Noisy clues to the origin of life

The origin of stable self-replicating molecules represents a fundamental obstacle to the origin of life. The low fidelity of primordial replicators places restrictions on the quantity of information encoded in a primitive nucleic acid alphabet. Further difficulties for the origin of life are the role of drift in small primordial populations, reducing the rate of fixation of superior replicators, and the hostile conditions increasing developmental noise. Thus, mutation, noise and drift are three different stochastic effects that are assumed to make the evolution of life improbable. Here we show, to the contrary, how noise present in hostile early environments can increase the probability of faithful replication, by amplifying selection in finite populations. Noise has negative consequences in infinite populations, whereas in finite populations, we observe a synergistic interaction among noise sources. Hence, two factors formerly considered inimical to the origin of life-developmental noise and drift in small populations-can in combination give rise to conditions favourable to robust replication.     

Genetic clues to the biological basis of autism

Autism, the prototypical pervasive developmental disorder, is characterized by impaired communication and social interaction, and by repetitive interests and behaviours. The core disorder probably affects around 5:10 000 individuals, of whom some three-quarters are male. Onset is in the first three years of life, and the disorder is associated with lifelong disabilities. Because of the clear evidence that idiopathic autism has a strong genetic basis, many groups are undertaking whole genome screens to identify susceptibility loci. We review the first results, and briefly consider the implications of molecular genetic findings for future research, diagnosis and management.     

Seven clues to the origin and structure of class-I ribonucleotide reductase intermediate X

Class-I ribonucleotide reductases (RNRs) are aerobic enzymes that catalyze the reduction of ribonucleotides to deoxyribonucleotides providing the required building blocks for DNA replication and repair. These ribonucleotide-to-deoxyribonucleotide reactions occur by a long range radical (or proton-coupled-electron-transfer) propagation mechanism initiated by a fairly stable tyrosine radical ("the pilot light"). When this pilot light goes out, the tyrosine radical is regenerated by a high-oxidation-state enzyme intermediate, called X. The active site of class-I RNR-X has been recognized as a spin coupled Fe(III)Fe(IV) center with S(total)=1/2 ground state. Although several clues have been obtained from M?ssbauer, (57)Fe, (1)H, (17)O(2), and H(2)(17)O ENDOR (electron-nuclear double resonance), EXAFS (extended X-ray absorption fine structure), and MCD (magnetic circular dichroism) experiments, the detailed structure of the intermediate X is still unknown. In the past three years, we have been studying the properties of a set of model clusters for RNR-X using broken-symmetry density functional theory (DFT), and have compared them with the available experimental results. Based on the detailed analysis and comparisons, we have proposed a definite form for the active site structure of class-I RNR intermediate X. The puzzle is now set: can you find any flaws in the argument or evidence? Can you add anything further to the current experimental picture? The argument is formulated from seven experimental clues with associated calculations and models.     

Plant development: Genetic clues to petal evolution.

A recent study of the expression of floral organ identity genes in buttercups, poppies and their relatives has shed light on the evolutionary origin of petals.     

Sticky bivalves from the Mesozoic: clues to the origin of the anomalodesmatan arenophilic system

Arenophilic glands represent the only molluscan example of multicellular organs solely concerned with adhesion of foreign particles to the external surfaces of an organism. The glands are exclusive to the bivalve clade Anomalodesmata, but do not occur in all component taxa, having been declared absent in a number of families, including Pholadomyidae. This paper records and describes for the first time the arenophilic apparatus of Pholadomya candida G. B. Sowerby I, 1823, and demonstrates that secretion from these glands is at times preserved in the fossil record. In P. candida , arenophilic glands in the middle mantle folds discharge their products on top of the shell as the animal grows, forming radial lines of secretion that comprise a meandering main strand and numerous thin threads projecting in tufts. The arrangement is similar to that of other families, corroborating the hypothesis that the glands are a synapomorphy of crown-group anomalodesmatans. Instances of preserved secretion in fossil Pholadomya , ranging in age almost to the initial appearance of the genus in the Late Triassic, suggest that fossilized arenophilic secretion may aid systematic studies of problematic fossil groups traditionally included in Anomalodesmata.     

Genetic clues to the molecular basis of tobacco addiction and progress towards personalized therapy

The molecular processes that underlie addiction are beginning to unfold. Genetically determined variations in dopaminergic neurotransmission predispose to nicotine dependence. In addition, tobacco use is likely to be governed by the rate at which smokers metabolize nicotine. Functional polymorphisms in CYTOCHROME P450 monooxygenases that metabolize nicotine have now been defined and it should soon be possible to identify fast nicotine metabolizers by DNA analysis. Here, we review the key neurotransmitter receptors and metabolic enzymes implicated in tobacco dependence. We explore the potential benefits of classifying smokers according to the molecular aetiology of their habit. One major benefit will be in planning effective strategies for smoking cessation. Methods of typing for alleles related to smoking behavior that might be suitable for use in clinical practice in the future will also be discussed     

Revisiting the chlamydial type III protein secretion system: clues to the origin of type III protein secretion

The bacterial type III secretion pathway delivers effector proteins into eukaryotic cells. Analysis of the type III system and flagellar export genes in the obligate parasites of the family Chlamydiales suggests that the type III system arose from the flagellar export system in chlamydiae or related bacteria.     

Genetic control of biennial bearing in apple

Although flowering in mature fruit trees is recurrent, floral induction can be strongly inhibited by concurrent fruiting, leading to a pattern of irregular fruiting across consecutive years referred to as biennial bearing. The genetic determinants of biennial bearing in apple were investigated using the 114 flowering individuals from an F(1) population of 122 genotypes, from a 'Starkrimson' (strong biennial bearer)×'Granny Smith' (regular bearer) cross. The number of inflorescences, and the number and the mass of harvested fruit were recorded over 6 years and used to calculate 26 variables and indices quantifying yield, precocity of production, and biennial bearing. Inflorescence traits exhibited the highest genotypic effect, and three quantitative trait loci (QTLs) on linkage group (LG) 4, LG8, and LG10 explained 50% of the phenotypic variability for biennial bearing. Apple orthologues of flowering and hormone-related genes were retrieved from the whole-genome assembly of 'Golden Delicious' and their position was compared with QTLs. Four main genomic regions that contain floral integrator genes, meristem identity genes, and gibberellin oxidase genes co-located with QTLs. The results indicated that flowering genes are less likely to be responsible for biennial bearing than hormone-related genes. New hypotheses for the control of biennial bearing emerged from QTL and candidate gene co-locations and suggest the involvement of different physiological processes such as the regulation of flowering genes by hormones. The correlation between tree architecture and biennial bearing is also discussed.     

The oldest cynodont: new clues on the origin and early diversification of the Cynodontia

Early mammaliaforms and their extinct relatives, nonmammaliaform cynodonts, have long been the focus of intense research in attempting to unravel how and when major changes toward mammalness occurred. The earliest well-known representatives of cynodonts are latest Late Permian in age. Here, we describe Charassognathus gracilis gen. et sp. nov. , from the early Late Permian of South Africa, representing the oldest cynodont yet found. This specimen displays a notch on the dentary in the same location as the base of the masseteric fossa in the basal cynodonts Procynosuchus and Dvinia , and represents the first indication in theriodonts of an invasion of occlusal musculature onto the dentary. A phylogenetic analysis of seven therocephalians and ten non-mammaliaform cynodonts and equally weighted characters resulted in nine most parsimonious trees, the strict consensus of which shows a basal polytomy in cynodonts, including Charassognathus , Dvinia , Procynosuchus and a clade including the remaining cynodonts. The basal polytomy in the majority rule consensus tree is reduced, as Procynosuchus and Dvinia form a clade. One most parsimonious tree, from an analysis using implied weights, positions Charassognathus as the most basal cynodont. This result implies that the Cynodontia initially diversified in Permian Gondwana, in what is now southern Africa.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 149 , 477–492.     

Genetic susceptibility to autoimmune disorders: clues from gene association and gene expression studies

Susceptibility to autoimmune disorders results from the interaction of multiple genetic factors that regulate the threshold of autoreactivity. Genome-wide microsatellite screens and large-scale single nucleotide polymorphism (SNP) association studies have identified chromosomal loci that are associated with specific disorders including systemic lupus erythematosus, rheumatoid arthritis, juvenile arthritis, multiple sclerosis, and diabetes. Numerous candidate gene association studies have in turn investigated the association of specific genes within these chromosomal regions, with susceptibility to autoimmune diseases (e.g. FcgammaReceptors, TYK2 and systemic lupus). More recently, large-scale differential gene expression studies performed on selected tissues from patients with autoimmune disorders, have led to the identification of gene signatures associated with the activation of specific pathways in these diseases (e.g. interferon signature in lupus). In the future, integrated analyses of gene (and protein) expression together with SNP data will allow us to sketch an intelligible picture of the genesis of autoimmunity in humans. This review sets out to illustrate how the most recent advances in the field of systemic lupus erythematosus, rheumatoid arthritis and juvenile arthritis have led to a better understanding of these disorders.     

Genetic continuity in the Franco-Cantabrian region: new clues from autochthonous mitogenomes

Background

The Late Glacial Maximum (LGM), ∼20 thousand years ago (kya), is thought to have forced the people inhabiting vast areas of northern and central Europe to retreat to southern regions characterized by milder climatic conditions. Archaeological records indicate that Franco-Cantabria might have been the major source for the re-peopling of Europe at the beginning of the Holocene (11.5 kya). However, genetic evidence is still scarce and has been the focus of an intense debate.

Methods/Principal Findings

Based on a survey of more than 345,000 partial control region sequences and the analysis of 53 mitochondrial DNA (mtDNA) genomes, we identified an mtDNA lineage, HV4a1a, which most likely arose in the Franco-Cantabrian area about 5.4 kya and remained confined to northern Iberia.

Conclusions/Significance

The HV4a1a lineage and several of its younger branches reveal for the first time genetic continuity in this region and long-term episodes of isolation. This, in turn, could at least in part explain the unique linguistic and cultural features of the Basque region.     

New clues on the origin of the Friedreich ataxia expanded alleles from the analysis of new polymorphisms closely linked to the mutation

Friedreichs ataxia (FRDA) is an autosomal recessive neurodegenerative disorder commonly caused by large expansions of a GAA repeat in the first intron of the frataxin gene, FRDA. The expansion of the triplet repeat is localized within an Alu sequence. FRDA GAA-repeat alleles can be divided into three classes depending on their lengths: short normal alleles (SN), long normal alleles (LN) and expanded pathological alleles (E). We made an accurate analysis of the Alu sequence containing the GAA repeat. We found a new single-nucleotide polymorphism (SNP) that is the closest one to the GAA repeat. We studied this new SNP and the polymorphic polyA region contiguous to the GAA triplets in two populations with different frequencies of FRDA. We found that, while both E and LN alleles seem to be genetically homogeneous and likely related, SN represents a more heterogeneous class of alleles. Indeed, one SNP variation (T) was more frequently associated with (GAA)₈ alleles, whereas the other one (C) with (GAA)₉ repeat(s). The long normal and expanded alleles presented the C haplotype. The same correlation was described for polyA-tract polymorphisms. Thus, 14A was commonly associated with (GAA)₈ alleles and 17A with (GAA)₉ alleles. The long normal alleles more frequently showed the 17A haplotype. Our data seem to suggest that all the E alleles come from LN alleles, while LN alleles come from a defined subclass of SN alleles.     

Genetic archaeologic perspective on the origin of Yakuts

Published data on two cases of linkage disequilibrium in Yakuts are analyzed. These are the disequilibria between loci HLA-A and HLA-B and between the mutation of gene SCA1 responsible for type 1 spinocerebellar ataxia and its flanking microsatellites D6S274 and D6S89. Both cases are regarded as consequences of the founder effect. The genetic archeological approach has been used to calculate the historical period when the mutant SCA1 gene and the HLA-A1\B17 haplotype spread in the population. It has been found that this was approximately 60-70 generations (1500-1750 years) ago in both cases. The time of the segregation of haplotype HLA-A1\B17 has also been calculated for some other populations. Caucasoids have proved to be the oldest carriers of this gene, which agrees with the well-known notion that HLA-A1 originated in Indo-Europeans. The general distribution of HLA genes in Yakuts is similar to that in east-central Asian Mongoloids; therefore, it is concluded that that Yakuts are east-central Asian Mongoloids by origin, except for the founder that had haplotype A1\B17. Historically, the time of the appearance of this haplotype coincided with the period when Saks conquered east-central Asia; therefore, it is hypothesized that the aforementioned founder was a Sak.     

Review. Genetic exchange and the origin of adaptations: prokaryotes to primates

Data supporting the occurrence of adaptive trait transfer (i.e. the transfer of genes and thus the phenotype of an adaptive trait through viral recombination, lateral gene transfer or introgressive hybridization) are provided in this review. Specifically, we discuss examples of lateral gene transfer and introgressive hybridization that have resulted in the transfer or de novo origin of adaptations. The evolutionary clades in which this process has been identified include all types of organisms. However, we restrict our discussion to bacteria, fungi, plants and animals. Each of these examples reflects the same consequence, namely that the transfer of genetic material, through whatever mechanism, may result in adaptive evolution. In particular, each of the events discussed has been inferred to impact adaptations to novel environmental settings in the recipient lineage.