska selection experiment and results achieved by hyperprolific selection schemes), overall results do not suggest that selection for litter size is impossible, only that it is difficult with limited resources. Artificial insemination is being used increasingly by pig breeding companies to accelerate rates of genetic improvement and to improve dissemination. Combining data from genetically connected herds and analyzing with BLUP computer programs to make efficient use of information on relatives makes selection for litter size feasible while maintaining selection pressure for growth and carcass traits. Although selection for lifetime productivity is impractical today, the knowledge and data accumulated from successful breeding programs for litter size may help make it the selection objective of the future. Meanwhile, the search continues for useful indirect criteria for selection, from testis size to molecular markers, and scientists are working with highly prolific breeds of Chinese pigs to better understand the physiologic and genetic basis of large litter size.

Animals↗

[Mental disorders in children: the value of epidemiology].

Epidemiological research on the mental health of children is not well developed in France, as demonstrated by the very small number of publications on the subject, especially in French. The purpose of this article is to show the contribution of epidemiology to an understanding of childhood mental illness. We emphasize descriptive epidemiology (currently the most developed component), but discuss analytic and evaluative epidemiology as well. We have thus considered methodological issues related to the advantages and limitations of techniques employed, using concrete examples from international publications. For example, an extensive review of the literature reveals considerable disparity in figures on the prevalence of psychiatric disorders, chiefly because of problems of variation in definitions used and in the places and techniques of data collection (especially screening tools and diagnostic classifications). Only studies carried out in representative samples of the general population allow reliable evaluation of frequency, but these are particularly difficult and costly. The same may be said for follow-up studies, in particular those on birth cohorts, whose principle importance is that they enable the identification of predictive factors for mental disorders, starting from earliest childhood. Entire areas are currently in need of development, such as the genetic epidemiology in mental illness, clinical trials, or the evaluation of programs. Epidemiology enables the evaluation of service needs, the identification of 'risk groups' and a scientific approach to explanatory factors. In a country such as France where nearly all children are in the school system from the age of 3 years on, schools should become a place for early detection, which assumes a considerable increase in the means available and an innovative policy in the training of health personnel, especially in the area of mental health.

Child↗

DNA fingerprints applied to gene introgression in breeding programs.

An application of DNA fingerprints (DFP) for gene introgression in breeding programs of both farm animals and plants is proposed. DFP loci, detectable by minisatellite probes, are extremely polymorphic. Individuals have unique patterns of DFP and thus can be selected for maximal genomic similarity to the recipient line, and minimal similarity to the donor line, using their DFP patterns as the criterion for similarity. This genomic selection (GS) can be performed at generations BC1, BC2 or both, and thus significantly reduce the required number of backcross generations in introgression breeding programs. The association between genomic and DFP similarity is demonstrated. Theoretical distributions and variances of the relative percentages of the donor and recipient genomes as the basis for the GS approach are presented.

Alleles↗

To shape a cell: an inquiry into the causes of morphogenesis of microorganisms.

We recognize organisms first and foremost by their forms, but how they grow and shape themselves still largely passes understanding. The objective of this article is to survey what has been learned of morphogenesis of walled eucaryotic microorganisms as a set of problems in cellular heredity, biochemistry, physiology, and organization. Despite the diversity of microbial forms and habits, some common principles can be discerned. (i) That the form of each organism represents the expression of a genetic program is almost universally taken for granted. However, reflection on the findings with morphologically aberrant mutants suggests that the metaphor of a genetic program is misleading. Cellular form is generated by a web of interacting chemical and physical processes, whose every strand is woven of multiple gene products. The relationship between genes and form is indirect and cumulative; therefore, morphogenesis must be addressed as a problem not of molecular genetics but of cellular physiology. (ii) The shape of walled cells is determined by the manner in which the wall is laid down during growth and development. Turgor pressure commonly, perhaps always, supplies the driving force for surface enlargement. Cells yield to this scalar force by localized, controlled wall synthesis; their forms represent variations on the theme of local compliance with global force. (iii) Growth and division in bacteria display most immediately the interplay of hydrostatic pressure, localized wall synthesis, and structural constraints. Koch's surface stress theory provides a comprehensive and quantitative framework for understanding bacterial shapes. (iv) In the larger and more versatile eucaryotic cells, expansion is mediated by the secretion of vesicles. Secretion and ancillary processes, such as cytoplasmic transport, are spatially organized on the micrometer scale. The diversity of vectorial physiology and of the forms it generates is illustrated by examples: apical growth of fungal hyphae, bud formation in yeasts, germination of fucoid zygotes, and development of cells of Nitella, Closterium, and other unicellular algae. (v) Unicellular organisms, no less than embryos, have a remarkable capacity to impose spatial order upon themselves with or without the help of directional cues. Self-organization is reviewed here from two perspectives: the theoretical exploration of morphogens, gradients, and fields, and experimental study of polarization in Fucus cells, extension of hyphal tips, and pattern formation in ciliates. Here is the heart of the matter, yet self-organization remains nearly as mysterious as it was a century ago, a subject in search of a paradigm.

Animals↗

Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites.

This paper presents a maximum likelihood approach to estimating the variation of substitution rate among nucleotide sites. We assume that the rate varies among sites according to an invariant+gamma distribution, which has two parameters: the gamma parameter alpha and the proportion of invariable sites theta. Theoretical treatments on three, four, and five sequences have been conducted, and computer program have been developed. It is shown that rho = (1 + theta alpha)/(1 + alpha) is a good measure for the rate heterogeneity among sites. Extensive simulations show that (1) if the proportion of invariable sites is negligible, i.e., theta = 0, the gamma parameter alpha can be satisfactorily estimated, even with three sequences; (2) if the proportion of invariable sites is not negligible, the heterogeneity rho can still be suitably estimated with four or more sequences; and (3) the distances estimated by the proposed method are almost unbiased and are robust against violation of the assumption of the invariant + gamma distribution.

Computer Simulation↗

Searching genomes for sequences with the potential to form intrastrand triple helices.

The canonical double-helix form of DNA is thought to predominate both in dilute solution and in living cells. Sequence-dependent fluctuations in local DNA shape occur within the double helix. Besides these relatively modest variations in shape, more extreme and remarkable structures have been detected in which some bases become unpaired. Examples include unusual three-stranded structures such as H-DNA. Certain RNA and DNA strands can also fold onto themselves to form intrastrand triplexes. Although they have been extensively studied in vitro, it remains unknown whether nucleic acid triplexes play natural roles in cells. If natural nucleic acid triplexes were identified in cells, much could be learned by examining the formation, stabilization, and function of such structures. With these goals in mind, we adapted a pattern-recognition program to search genetic databases for a type of potential triplex structure whose presence in genomes has not been previously investigated. We term these sequences Potential Intrastrand Triplex (PIT) elements. The formation of an intrastrand triplex requires three consecutive sequence domains with appropriate symmetry along a single nucleic acid strand. It is remarkable that we discovered multiple copies of sequence elements with the potential to form one particular class of intrastrand triplexes in the fully sequenced genomes of several bacteria. We then focused on the characterization of the 25 copies of a particular approximately 37 nt PIT sequence detected in Escherichia coli. Through biochemical studies, we demonstrate that an isolated DNA strand from this family of E. coli PIT elements forms a stable intrastrand triplex at physiological temperature and pH in the presence of physiological concentrations of Mg(2+).

Algorithms↗

Telomeres and telomerase in the fetal origins of cardiovascular disease: a review.

Telomeres are noncoding functional DNA repeat sequences at the ends of chromosomes that decrease in length by a predictable amount at each cell division. When the telomeres become critically short, the cell is no longer able to replicate and enters cellular senescence. Recent work has shown that within individuals, telomere length tracks with cardiovascular health and aging and is also affected by growth variation, both prenatally and postnatally. Therefore telomere length can be a marker of both growth history (cell division) and tissue function (senescence). Relationships between early growth and later health have emerged as a research focus in the epidemiology of chronic diseases of aging, such as heart disease and diabetes. The "fetal origins" literature has demonstrated that hormonal and nutritional aspects of the intrauterine environment not only affect fetal growth but also can permanently alter the metabolic program of the individual. Smaller infants tend to have a higher risk of developing cardiovascular disease. Much less attention has been paid to possible genetic links between the processes of early growth and later disease. Our aim in this review is to summarize evidence for one such genetic mechanism, telomere attrition, that may underlie the fetal origins of cardiovascular disease and to discuss this mechanism in light of the evolution of senescence.

Aging↗