Does the Genetic Code Have A Eukaryotic Origin?

In the RNA world, RNA is assumed to be the dominant macromolecule performing most, if not all, core "house-keeping" functions. The ribo-cell hypothesis suggests that the genetic code and the translation machinery may both be born of the RNA world, and the introduction of DNA to ribo-cells may take over the informational role of RNA gradually, such as a mature set of genetic code and mechanism enabling stable inheritance of sequence and its variation. In this context, we modeled the genetic code in two content variables-GC and purine contents-of protein-coding sequences and measured the purine content sensitivities for each codon when the sensitivity (% usage) is plotted as a function of GC content variation. The analysis leads to a new pattern-the symmetric pattern-where the sensitivity of purine content variation shows diagonally symmetry in the codon table more significantly in the two GC content invariable quarters in addition to the two existing patterns where the table is divided into either four GC content sensitivity quarters or two amino acid diversity halves. The most insensitive codon sets are GUN (valine) and CAN (CAR for asparagine and CAY for aspartic acid) and the most biased amino acid is valine (always over-estimated) followed by alanine (always under-estimated). The unique position of valine and its codons suggests its key roles in the final recruitment of the complete codon set of the canonical table. The distinct choice may only be attributable to sequence signatures or signals of splice sites for spliceosomal introns shared by all extant eukaryotes.     

Does Aging Have a Purpose?

Ideas of proponents and opponents of programmed aging concerning the expediency of this phenomenon for the evolution of living organisms are briefly considered. We think that evolution has no “gerontological” purpose, because the obligate restriction of cell proliferation during the development of multicellular organisms is a factor that “automatically” triggers aging due to the accumulation of various macromolecular lesions in cells as a result of the suppression, or even complete cessation of emergence of new, intact cells. This leads to the “dilution” of stochastic damage (the most important of which is DNA damage) at the level of the entire cellular population. Some additional arguments in favor of the inexpediency of aging for both species and individuals are also listed.     

Is There a Genetic Basis for Fluctuating Asymmetry and Does it Predict Fitness in the Plant Lotus corniculatus Grown in Different Environmental Conditions?

Fluctuating asymmetry (FA) is considered to be a good measure of developmental stability. We measured the asymmetry of leaves and flowers of 16 different genotypes of Lotus corniculatus grown in four different experimental environments to estimate the plasticity or developmental stability of asymmetry itself. We found that an index of FA (absolute difference between size of left and right sides, corrected for trait size) differed significantly across environments, with the treatment CO2+/N+ inducing the greatest FA for both flowers and leaves. Genotypes did not differ in FAs. Individual plants showed significantly different FAs only for flowers. At the individual level, we found no significant relationship between flower FA and fitness. Previous work indicates that change in asymmetry in a poor or perturbing environment versus a good environment could reflect the intrinsic quality of a particular genotype. However, in our experiment, genotype effect was significant only for change in asymmetry of leaves, and this last trait was not significantly correlated with our fitness estimate for each genotype in either the most or the least perturbing environment.     

Opening the “Black Box”: The Genetic and Biochemical Basis of Eye Evolution

Eyes provide a rich narrative for understanding evolution, having attracted the attention of preeminent scientists and communicators alike. Until recently, this narrative has focused primarily on the evolution of eye structure and far less on biochemistry or genetics. Although eye biochemistry was once likened to an unknown “black box;” the flood of discoveries in biochemistry is now allowing an increasingly detailed understanding of the processes involved in vision. As a result, evolutionary comparative (“tree-thinking”) analyses that use these data currently allow a new and still unfolding narrative, both richer in detail and more comprehensive in scope. Rather than toppling evolutionary theory by finding irreducibly complex molecular machines, eye evolution provides detailed accounts of how natural processes tinker with existing genetic components, duplicating and recombining them, to yield complex, intricate, and highly functional eyes. Understanding the new biochemical narrative is critical for researchers and teachers alike, in order to answer anti-evolutionist claims, and to provide an up-to-date account of the state of knowledge on the subject of eye evolution.     

Language Evolution: What Do Chimpanzees Have to Say?

Although unique in important ways, language shares some properties with other animal communication systems. Comparative analyses of nonhuman primate vocalizations can shed light on the evolution of language's special features.     

Evolution of Cooperation: Does Selfishness Restraint Lie within?

Traditional models of how cooperative strategies succeed in evolution have largely focused on social interactions among individuals and selection acting at kin and group levels. A recent study at the genetic level suggests that cooperation may also be promoted by the evolution of gene-trait relationships that limit the range of possible cheating mechanisms that can evolve.     

Genetic Changes Accompanying the Domestication of Pisum sativum: Is there a Common Genetic Basis to the ‘Domestication Syndrome’ for Legumes?

BACKGROUND AND AIMS: The changes that occur during the domestication of crops such as maize and common bean appear to be controlled by relatively few genes. This study investigates the genetic basis of domestication in pea (Pisum sativum) and compares the genes involved with those determined to be important in common bean domestication. METHODS: Quantitative trait loci and classical genetic analysis are used to investigate and identify the genes modified at three stages of the domestication process. Five recombinant inbred populations involving crosses between different lines representing different stages are examined. KEY RESULTS: A minimum of 15 known genes, in addition to a relatively few major quantitative trait loci, are identified as being critical to the domestication process. These genes control traits such as pod dehiscence, seed dormancy, seed size and other seed quality characters, stem height, root mass, and harvest index. Several of the genes have pleiotropic effects that in species possessing a more rudimentary genetic characterization might have been interpreted as clusters of genes. Very little evidence for gene clustering was found in pea. When compared with common bean, pea has used a different set of genes to produce the same or similar phenotypic changes. CONCLUSIONS: Similar to results for common bean, relatively few genes appear to have been modified during the domestication of pea. However, the genes involved are different, and there does not appear to be a common genetic basis to 'domestication syndrome' in the Fabaceae.     

Does Aβ 42 Have a Function Related to Blood Homeostasis?

In this review, I discuss the possibility that Aβ42 has a physiologic function in blood vessel homeostasis and the consequences that this might have for theories concerning the pathogenesis of Alzheimer’s disease and for treatment. Dedicated with affection to John Blass, who is always willing to talk about new ideas.     

Assessing Genetic Heterogeneity within Bacterial Species Isolated from Gastrointestinal and Environmental Samples: How Many Isolates Does It Take?

Strain typing of bacterial isolates is increasingly used to identify sources of infection or product contamination and to elucidate routes of transmission of pathogens or spoilage organisms. Usually, the number of bacterial isolates belonging to the same species that is analyzed per sample is determined by convention, convenience, laboratory capacity, or financial resources. Statistical considerations and knowledge of the heterogeneity of bacterial populations in various sources can be used to determine the number of isolates per sample that is actually needed to address specific research questions. We present data for intestinal Escherichia coli, Listeria monocytogenes, Klebsiella pneumoniae, and Streptococcus uberis from gastrointestinal, fecal, or soil samples characterized by ribotyping, pulsed-field gel electrophoresis, and PCR-based strain-typing methods. In contrast to previous studies, all calculations were performed with a single computer program, employing software that is freely available and with in-depth explanation of the choice and derivation of prior distributions. Also, some of the model assumptions were relaxed to allow analysis of the special case of two (groups of) strains that are observed with different probabilities. Sample size calculations, with a Bayesian method of inference, show that from 2 to 20 isolates per sample need to be characterized to detect all strains that are present in a sample with 95% certainty. Such high numbers of isolates per sample are rarely typed in real life due to financial or logistic constraints. This implies that investigators are not gaining maximal information on strain heterogeneity and that sources and transmission pathways may go undetected.     

Is There a Genetic Basis for the Deposition of β-Amyloid After Fatal Head Injury?

1. Alzheimer's disease is a heterogeneous disorder that may be caused by genetic or environmental factors or by a combination of both. Abnormalities in chromosomes 1, 14, and 21 have all been implicated in the pathogenesis of the early-onset form of the disease, while the 4 allele of the apolipoprotein E gene (on chromosome 19) is now recognized as a risk factor for early- and late-onset sporadic and familial Alzheimer's disease.2. The best-established environmental trigger for the disease is a head injury, based on epidemiological and neuropathological evidence. Approximately 30% of patients who die after a single episode of severe head injury show intracerebral deposition of -amyloid protein (A), a protein that is thought to be central to the pathogenesis of Alzheimer's disease.3. Recent studies have revealed an over-representation of the apoE 4 allele in those head-injured patients displaying A pathology, thus providing the first evidence for a link between a genetic susceptibility (apoE 4) and an environmental trigger (head injury) in the development of Alzheimer-type pathology.     

Environmental mycobacteria: a threat to human health?

In many cases, bacterial pathogens are close relatives to nonpathogens. Pathogens seem to be limited lineages within nonpathogenic bacteria. Nonpathogenic isolates are generally more diverse and widespread in the environment and it is generally considered that environmental bacteria do not pose a risk to human health as clinical isolates do; this may not be the case with mycobacteria, but environmental mycobacteria have not been well studied. It is documented that several environmental mycobacteria constitute a source for human infections. Diverse mycobacterial environmental isolates are rarely involved in human disease. Environmental mycobacteria may have a role in degradation of different compounds. Environmental mycobacteria have had a long interaction with humans, maybe as long as the human species, and may have contributed to human evolution.     

Brain Evolution: When Is a Group Not a Group?

In testing the 'social brain hypothesis' with comparative data, most research has used group size as an index of cognitive challenge. Recent work suggests that this measure is too crude to apply to a wide range of species, and biologists may need to develop other ways of extending these analyses.     

Genetic rescue: a safe or risky bet?

Small and isolated populations face threats from genetic drift and inbreeding. To rescue populations from these threats, conservation biologists can augment gene flow into small populations to increase variation and reduce inbreeding depression. Spectacular success stories include greater prairie chickens in Illinois (Westermeier et al. 1998 ), adders in Sweden (Madsen et al. 1999 ) and panthers in Florida (Johnson et al. 2010 ). However, we also know that performing such crosses risks introducing genes that may be poorly adapted to local conditions or genetic backgrounds. A classic example of such ‘outbreeding depression’ occurred when different subspecies of ibex from Turkey and the Sinai were introduced to assist recovery of an ibex population in Czechoslovakia (Templeton 1986 ). Despite being fertile, the hybrids birthed calves too early, causing the whole population to disappear. In the face of uncertainty, conservation biologists have tended to respect genetic identity, shying away from routinely crossing populations. In this issue of Molecular Ecology, Frankham ( 2015 ) compiles empirical data from experimental studies to assess the costs and benefits of between‐population crosses (Fig.  1 ). Crosses screened to exclude those involving highly divergent populations or distinct habitats show large heterosis with few apparent risks of outbreeding depression. This leads Frankham to advocate for using assisted gene flow more widely. But do the studies analysed in this meta‐analysis adequately test for latent outcrossing depression?