Inferring gene function from evolutionary change in signatures of translation efficiency

Background

The genetic code is redundant, meaning that most amino acids can be encoded by more than one codon. Highly expressed genes tend to use optimal codons to increase the accuracy and speed of translation. Thus, codon usage biases provide a signature of the relative expression levels of genes, which can, uniquely, be quantified across the domains of life.

Results

Here we describe a general statistical framework to exploit this phenomenon and to systematically associate genes with environments and phenotypic traits through changes in codon adaptation. By inferring evolutionary signatures of translation efficiency in 911 bacterial and archaeal genomes while controlling for confounding effects of phylogeny and inter-correlated phenotypes, we linked 187 gene families to 24 diverse phenotypic traits. A series of experiments in Escherichia coli revealed that 13 of 15, 19 of 23, and 3 of 6 gene families with changes in codon adaptation in aerotolerant, thermophilic, or halophilic microbes. Respectively, confer specific resistance to, respectively, hydrogen peroxide, heat, and high salinity. Further, we demonstrate experimentally that changes in codon optimality alone are sufficient to enhance stress resistance. Finally, we present evidence that multiple genes with altered codon optimality in aerobes confer oxidative stress resistance by controlling the levels of iron and NAD(P)H.

Conclusions

Taken together, these results provide experimental evidence for a widespread connection between changes in translation efficiency and phenotypic adaptation. As the number of sequenced genomes increases, this novel genomic context method for linking genes to phenotypes based on sequence alone will become increasingly useful.     

Case oriented approach to co-occurrence of risk lifestyle behavior with overweight, excess abdominal fat and high blood pressure: the CroHort study

Objective of this paper is to estimate interim risk factors (INTF) proportions and changes within 5-years of groups with at least one risk health behavior (BEHF) in CroHort population. Results show that CroHort 2008 group has higher proportions of excess abdominal fat and overweight. Men older than 65 without any BEHF have smaller proportions of INTF in 2008 than in 2003. Proportion of people with high blood pressure is smaller in 2008 for all groups except for young women who show increase. Analysis of middle age group shows significant increase in all INTF in women smokers while men smokers have the highest increase in abdominal fat. Physical inactivity in women is associated with increase of all INTF, while men have decrease in overweight INTF. Alcohol intake has protective effect on middle aged men, except for increase in waist circumference. Women show constant increase in all INTF with heavy alcohol intake.     

Prevalence and five-year cumulative incidence of psychological distress: the CroHort study

The aims of this paper are to investigate the change in prevalence of psychological distress (PD), to investigate the cumulative incidence of the psychological distress and to indicate are there any differences between genders and various age groups in Croatian adult population. Psychological distress status was measured by the five-item Mental Health Scale (MHI-5) of the Short Form questionnaire (SF-36). Psychological distress was present in 28.5% (95% CI 25.7%-31.2%) of men and 32.1% (95% CI 30.1%-34.0%) of women in 2003. In 2008 PD was present in 33.0% (95% CI 30.1%-35.9%) of men and 34.1% (95% CI 32.1%-36.0%) of women. The highest incidence of PD, both for men and women, was in the oldest age group (> 65 years). Results of this study demonstrating the fact that every third adult men and woman in Croatia are in psychological distress, the fact that there is an increase in PD prevalence for men and women should be taken into account in the future mental health policy planning.     

Risk factors for cardiovascular disease in rural area of Croatia

Rural areas, where 47.6% of the Croatian population lives are not generally the focus of research; yet there are challenges which affect the rural population that often go unreported. These communities often exhibit disadvantages in many areas of health. The aim of this study is to examine the specific health needs and related determinants of rural populations influenced by transition that were affected by the consequences of war. The focus of the research is rural lifestyle, behaviour and cardiovascular risk factors in three villages of Sisacko-moslavacka County. Results show that participants generally understand that their own lifestyles influence their health, but they often neglect to change their behaviour to improve their health. This can be explained through complex socio-economic conditions and traditional values of their heritage. These results suggest a need for further research on health status, attitude, and behaviour of Croatia's rural population. Specific public health intervention and services for rural populations must be promoted.     

Complete chloroplast genome sequence of Elodea canadensis and comparative analyses with other monocot plastid genomes

Elodea canadensis is an aquatic angiosperm native to North America. It has attracted great attention due to its invasive nature when transported to new areas in its non-native range. We have determined the complete nucleotide sequence of the chloroplast (cp) genome of Elodea. Taxonomically Elodea is a basal monocot, and only few monocot cp genomes representing early lineages of monocots have been sequenced so far. The genome is a circular double-stranded DNA molecule 156,700bp in length, and has a typical structure with large (LSC 86,194bp) and small (SSC 17,810bp) single-copy regions separated by a pair of inverted repeats (IRs 26,348bp each). The Elodea cp genome contains 113 unique genes and 16 duplicated genes in the IR regions. A comparative analysis showed that the gene order and organization of the Elodea cp genome is almost identical to that of Amborella trichopoda, a basal angiosperm. The structure of IRs in Elodea is unique among monocot species with the whole cp genome sequenced. In Elodea and another monocot Lemna minor the borders between IRs and LSC are located upstream of rps19 gene and downstream of trnH-GUG gene, while in most monocots, IR has extended to include both trnH and rps19 genes. A phylogenetic analysis conducted using Bayesian method, based on the DNA sequences of 81 chloroplast genes from 17 monocot taxa provided support for the placement of Elodea together with Lemna as a basal monocot and the next diverging lineage of monocots after Acorales. In comparison with other monocots, the Elodea cp genome has gone through only few rearrangements or gene losses. IR of Elodea has a unique structure among the monocot species studied so far as its structure is similar to that of a basal angiosperm Amborella. This result together with phylogenetic analyses supports the placement of Elodea as a basal monocot to the next diverging lineage of monocots after Acorales. So far, only few cp genomes representing early lineages of monocots have been sequenced and, therefore, this study provides valuable information about the course of evolution in divergence of monocot lineages.     

1H-NMR-based metabolic profiling of maternal and umbilical cord blood indicates altered materno-foetal nutrient exchange in preterm infants

Background

Adequate foetal growth is primarily determined by nutrient availability, which is dependent on placental nutrient transport and foetal metabolism. We have used ¹H nuclear magnetic resonance (NMR) spectroscopy to probe the metabolic adaptations associated with premature birth.

Methodology

The metabolic profile in ¹H NMR spectra of plasma taken immediately after birth from umbilical vein, umbilical artery and maternal blood were recorded for mothers delivering very-low-birth-weight (VLBW) or normo-ponderal full-term (FT) neonates.

Principal Findings

Clear distinctions between maternal and cord plasma of all samples were observed by principal component analysis (PCA). Levels of amino acids, glucose, and albumin-lysyl in cord plasma exceeded those in maternal plasma, whereas lipoproteins (notably low-density lipoprotein (LDL) and very low-density lipoprotein (VLDL) and lipid levels were lower in cord plasma from both VLBW and FT neonates. The metabolic signature of mothers delivering VLBW infants included decreased levels of acetate and increased levels of lipids, pyruvate, glutamine, valine and threonine. Decreased levels of lipoproteins glucose, pyruvate and albumin-lysyl and increased levels of glutamine were characteristic of cord blood (both arterial and venous) from VLBW infants, along with a decrease in levels of several amino acids in arterial cord blood.

Conclusion

These results show that, because of its characteristics and simple non-invasive mode of collection, cord plasma is particularly suited for metabolomic analysis even in VLBW infants and provides new insights into the materno-foetal nutrient exchange in preterm infants.     

Intraclonal competition inhibits the formation of high-affinity antibody-secreting cells

Protective immunity requires a diverse, polyclonal B cell repertoire. We demonstrate that affinity maturation of the humoral response to a hapten is impaired when preexisting clonally restricted cells recognizing the hapten are dominant in the B cell repertoire. B1-8i(+/-) mice, which feature a high frequency of B cells with nitrophenyl (NP)-binding specificity, respond to NP-haptenated proteins with the production of NP-specific Abs, but affinity maturation is impaired due to insufficient generation of high-affinity Ab-producing cells. We manipulated the frequency of NP-specific B cells by adoptive transfer of B1-8 B cells into naive, wild-type recipients. Remarkably, when 10(4) B1-8 B cells were transferred, these cells supported efficient affinity maturation and plasma cell differentiation. In contrast, when 10(6) B1-8 cells were transferred, affinity maturation did not occur. These data indicate that restricting the frequency of clonally related B cells is required to support affinity maturation.     

Towards the first inhibitors of trihydroxynaphthalene reductase from Curvularia lunata: synthesis of artificial substrate, homology modelling and initial screening

Trihydroxynaphthalene reductase (3HNR) is an essential enzyme in the biosynthesis of fungal melanin and it represents an emerging target for the development of new fungicides and antimicotics. To promote the discovery of new inhibitors, an improved chemical synthesis of the artificial substrate 2,3-dihydro-2,5-dihydroxy-4H-benzopyran-4-one (DDBO) was developed. A series of compounds were screened on 3HNR from Curvularia lunata, a known plant pathogen and an opportunistic human pathogen, and several structurally diverse hits were obtained. Homology modelling of 3HNR from C. lunata can explain their binding modes and will enable further structure-based design of new and improved inhibitors.     

Effect of erythropoietin in a patient with severe congestive heart failure--a case report

Erythropoietin (EPO), traditionally known as a hematopoietic hormone, has recently been shown to have effects beyond hematopoiesis such as prevention of neuronal and cardiac apoptosis secondary to ischemia and induction of neoangiogenesis. Patients with congestive heart failure (CHF) suffer considerable morbidity and mortality despite advances in therapy. Anemia, CHF, and chronic kidney insuficiency often coexist and interact to cause or worsen each other in the so-called cardio-renal anemia syndrome. Treatment with EPO has shown promise in such patients. The paper reviews a case of a successful recovery of cardiac function in a patient with a severe CHF during the treatment with EPO.     

The protein phosphatase 7 regulates phytochrome signaling in Arabidopsis

The psi2 mutant of Arabidopsis displays amplification of the responses controlled by the red/far red light photoreceptors phytochrome A (phyA) and phytochrome B (phyB) but no apparent defect in blue light perception. We found that loss-of-function alleles of the protein phosphatase 7 (AtPP7) are responsible for the light hypersensitivity in psi2 demonstrating that AtPP7 controls the levels of phytochrome signaling. Plants expressing reduced levels of AtPP7 mRNA display reduced blue-light induced cryptochrome signaling but no noticeable deficiency in phytochrome signaling. Our genetic analysis suggests that phytochrome signaling is enhanced in the AtPP7 loss of function alleles, including in blue light, which masks the reduced cryptochrome signaling. AtPP7 has been found to interact both in yeast and in planta assays with nucleotide-diphosphate kinase 2 (NDPK2), a positive regulator of phytochrome signals. Analysis of ndpk2-psi2 double mutants suggests that NDPK2 plays a critical role in the AtPP7 regulation of the phytochrome pathway and identifies NDPK2 as an upstream element involved in the modulation of the salicylic acid (SA)-dependent defense pathway by light. Thus, cryptochrome- and phytochrome-specific light signals synchronously control their relative contribution to the regulation of plant development. Interestingly, PP7 and NDPK are also components of animal light signaling systems.