Avoidance of Long Mononucleotide Repeats in Codon Pair Usage

Protein is an essential component for life, and its synthesis is mediated by codons in any organisms on earth. While some codons encode the same amino acid, their usage is often highly biased. There are many factors that can cause the bias, but a potential effect of mononucleotide repeats, which are known to be highly mutable, on codon usage and codon pair preference is largely unknown. In this study we performed a genomic survey on the relationship between mononucleotide repeats and codon pair bias in 53 bacteria, 68 archaea, and 13 eukaryotes. By distinguishing the codon pair bias from the codon usage bias, four general patterns were revealed: strong avoidance of five or six mononucleotide repeats in codon pairs; lower observed/expected (o/e) ratio for codon pairs with C or G repeats (C/G pairs) than that with A or T repeats (A/T pairs); a negative correlation between genomic GC contents and the o/e ratios, particularly for C/G pairs; and avoidance of C/G pairs in highly conserved genes. These results support natural selection against long mononucleotide repeats, which could induce frameshift mutations in coding sequences. The fact that these patterns are found in all kingdoms of life suggests that this is a general phenomenon in living organisms. Thus, long mononucleotide repeats may play an important role in base composition and genetic stability of a gene and gene functions.

Conformational diversity versus nucleic acid triplex stability, a combinatorial study

The stability of a triple helix formed between a DNA duplex and an incoming oligonucleotide strand strongly depends on the solvent conditions and on intrinsic chemical and conformational factors. Attempts to increase triple helix stability in the past included chemical modification of the backbone, sugar ring, and bases in the third strand. However, the predictive power of such modifications is still rather poor. We therefore developed a method that allows for rapid screening of conformationally diverse third strand oligonucleotides for triplex stability in the parallel pairing motif to a given DNA double helix sequence. Combinatorial libraries of oligonucleotides of the requisite (fixed) base composition and length that vary in their sugar unit (ribose or deoxyribose) at each position were generated. After affinity chromatography against their corresponding immobilized DNA target duplex, utilizing a temperature gradient as the selection criterion, the oligonucleotides forming the most stable triple helices were selected and characterized by physicochemical methods. Thus, a series of oligonucleotides were identified that allowed us to define basic rules for triple helix stability in this conformationally diverse system. It was found that ribocytidines in the third strand increase triplex stability relative to deoxyribocytidines independently of the neighboring bases and position along the strand. However, remarkable sequence-dependent differences in stability were found for (deoxy)thymidines and uridines

Decreased phosphatidylcholine plasmalogens - A putative novel lipid signature in patients with stable coronary artery disease and acute myocardial infarction.

OBJECTIVE Glycerophospholipids and sphingolipids are structurally heterogeneous due to differences in the O- and N-linked fatty acids and head groups. Sphingolipids also show a heterogeneity in their sphingoid base composition which up to now has been little appreciated. The aim of this study was to investigate the association of certain glycerophospholipid and sphingolipid species with stable coronary artery disease (CAD) and acute myocardial infarction (AMI). METHODS The lipid profile in plasma from patients with stable CAD (n = 18) or AMI (n = 17) was compared to healthy subjects (n = 14). Sixty five glycerophospholipid and sphingolipid species were quantified by LC-MS. The relative distribution of these lipids into lipoprotein fractions was analyzed. RESULTS In the CAD cohort, 45 glycerophospholipid and sphingolipid species were significantly lower compared to healthy controls. In the AMI group, 42 glycerophospholipid and sphingolipid species were reduced. Four PC plasmalogens (PC33:1, PC33:2, PC33:3 and PC35:3) showed the most significant difference. Out of eleven analyzed sphingoid bases, four were lower in the CAD and six in the AMI group. Sphingosine-1-phosphate (S1P) levels were reduced in the AMI group whereas an atypical C16:1 S1P was lower in both groups. Phosphatidylcholine and sphingomyelin species were exclusively present in lipoprotein particles, whereas lysophosphatidylcholines were mainly found in the lipoprotein-free fraction. The observed differences were not explained by the use of statins as confirmed in a second, independent cohort. CONCLUSIONS Reduced levels of four PC plasmalogens (PC33:1, PC33:2, PC33:3 and PC35:3) were identified as a putatively novel lipid signature for CAD and AMI.

Randomized, Double-Blind Trial of the Effect of Fluid Composition on Electrolyte, Acid-Base, and Fluid Homeostasis in Patients Early After Subarachnoid Hemorrhage.

Hyper- and hyponatremia are frequently observed in patients after subarachnoidal hemorrhage, and are potentially related to worse outcome. We hypothesized that the fluid regimen in these patients is associated with distinct changes in serum electrolytes, acid-base disturbances, and fluid balance.

Provenance versus weathering control on the composition of tropical river mud (southern Africa)

This study presents an integrated mineralogical-geochemical data base on fine-grained sediments transported by all major rivers of southern Africa, including the Zambezi, Okavango, Limpopo, Olifants, Orange and Kunene. Clay mineralogy, bulk geochemistry, Sr and Nd isotopic signatures of river mud, considered as proxy of suspended load, are used to investigate the influence of source-rock lithology and weathering intensity on the composition of clay and silt produced in subequatorial to subtropical latitudes. Depletion in mobile alkali and alkaline-earth metals, minor in arid Namibia, is strong in the Okavango, Kwando and Upper Zambezi catchments, where recycling is also extensive. Element removal is most significant for Na, and to a lesser extent for Sr. Depletion in K, Ca and other elements, negligible in Namibia, is moderate elsewhere. The most widespread clay minerals are smectite, dominant in muds derived from Karoo or Etendeka flood basalts, or illite and chlorite, dominant in muds derived from metasedimentary rocks of the Damara Orogen or Zimbabwe Craton. Kaolinite represents 30-40% of clay minerals only in Okavango and Upper Zambezi sediments sourced in humid subequatorial Angola and Zambia. After subtracting the effects of recycling and of local accumulation of authigenic carbonates in soils, the regional distribution of clay minerals and chemical indices consistently reflect weathering intensity primarily controlled by climate. Bulk geochemistry identifies most clearly volcaniclastic sediments and mafic sources in general, but cannot discriminate the other sources of detritus in detail. Instead, Sr and Nd isotopic fingerprints are insensitive to weathering, and thus mirror faithfully the tectonic structure of the southern African continent. Isotopic tools thus represent a much firmer basis than bulk geochemistry or clay mineralogy in the provenance study of mudrocks.