Selfish genetic elements favor the evolution of a distinction between soma and germline

Many multicellular organisms have evolved a dedicated germline. This can benefit the whole organism, but its advantages to genetic parasites have not been explored. Here I model the evolutionary success of a selfish element, such as a transposable element or endosymbiont, which is capable of creating or strengthening a germline-soma distinction in a primitively multicellular host, and find that it will always benefit the element to do so. Genes causing germline sequestration can therefore spread in a population even if germline sequestration is maladaptive for the host organism. Costly selfish elements are expected to survive only in sexual populations, so sexual species may experience an additional push toward germline-soma distinction, and hence toward cell differentiation and multicellularity.     

Genotype-by-environment interaction and the genetic covariance between environments: multilocus genetics

Explicit multi-locus expressions for the genetic variance of a phenotypically plastic trait over a range of environments are derived. The link becomes apparent between the genetic covariance, the genotype-by-environment interaction variance and the variance for the main effect genotype in a two-factor analysis of variance over two environments and many known genotypes. The genetic correlation can be +1 even if the genotype-by-environment interaction variance is greater than zero.     

Path analysis in genetic epidemiology: a critique

Path analysis, a form of general linear structural equation models, is used in studies of human genetics data to discern genetic, environmental, and cultural factors contributing to familial resemblance. It postulates a set of linear and additive parametric relationships between phenotypes and genetic and cultural variables and then essentially uses the assumption of multivariate normality to estimate and perform tests of hypothesis on parameters. Such an approach has been advocated for the analysis of genetic epidemiological data by D. C. Rao, N. Morton, C. R. Cloninger, L. J. Eaves, and W. E. Nance, among others. This paper reviews and evaluates the formulations, assumptions, methodological procedures, interpretations, and applications of path analysis. To give perspective, we begin with a discussion of path analysis as it occurs in the form of general linear causal models in several disciplines of the social sciences. Several specific path analysis models applied to lipoprotein concentrations, IQ, and twin data are then reviewed to keep the presentation self-contained. The bulk of the critical discussion that follows is directed toward the following four facets of path analysis: (1) coherence of model specification and applicability to data; (2) plausibility of modeling assumptions; (3) interpretability and utility of the model; and (4) validity of statistical and computational procedures. In the concluding section, a brief discussion of the problem of appropriate model selection is presented, followed by a number of suggestions of essentially model-free alternative methods of use in the treatment of complex structured data such as occurs in genetic epidemiology.     

Some fundamental aspects of epidemiology: a guide for laboratory scientists.

Epidemiologic methods used to study human diseases are often unfamiliar to the laboratory scientist. This paper outlines the standard method by which epidemiologic studies are classified, explains the methodologic strengths and weaknesses of different kinds of studies, and notes the kinds of inferences that can be drawn from each. Surveys on populations are treated first, followed by sample surveys. Prospective (follow-up) studies, in which groups of subjects are followed in time, are a basic epidemiologic method. Alternatives to these studies that do not require similar time commitments but may allow similar inferences are record studies. Retrospective, or case-control studies, are often the only feasible method for studying rare diseases. However, diseases with long latency periods and problems in control selection can make these studies difficult to analyze and interpret.     

EST-SSRs reveal genetic distinction between lac and grain yielding genotypes of pigeonpea

Journal of Plant Biochemistry and Biotechnology - Pigeonpea, an important legume crop is a good host plant for lac cultivation in North East India. In the present study, sixty-three polymorphic EST...     

Evolutionary ecology of egg size and number in a seed beetle: genetic trade-off differs between environments

Abstract In many organisms, large offspring have improved fitness over small offspring, and thus their size is under strong selection. However, due to a trade-off between offspring size and number, females producing larger offspring necessarily must produce fewer unless the total amount of reproductive effort is unlimited. Because differential gene expression among environments may affect genetic covariances among traits, it is important to consider environmental effects on the genetic relationships among traits. We compared the genetic relationships among egg size, lifetime fecundity, and female adult body mass (a trait linked to reproductive effort) in the seed beetle, Stator limbatus , between two environments (host-plant species Acacia greggii and Cercidium floridum ). Genetic correlations among these traits were estimated through half-sib analysis, followed with artificial selection on egg size to observe the correlated responses of lifetime fecundity and female body mass. We found that the magnitude of the genetic trade-off between egg size and lifetime fecundity differed between environments–a strong trade-off was estimated when females laid eggs on C. floridum seeds, yet this trade-off was weak when females laid eggs on A. greggii seeds. Also differing between environments was the genetic correlation between egg size and female body mass–these traits were positively genetically correlated for egg size on A. greggii seeds, yet uncorrelated on C. floridum seeds. On A. greggii seeds, the evolution of egg size and traits linked to reproductive effort (such as female body mass) are not independent from each other as commonly assumed in life-history theory.     

Microbial diversity in natural environments: focusing on fundamental questions

Interactions with Gijs Kuenen and other Dutch scientists have led my lab to fundamental insights into the composition, structure and function of a hot spring cyanobacterial mat community that should influence our thinking about all microbial communities. By focusing on the distribution of molecular sequence variants of predominant mat phototrophs, we have discovered that small-scale sequence variation can be ecologically meaningful. By applying novel cultivation approaches, we have been able to obtain genetically relevant community members and thus to test the hypothesis that closely related sequence variants arose via adaptive evolutionary radiation. By applying the analytical tools of organic geochemistry we have gained insight into the metabolisms of major phototrophic members of the mat community as well as interactions between phototrophic guilds. These observations challenge traditional paradigms about prokaryotic species and cause us to consider evolutionary ecology theory as we develop genome-based methods for high-resolution analysis of the species-like fundamental units comprising microbial communities, and for investigating how such units coordinate the physiological activities within guilds of the community.     

Beyond strain typing and molecular epidemiology: integrated genetic epidemiology of infectious diseases

In the past 20 years, genetic and molecular methods for characterizing pathogen strains have taken a major place in modern approaches to epidemiology of parasitic and other infectious diseases. Here, Michel Tibayrenc explains the main concepts used in this field of research, with special emphasis on the approaches developed in his team, and suggests future avenues to explore.     

Lipopeptides: adjuvanticity in conventional and genetic immunization

Synthetic lipopeptides derived from the bacterial cell wall component lipoprotein activate B-lymphocytes and macrophages/monocytes in vitro. In vivo they constitute potent immunoadjuvants for a broad range of different antigens and species comparable or superior to Freund's adjuvant. Here, we demonstrate that P(3)CSK(4), representing a highly active lipopentapeptide derivative in vitro, significantly enhances and accelerates the humoral immune response to tetanus toxoid. P(3)CSK(4) could substitute for up to 90% of the antigen without any decrease in the specific IgG level, and the presence of the lipopeptide resulted in a prolonged production of specific IgG in time. Investigations using P(3)CSK(4) as an adjuvant in genetic immunization confirmed earlier data demonstrating that lipopeptides constitute adjuvants for low-immunogenic DNA constructs and/or for application routes resulting in weak immune responses. We monitored a lipopeptide-dependent shift from a Th1-type to Th2-type response, when DNA immunization was followed by i.p. administration of the lipopeptide adjuvant.     

Penetrance of von Recklinghausen neurofibromatosis: a distinction between predecessors and descendants.

This paper reviews the concepts of penetrance and expressivity and examines their application to the specific disorder von Recklinghausen neurofibromatosis. The data suggest that assessments of penetrance among predecessors to probands yield results different from those of assessments of penetrance among descendants to probands. For descendants at risk, penetrance is very close to 100%. For predecessors at risk, extremely variable expressivity may confound estimates of penetrance; as a specific example, a family is described in which two brothers have bona fide von Recklinghausen neurofibromatosis and their mother manifests the neurofibromatosis mutation only as iris Lisch nodules.     

Molecular distinction between arteries and veins

The vertebrate vascular system is essential for the delivery and exchange of gases, hormones, metabolic wastes and immunity factors. These essential functions are carried out in large part by two types of anatomically distinct blood vessels, namely arteries and veins. Previously, circulatory dynamics were thought to play a major role in establishing this dichotomy, but recently it has become clear that arterial and venous endothelial cells are molecularly distinct even before the output of the first embryonic heartbeat, thus revealing the existence of genetic programs coordinating arterial-venous differentiation. Here we review some of the molecular mechanisms involved in this process.The first two authors contributed equally to this work     

The distinction between transudates and exudates

Summary The first step in the diagnosis of pleural effusions is the distinction between exudates and transudates. The aim of this study was to evaluate the usefulness of various parameters for the differentiation of pleural exudates and transudates. We recorded clinical characteristics, final diagnoses, and measured pleural fluid and serum levels of albumin, protein, LDH, cholesterol, and bilirubin of 381 consecutive patients with pleural effusion. Seventy-one (23%) pleural effusions were transudates and 236 were exudates. As a single criterion, the pleural fluid to serum albumin ratio >0.5 was the most accurate parameter (88.4%). An albumin gradient of 12 g/l had an accuracy of 75% in the whole population but it detected 96% of transudative effusions in patients treated with diuretics. Light’s criteria and abbreviated Light’s criteria had similar accuracies, 87.8% vs. 88.2%, respectively. In conclusions, different alternatives can be used instead of Light’s criteria.     

Family based studies and genetic epidemiology: theory and practice

Family based studies have underpinned many successes in uncovering the causes of monogenic and oligogenic diseases. Now research is focussing on the identification and characterisation of genes underlying common diseases and it is widely accepted that these studies will require large population based samples. Population based family study designs have the potential to facilitate the analysis of the effects of both genes and environment. These types of studies integrate the population based approaches of classic epidemiology and the methods enabling the analysis of correlations between relatives sharing both genes and environment. The extent to which such studies are feasible will depend upon population- and disease-specific factors. To review this topic, a symposium was held to present and discuss the costs, requirements and advantages of population based family study designs. This article summarises the features of the meeting held at The University of Sheffield, August 2006.     

Clustered cadherin genes: a sequence-ready contig for the desmosomal cadherin locus on human chromosome 18

We describe the assembly of a cosmid and PAC contig of approximately 700 kb on human chromosome 18q12 spanning the DSC and DSG genes coding for the desmocollins and desmogleins. These are members of the cadherin superfamily of calcium-dependent cell adhesion proteins present in the desmosome type of cell junction found especially in epithelial cells. They provide the strong cell-cell adhesion generated by this type of cell junction for which expression of both a desmocollin and a desmoglein is required. In the autoimmune skin diseases pemphigus foliaceous and pemphigus vulgaris (PV), where the autoantigens are, respectively, encoded by the DSG1 and DSG3 genes, severe areas of acantholysis (cell separation), potentially life-threatening in the case of PV, are evident. Dominant mutations in the DSG1 gene causing striate palmoplantar keratoderma result in hyperkeratosis of the skin on the parts of the body where pressure and abrasion are greatest, viz., on the palms and soles. These genes are also candidate tumor suppressor genes in squamous cell carcinomas and other epithelial cancers. We have screened two chromosome 18-specific cosmid libraries by hybridization with previously isolated YAC clones and DSC and DSG cDNAs, and a whole genome PAC library, both by hybridization with the YACs and by screening by PCR using cDNA sequences and YAC end sequence. The contigs were extended by further PCR screens using STSs generated by vectorette walking from the ends of the cosmids and PACs, together with sequence from PAC ends. Despite screening of two libraries, the cosmid contig still had four gaps. The PAC contig filled these gaps and in fact covered the whole locus. The positions of 45 STSs covering the whole of this region are presented. The desmocollin and desmoglein genes, which are about 30-35 kb in size, are quite well separated at approximately 20-30 kb apart and are arranged in two clusters, one DSC cluster and one DSG cluster, which are transcribed outward from the interlocus region. The order of the genes is correlated with the spatial order of gene expression in the developing mouse embryo, and this, and previous transgenic experiments, suggests that long-range genetic elements that coordinate expression of these genes may be present. The complete bacterial clone contig described in this paper is thus a resource not only for future sequencing but also for investigations into the control of expression of these clustered genes.     

Clustered arg genes on a BamHI segment of the Escherichia coli chromosome.

BamHI cleavage of DNAs from transducing phages gamma darg13 (ppc, argECBH, bfe), gamma darg14 (ppc, argECBH) and gamma darg23 (argECBH) yields three purely gamma DNA segments (and, in one case, a fourth), as well as several Excherichia coli-DNA-containing segments. The length (in kilobases, kb) of the segments, determined by electron microscopy and ararose gel electrophoresis is 4.2, 7.5, 8.4, 6.2, 6.9, and 6.4 kb for gamma darg13; 13.0, 7.5, 4.7, 6.2, 6.9, and 6.4 kb for gamma darg 14: and 5.3, 11.0, 4.7, 6.2, 6.9, and 6.4 kb for gamma darg23. Ordering of the segments (in relation to the gamma genetic map and with the direction from left to right corresponding to the clockwise orientation of the E. coli genetic map and to each of the numerical sequences given) reveals, on 26 kb of bacterial DNA, two cleavage sites defining the 7.5-kb segment obtainable from the DNA of either gamam darg13 or gamma darg14. These and analogous findings with argEC and argCB deletion-bearing strains, together with results from heteroduplex experiments, locate argE, argC, argB, and presumably argH on the 7.5-kb segment.