Synonymous codon usage pattern among the S,M, and L segments in Crimean-congo hemorrhagic fever virus

Crimean-Congo hemorrhagic fever (CCHF) virus is one among the major zoonosis viral diseases that use the Hyalomma ticks as their transmission vector to cause viral infection to the human and mammalian community. The fatality of infectious is high across the world especially in Africa, Asia, Middle East, and Europe. This study regarding codon usage bias of S, M, and L segments of the CCHF virus pertaining to the host Homo sapiens, reveals in-depth information about the evolutionary characteristics of CCHFV. Relative Synonymous Codon Usage (RSCU), Effective number of codons (ENC) were calculated, to determine the codon usage pattern in each segment. Correlation analysis between Codon adaptation index (CAI), GRAVY (Hydrophobicity), AROMO (Aromaticity), and nucleotide composition revealed bias in the codon usage pattern. There was no strong codon bias found among any segments of the CCHF virus, indicating both the factors i.e., natural selection and mutational pressure shapes the codon usage bias.     

Codon Usage in Pathogenic Entamoeba histolytica

Summary An analysis of 4680 codons expressed by pathogenic Entamoeba histolytica showed the A+U content of coding sequences to be 67%. The preference for A+U resulted in an unusual codon usage with an A+U content of 84% in the third codon position. The data show a remarkable similarity to those obtained for Plasmodium falciparum.     

五个鸡群中催乳素基因密码子使用频率与产蛋量的关系分析

通过鸡催乳素基因编码区基因扫描,发现3个SNP位点,分别是外显子2的C1607T、外显子5的C5749T和T5821C,3个SNP均没有改变氨基酸的编码.同时发现不同的单倍型间存在不同的密码子使用频率.对5个鸡群共370只鸡进行SSCP的基因型检测,共发现7种单倍型,结合44周龄产蛋量分析,发现不同单倍型的平均产蛋量存在显著性差异.结合密码子使用频率分析,发现使用高频密码子的单倍型个体产蛋量相对高.通过酶联免疫方法检测催乳素表达量,结果显示,使用高频密码子的个体,激素水平较高,其中使用2个高频密码子的单倍型个体和使用1.5个密码子的单倍型个体之间存在极显著差异.研究结果表明,密码子使用频率与产蛋量在一定的范围内呈现正相关趋势.     

几种鳞毛蕨科药用蕨类植物的抑菌特性分析

研究了6种鳞毛蕨科药用蕨类植物的不同浸提液对几种常见微生物生长的影响情况,结果表明它们普遍表现了很好的抑菌效果,其中对金黄色葡萄球菌(Staphylococcus aureus)的抑制效果最好,最大的抑菌率达到90.4%;通过对鳞毛蕨科3个属的抑菌作用比较,耳蕨属(Polystichum)的普遍抑菌作用占优势;从浸提方法上看,醇提取的方法并不比水提取的方法有明显的优势.     

Impact of plant nutrients on the relationship between a herbivorous insect and its symbiotic bacteria

The interactions between herbivorous insects and their symbiotic micro-organisms can be influenced by the plant species on which the insects are reared, but the underlying mechanisms are not understood. Here, we identify plant nutrients, specifically amino acids, as a candidate factor affecting the impact of symbiotic bacteria on the performance of the phloem-feeding aphid Aphis fabae. Aphis fabae grew more slowly on the labiate plant Lamium purpureum than on an alternative host plant Vicia faba, and the negative effect of L. purpureum on aphid growth was consistently exacerbated by the bacterial secondary symbionts Regiella insecticola and Hamiltonella defensa, which attained high densities in L. purpureum-reared aphids. The amino acid content of the phloem sap of L. purpureum was very low; and A. fabae on chemically defined diets of low amino acid content also grew slowly and had elevated secondary symbiont densities. It is suggested that the phloem nutrient profile of L. purpureum promotes deleterious traits in the secondary symbionts and disturbs insect controls over bacterial abundance.     

Chloroplast phylogeny indicates that bryophytes are monophyletic

Opinions on the basal relationship of land plants vary considerably and no phylogenetic tree with significant statistical support has been obtained. Here, we report phylogenetic analyses using 51 genes from the entire chloroplast genome sequences of 20 representative green plant species. The analyses, using translated amino acid sequences, indicated that extant bryophytes (mosses, liverworts, and hornworts) form a monophyletic group with high statistical confidence and that extant bryophytes are likely sisters to extant vascular plants, although the support for monophyletic vascular plants was not strong. Analyses at the nucleotide level could not resolve the basal relationship with statistical confidence. Bryophyte monophyly inferred using amino acid sequences has a good statistical foundation and is not rejected statistically by other data sets. We propose bryophyte monophyly as the currently best hypothesis.     

Investigation of differentially expressed genes during the development of mouse cerebellum

Before the discovery of DNA microarray and DNA chip technology, the expression of only a small number of genes could be analyzed at a time. Currently, such technology allows us the simultaneous analysis of a large number of genes to systematically monitor their expression patterns that may be associated with various biological phenomena. We utilized the Affymetrix GeneChip Mu11K to analyze the gene expression profile in developing mouse cerebellum to assist in the understanding of the genetic basis of cerebellar development in mice. Our analysis showed 81.6% (10,321/12,654) of the genes represented on the GeneChip were expressed in the postnatal cerebellum, and among those, 8.7% (897/10,321) were differentially expressed with more than a two-fold change in their maximum and minimum expression levels during the developmental time course. Further analysis of the differentially expressed genes that were clustered in terms of their expression patterns and the function of their encoded products revealed an aspect of the genetic foundation that lies beneath the cellular events and neural network formation that takes place during the development of the mouse cerebellum.     

Tetracoding increases with body temperature in Lepidosauria

Codons expanded by a silent position (quadruplet or tetracodons) may solve the conundrum that at life's origins, the weak tricodon–anticodon interactions could not promote translation in the absence of complex ribosomes. Modern genomes have isolated tetracodons resulting from insertion mutations. Some bioinformatic analyses suggest that tetracoding stretches overlap with regular mitochondrial protein coding genes. These tetragenes are probably decoded by (antisense) tRNAs with expanded anticodons. They are GC-rich, which produce stronger basepairs than A:T interactions, suggesting expression at high temperatures. The hypothesis that tetracoding is an adaptation to high temperatures is tested here by comparing predicted mitochondrial tetracoding in Lepidosauria (lizards, amphisbaenia, and Sphenodon), in relation to body temperature, expecting more tetracoding in species with high body temperature. The association between tRNAs with expanded anticodons and tetracoding previously described for mammals and Drosophila is confirmed for Lepidosauria. Independent evidence indicates that tetracoding increases with body temperature, supporting the hypothesis that tetracoding is an adaptation for efficient translation when conditions (temperature) make triplet codon-anticodons too unstable to allow efficient protein elongation.