Is there a twenty third amino acid in the genetic code?

The universal genetic code includes 20 common amino acids. In addition, selenocysteine (Sec) and pyrrolysine (Pyl), known as the twenty first and twenty second amino acids, are encoded by UGA and UAG, respectively, which are the codons that usually function as stop signals. The discovery of Sec and Pyl suggested that the genetic code could be further expanded by reprogramming stop codons. To search for the putative twenty third amino acid, we employed various tRNA identification programs that scanned 16 archaeal and 130 bacterial genomes for tRNAs with anticodons corresponding to the three stop signals. Our data suggest that the occurrence of additional amino acids that are widely distributed and genetically encoded is unlikely.     

Was the evolution of plastid genetic machinery discontinuous?

The plastid nucleoid consists of plastid DNA and various, mostly uncharacterized, DNA-binding proteins. The plastid DNA undoubtedly originated from an ancestral cyanobacterial genome, but the origin of the nucleoid proteins appears complex. Initial biochemical analysis of these proteins, as well as comparative genome informatics, suggest that proteins of eukaryotic origin replaced most of the original prokaryotic proteins during the evolution of plastids in the lineage of green plants.     

Is the Central Valley of Costa Rica a genetic isolate?

In the last decade, the Costa Rican Central Valley population (CRCV), has received considerable scientific attention, attributed in part to a particularly interesting population structure. Two different and contradictory explanations have emerged: (1) An European-Amerindian-African admixed population, with some regional genetic heterocigosity and moderate degrees of consanguinity, similar to other Latin-American populations. (2) A genetic isolate, with a recent founder effect of European origin, genetically homogeneous, with a high intermarriage rate, and with a high degree of consanguinity. Extensive civil and religious documentation, since the settlement of the current population, allows wide genealogy and isonymy studies useful in the analysis of both hypotheses. This paper reviews temporal and spatial aspects of endogamy and consanguinity in the CRCV as a key to understand population history. The average inbreeding coefficients (a) between 1860 and 1969 show a general decrease within time. The consanguinity in the CRCV population is not homogeneous, and it is related to a variable geographic pattern. Results indicate that the endogamy frequencies are high but in general it was not correlated with a values. The general tendency shows a consanguinity decrease in time, and from rural to urban communities, repeating the tendencies observed in other countries with the same degree of development, and follows the general Western World tendency. Few human areas or communities in the world can be considered true genetic isolates. As shown, during last century, the CRCV population has had consanguinity values that definitively do not match those of true genetic isolates. A clear knowledge of the Costa Rican population genetic structure is needed to explain the origin of genetic diseases and its implications to the health system.     

Is there a higher level genetic code that directs evolution?

Summary Because the genetic code is redundant for most amino acids, different codons can be used in a given position without altering the structure of the protein for which the gene codes. This flexibility permits information encoding structural, and therefore functional, properties of RNA and DNA to be transmitted simultaneously by a protein-coding sequence of DNA. Among the other messages that might be transmitted, it is proposed, is one modulating the evolution of the DNA itself.     

Evolution of the genetic machinery of the visual cycle: a novelty of the vertebrate eye?

The discovery in invertebrates of ciliary photoreceptor cells and ciliary (c)-opsins established that at least two of the three elements that characterize the vertebrate photoreceptor system were already present before vertebrate evolution. However, the origin of the third element, a series of biochemical reactions known as the "retinoid cycle," remained uncertain. To understand the evolution of the retinoid cycle, I have searched for the genetic machinery of the cycle in invertebrate genomes, with special emphasis on the cephalochordate amphioxus. Amphioxus is closely related to vertebrates, has a fairly prototypical genome, and possesses ciliary photoreceptor cells and c-opsins. Phylogenetic and structural analyses of the amphioxus sequences related with the vertebrate machinery do not support a function of amphioxus proteins in chromophore regeneration but suggest that the genetic machinery of the retinoid cycle arose in vertebrates due to duplications of ancestral nonvisual genes. These results favor the hypothesis that the retinoid cycle machinery was a functional innovation of the primitive vertebrate eye.     

Is there a physical chemical basis for the present genetic code?

Summary Recent experiments on the interaction of amino acids with homopolyribonucleic acids as measured by proton magnetic resonance spectroscopy and on the interactions of ribonucleoside 5-monophosphates with immobilized amino acids give relative binding strengths that are not reconcilable with the present genetic code in any simple way.     

Is cystic fibrosis genetic medicine's canary?

In 1989 the gene that causes cystic fibrosis (CF) was identified in a search accompanied by intense anticipation that the gene, once discovered, would lead rapidly to gene therapy. Many hoped that the disease would effectively disappear. Those affected were going to inhale vectors packed with functioning genes, which would go immediately to work in the lungs. It was a bewitching image, repeatedly invoked in both scientific and popular texts. Gene therapy clinical trials were carried out with a range of strategies and occasionally success seemed close, but by 1996 the idea that gene therapy for CF would quickly provide a cure was being abandoned by the communities engaged with treatment and research. While conventional wisdom holds that the death of Jesse Gelsinger in an unrelated gene therapy trial in 1999 produced new skepticism about gene therapy, the CF story suggests a different trajectory, and some different lessons. This article considers the rise and fall of gene therapy for CF and suggests that CF may provide a particularly compelling case study of a failed genomic technology, perhaps even of a medical "canary." The story of CF might be a kind of warning to us that genetic medicine may create as many problems as it solves, and that moving forward constructively with these techniques and practices requires many kinds of right information, not just about biology, but also about values, priorities, market forces, uncertainty, and consumer choice.     

Is skeletal mechanotransduction under genetic control?

Studies of twins have established that peak bone mass is about 70% heritable. The skeletal response to exercise contributes to peak bone mass, as mechanical loading increases skeletal mass during growth and development. It is possible that the skeletal responsiveness to mechanical loading is under genetic control, so that some individuals will build stronger bones with exercise. This appears to be the case in mice. Long bones in mice of the C3H/He strain are largely unresponsive to mechanical loading. Ironically, this strain of mice has very high bone density. Perhaps the genes that regulate BMD are not the same as those that regulate mechanical loading response. Studies of recombinant inbred and congenic strains derived from C3H mice will help to identify genes influencing bone size, density and responsiveness to mechanical loading.     

Is a genetic defect in Fkbp6 a common cause of azoospermia in humans?

FK506-binding protein 6 (Fkbp6) is a member of a gene family containing a prolyl isomerase/FK506-binding domain and tetratricopeptide protein-protein interaction domains. Recently, the targeted inactivation of Fkbp6 in mice has been observed to result in aspermic males and the absence of normal pachytene spermatocytes. The loss of Fkbp6 results in abnormal pairing and a misalignment of the homologous chromosomes, and in non-homologous partner switches and autosynapsis of the X chromosome cores in meiotic spermatocytes. In this study, we analyzed whether human FKBP6 gene defects might be associated with human azoospermia. We performed a mutation analysis in all the coding regions of the human FKBP6 gene in 19 patients with azoospermia resulting from meiotic arrest. The expression of the human FKBP6 gene was specific to the testis, and a novel polymorphism site, 245C → G (Y60X) could be found in exon 3. Our findings suggest that the human FKBP6 gene might be imprinted in the testis based on an analysis using two polymorphism sites. These authors equally contributed to this paper     

Is it possible to produce succinic acid at a low pH?

Bio-based succinate is still a matter of special emphasis in biotechnology and adjacent research areas. The vast majority of natural and engineered producers are bacterial strains that accumulate succinate under anaerobic conditions. Recently, we succeeded in obtaining an aerobic yeast strain capable of producing succinic acid at low pH. Herein, we discuss some difficulties and advantages of microbial pathways producing "succinic acid" rather than "succinate." It was concluded that the peculiar properties of the constructed yeast strain could be clarified in view of a distorted energy balance. There is evidence that in an acidic environment, the majority of the cellular energy available as ATP will be spent for proton and anion efflux. The decreased ATP:ADP ratio could essentially reduce the growth rate or even completely inhibit growth. In the same way, the preference of this elaborated strain for certain carbon sources could be explained in terms of energy balance. Nevertheless, the opportunity to exclude alkali and mineral acid waste from microbial succinate production seems environmentally friendly and cost-effective.     

Is a multivariate consensus representation of genetic relationships among populations always meaningful?

To determine the relationships among closely related populations or species, two methods are commonly used in the literature: phylogenetic reconstruction or multivariate analysis. The aim of this article is to assess the reliability of multivariate analysis. We describe a method that is based on principal component analysis and Mantel correlations, using a two-step process: The first step consists of a single-marker analysis and the second step tests if each marker reveals the same typology concerning population differentiation. We conclude that if single markers are not congruent, the compromise structure is not meaningful. Our model is not based on any particular mutation process and it can be applied to most of the commonly used genetic markers. This method is also useful to determine the contribution of each marker to the typology of populations. We test whether our method is efficient with two real data sets based on microsatellite markers. Our analysis suggests that for closely related populations, it is not always possible to accept the hypothesis that an increase in the number of markers will increase the reliability of the typology analysis.     

Is the black robin in genetic peril?

In 1980 the entire black robin species Petroica traversi comprised only five birds, and the current population of ≊ 200 individuals is known to be derived from a single breeding pair. We show here that levels of minisatellite DNA variation in the black robin are among the lowest reported for any avian species in the wild. Surprisingly, similarly bottlenecked control populations of a closely related species ( P. australis australis ) exhibit significantly higher levels of genetic variation. This suggests that the black robin's persistence in a single small population for the last 100 years, rather than the recent bottleneck itself, accounts for the low genetic variation observed. Despite apparent genetic impoverishment, survival and reproductive performance indicate that the black robin is viable under existing conditions. This example illustrates that significant levels of genetic variation are not a necessary prerequisite for endangered species' survival.     

Birth defects in Arkansas: Is folic acid fortification making a difference?

BACKGROUND: Since 1998, fortification of grain products with folic acid has been mandated in the United States, in an effort to reduce the prevalence of neural tube defects (NTDs). Published reports have shown a reduction in the prevalence of spina bifida since fortification was mandated, but no published studies have reported a reduction in birth defects, other than NTDs, that are postulated to be associated with folic acid deficiency. This study was performed to determine if fortification has reduced the prevalence of NTDs and other birth defects in Arkansas. METHODS: Using data from the Arkansas Reproductive Health Monitoring System, prevalences were computed for thirteen specific birth defects with prior evidence supporting a protective effect of folic acid or multivitamins. Prevalences were calculated using data for live births to Arkansas residents for 1993-2000. Exposure to folic acid fortification was classified by birth year as "pre-fortification" (1993-1995), "transition" (1996-1998) or "post-fortification" (1999-2000). Logistic regression analysis was used to compute crude and adjusted prevalence odds ratios comparing the identified time periods. RESULTS: Prevalences decreased between the pre- and post-fortification periods for spina bifida, orofacial clefts, limb reduction defects, omphalocele, and Down syndrome, but only the decrease in spina bifida was statistically significant (prevalence odds ratio 0.56; 95% confidence interval, 0.37, 0.83). CONCLUSION: In Arkansas, the prevalence of spina bifida has decreased since folic acid fortification of foods was implemented. Similar studies by other birth defects surveillance systems are needed to confirm a preventive effect of fortification for malformations other than spina bifida.