Codon–anticodon interaction and the genetic code evolution

The evolution of the genetic code, with 20 amino acids encoded from the beginning, is analyzed from the viewpoint of codon–anticodon interaction. Imposing a minimum principle for the interaction, in the framework of the so called crystal basis model of the genetic code, we determine the structure of the anticodons in the ancient, archetypal and early genetic codes, that are all reconciled in a unique frame. Most of our results agree with the generally accepted scheme.     

Two genetic stocks of Steindachneridion melanodermatum living in sympatry in nature and genetic variability of wild parents and F₁ generation

Steindachneridion melanodermatum is a large Brazilian catfish, highly prized for sport fishing and for its meat. Specimens of this species, both caught in nature from Iguacu River and F(1) fish born in captivity, were analyzed with regard to patterns of RAPD molecular markers. Genetic similarity ranged from 0.57 to 0.95; two groups were determined for the wild specimens. The results suggest different genetic lineages in sympatry in nature. Heterozygosity and percentage of polymorphic loci were 0.31 and 79% and 0.23 and 62%, respectively, for the two populations of wild specimens and 0.26 and 66%, respectively, for those born in captivity.     

Indirect genetic effects and the lek paradox: inter-genotypic competition may strengthen genotype × environment interactions and conserve genetic variance

Understanding the evolutionary mechanisms that maintain genetic variation in natural populations is one of the fundamental goals of evolutionary biology. There is growing evidence that genotype-by-environment interaction (G × E) can maintain additive genetic variance (V _A), but we lack information on the relative performance of genotypes under the competitive situations encountered in the field. Competing genotypes may influence each other, and this interaction is also subject to selection through indirect genetic effects (IGE). Here, we explore how genotypes perform when interacting and evaluate IGE in order to understand its influence on V _A for sexually-selected traits in the lesser waxmoth, Achroia grisella. We found that inter-genotype differences and crossover interactions under joint rearing are equal to or greater than values when reared separately. A focal genotype exhibited different performances when jointly reared with various genotypes—suggesting that IGE may be responsible for the increased levels of crossover and differences in performance observed. We suggest that some genotypes are superior competitors for food acquisition in the larval stage, and that these differences influence the development and evolution of other genotypes through IGE. We reaffirm the role of G × E in maintaining V _A and note the general importance of IGE in studies of evolutionary mechanisms.     

Agyria — pachygyria and Miller-Dieker syndrome: clinical,genetic and chromosome studies

Summary Twelve cases of lissencephaly are reported. A high resolution chromosome study was performed on each in order to detect small chromosomal anomalies, undetectable with routine techniques. Only one case was shown to have an unbalanced karyotype with a microdeletion of the short arm of chromosome 17(del 17p). This child also had symptoms of the Miller-Dieker syndrome, consisting of lissencephaly, characteristic facies, pre- and post-natal growth retardation and other birth defects. As proposed by Dobyns, it seems justifiable to classify lissencephalies into four different groups, according to other clinical manifestations and results of chromosome studies.     

Plasma norepinephrine and dopamine-β-hydroxylase in genetic hypertensive rats

The relationship between blood pressure, plasma norepinephrine (NE), dopamine-β-hydroxylase (DBH) activity and age was investigated in spontaneously hypertensive rat (SHR), a stroke-prone substrain of the SHR and control Wistar-Kyoto rat (WKR). Blood pressure of both SHR strains increased with age and was significantly higher than that of the WKR at all ages tested (3 15 weeks). The blood pressure of stroke-prone SHR was significantly higher than that of the regular SHR after 6 weeks of age. Plasma DBH activity decreased with age in each strain, although the SHR, and especially the stroke-prone SHR, had significantly higher DBH than the controls at an early age. Plasma NE in the WKR did not change with age. Increased plasma NE was observed only in the young SHRs. The highest values were found in the 6 week old stroke-prone SHR. These data suggest that plasma DBH activity is not correlated directly with plasma NE or blood pressure, but that increased sympathetic nerve activity may occur during the development of hypertension in the SHR and the stroke-prone SHR.     

Dy and Nd induced genetic mutation of bacillus α-amylase

After treatment with DyCl₃ and NdCl₃, two strains of mutated bacilli showing increased α-amylase activity were isolated. The α-amylase genes were amplified, cloned, and sequenced. Sequencing revealed that there were either 11 or 14 bases altered in the two genes. These alterations took the form of base substitutions, and transversion was more common than transition. Based on these results, it was concluded that the rare earth compounds DyCl₃ and NdCl₃ were mutagens.     

Insurance and genetic testing: where are we now?

Basic research will spur development of genetic tests that are capable of presymptomatic prediction of disease, disability, and premature death in presently asymptomatic individuals. Concerns have been expressed about potential harms related to the use of genetic test results, especially loss of confidentiality, eugenics, and discrimination. Existing laws and administrative policies may not be sufficient to assure that genetic information is used fairly. To provide factual information and conceptual principles upon which sound social policy can be based, the Human Genome Initiative established an Ethical, Legal, and Social Issues Program. Among the first areas to be identified as a priority for study was insurance. This paper provides a review of life, health, and disability insurance systems, including basic principles, risk classification, and market and regulatory issues, and examines the potential impact of genetic information on the insurance industry.     

Does habitat fragmentation reduce genetic diversity and subpopulation connectivity?

The estimation of levels of genetic variation has received considerable attention because it is generally thought to be indicative of overall species vitality and the potential for evolutionary responses to environmental changes. Here, we use allozymes markers and two distinct collections of Cakile maritima, an annual species from sandy coastal habitats (2000 generation and 2005 generation collected from 9 populations in their natural habitats), to assess the magnitude of expected genetic change. We compared genetic diversity between generations (all populations combined), and then between populations at each generation. Based on 13 loci scored from the eight enzymes examined, a high genetic diversity was detected at both the population and generation level as compared to other herbaceous species. However, allelic richness reduction in the 2005 generation suggested restricted gene flow and a high risk of future genetic bottlenecks, if larger tracts of coastal areas disappear. Most loci showed deviation from Hardy‐Weinberg equilibrium due to excess of heterozygotes in all populations suggesting that this species has an allogamic mode of reproduction. It appears most likely that this species has experienced a recent decrease in population size, and that genetic drift in small populations has resulted in a loss of alleles occurring at low frequency. Despite the deterioration process, maintenance of high genetic diversity suggests that there are some ecological factors determining population structure.     

Microbial acid-stable α-amylases: Characteristics,genetic engineering and applications

Among the wide variety of amylolytic enzymes synthesized by microorganisms, α-amylases are the most widely used biocatalysts in starch saccharification, baking industries and textile desizing. These enzymes randomly cleave the α-1,4-glycosidic linkages in starch, generating maltose and malto-oligosaccharides. The commercially available α-amylases have certain limitations, such as limited activity at low pH and Ca²⁺-dependence, and therefore, the search for novel acid-stable and thermostable amylases from extremophilic microorganisms and the engineering of the already available enzymes have been the major areas of research in this field over the years. Several attempts have been made to find suitable microbial sources of acid-stable and thermostable α-amylases. Acid-stable α-amylases have been reported in fungi, bacteria and archaea. α-Amylases that are active at elevated temperatures have been reported in bacteria as well as in archaea. α-Amylases that possess both characteristics, to the extent required for their various applications are very scarce. The developments that have been made in molecular biology, directed evolution and structural conformation studies of α-amylases for improving their properties to suit various industrial applications are discussed in this review.     

β-Turn-driven early evolution: The genetic code and biosynthesis pathways

Summary The physicochemical properties of -turns suggest their biological importance prior to the formation of the genetic code. These properties include ones potentially affecting the preference for eitherl- ord-amino acids. The abundance of certain amino acids in -turns is correlated with their assignment to a small, well-defined part of the genetic code and with their role as metabolic precursors for other amino acids. It is proposed that in the prebiotic environment, -turns became objects of selection that influenced the evolution of the genetic code and biosynthetic pathways for amino acids.     

Current applications of wheat and wheat–alien precise genetic stocks

A comprehensive collection of wheat aneuploids, whole chromosome substitutions (both intervarietal and interspecific) and wheat–alien addition lines, along with various introgression and near-isogenic lines, has been created over a period of years, primarily to provide the means of localizing the genes underpinning traits and to introduce novel genes into the bread wheat genome. For a time, interest in this class of genetic material was on the wane, but more recently it has revived in the context, for example, of localizing DNA-based markers, designing chromosome-specific bacterial artificial chromosome libraries, and establishing functional differences between alleles and homoeoalleles. Here, a brief review is provided of recent applications of precise genetic stocks in the field of molecular genetics, functional genetics and genomics of the Triticeae species.     

The polyphyly of Neotragus – Results from genetic and morphometric analyses

Dwarf antelope species were commonly united in the tribe “Neotragini” (Bovidae, Mammalia) due to their general morphological appearance. However, phylogenetic analyses have shown that not all dwarf antelopes are closely related, so it was suggested to restrict the name Neotragini to the type genus Neotragus. In our study we use mitochondrial cytochrome b sequences and linear skull measurements to further investigate the similarity of all three Neotragus species. Our analyses support the close relationship of N. moschatus and N. batesi. However, N. pygmaeus – the type species, which was never before included in phylogenetic analyses – is not closely related. It might share a most recent common ancestor with another “dwarf antelope”, the Klipspringer Oreotragus oreotragus, and the duikers in the taxon Cephalophini. Hence, we suggest resurrecting the genus Nesotragus von Dueben, 1846 for Nesotragus moschatus and N. batesi.     

Geographic variation of genetic and behavioral traits in northern and southern tüngara frogs

We use a combination of microsatellite marker analysis and mate-choice behavior experiments to assess patterns of reproductive isolation of the túngara frog Physalaemus pustulosus along a 550-km transect of 25 populations in Costa Rica and Panama. Earlier studies using allozymes and mitochondrial DNA defined two genetic groups of túngara frogs, one ranging from Mexico to northern Costa Rica (northern group), the second ranging from Panama to northern South America (southern group). Our more fine-scale survey also shows that the northern and southern túngara frogs are genetically different and geographically separated by a gap in the distribution in central Pacific Costa Rica. Genetic differences among populations are highly correlated with geographic distances. Temporal call parameters differed among populations as well as between genetic groups. Differences in calls were explained better by geographic distance than by genetic distance. Phonotaxis experiments showed that females preferred calls of males from their own populations over calls of males from other populations in about two-thirds to three-fourths of the contrasts tested. In mating experiments, females and males from the same group and females from the north with males from the south produced nests and tadpoles. In contrast, females from the south did not produce nests or tadpoles with males from the north. Thus, northern and southern túngara frogs have diverged both genetically and bioacoustically. There is evidence for some prezygotic isolation due to differences in mate recognition and fertilization success, but such isolation is hardly complete. Our results support the general observation that significant differences in sexual signals are often not correlated with strong genetic differentiation.     

Prevalence and genetic analysis of α-thalassemia and β-thalassemia in Chongqing area of China

Background and aims

Thalassemia is one of the most common hereditary disorders. This study aimed to investigate the prevalence of thalassemia and the mutation spectrum in Chongqing, the southern area of China.

Methods

A total of 1057 children were recruited from Chongqing. Hematological parameters were examined and globin genes were genetically analyzed.

Results

The total frequency of thalassemia carriers was 7.76% in this group of children. Among these, α-thalassemia was 5.20%, β-thalassemia was 1.99% and abnormal hemoglobin variant was 0.57%. Furthermore, 24 cases of α-triplication were detected, frequency of which was 2.55%. The true prevalence of silent α-thalassemia was first reported in this study. In addition, six novel mutations that give rise to α-thalassemia and two rare abnormal hemoglobin variants were first identified in Chinese population.

Conclusions

Our data suggested that the population in Chongqing are at high risk of α- and β-thalassemia. The findings will be useful for genetic counseling and the prevention of severe thalassemias in this area.     

Folic acid - vitamin and panacea or genetic time bomb?

We live in a health-conscious age - many of us supplement our diet with essential micronutrients through the discretionary use of multivitamin pills or judicious selection of foods that have a health benefit beyond that conferred by the nutrient content alone - the so-called 'functional foods'. Indeed, the citizens of some nations have little choice, with a mandatory fortification policy in place for certain vitamins. But do we ever stop to consider the consequences of an increased exposure to micronutrients? We examine this issue in relation to the B-group vitamin folic acid, and ask whether supplementation with this vitamin could introduce a strong genetic selection pressure - one that has the side effect of increasing the prevalence of some of the most significant, human life-threatening diseases. Are we affecting our genetics - is this a case of human evolution in progress by altering our diet?     

DNA polymerases and SOS mutagenesis: can one reconcile the biochemical and genetic data?

Until recently, it had been concluded from genetic evidence that DNA polymerase III (Pol III, the main replicative polymerase in E. coli) was also responsible for mutagenic translesion synthesis on damaged templates, albeit under the influence of inducible proteins UmuD' and UmuC. Now it appears that these proteins themselves have polymerase activity (and are now known as Pol V) and can carry out translesion synthesis in vitro in the absence of Pol III. Here I discuss the apparent contradictions between genetics and biochemistry with regard to the role of Pol III in translesion synthesis. Does Pol V interact with Pol III and constitute an alternative component of the replication factory (replisome)? Where do the other three known polymerases fit in? What devices does the cell have to ensure that the "right" polymerase is used in a given situation? The debate about the role of Pol III in translesion synthesis reveals a deeper divide between models that interpret everything in terms of mass action effects and those that embrace a replisome held together by protein-protein interactions and located as a structural entity within the cell.