Complete mitochondrial genome of a forensically important muscid, Hydrotaea chalcogaster (Diptera: Muscidae), with notes on its phylogenetic position

Muscidae are a dipteran family which is important for forensic investigations. However, it has received limited attention in forensic entomological experiments as a reason of identification issues. It is hard to identify specimens by morphological methods, especially in developmental stages. Therefore, complete mitochondrial genome sequences can be important tool in forensic entomology for identifying species. In this study we sequenced and analyzed the first complete mitochondrial genome from a forensically important Muscidae species Hydrotaea (=Ophyra) chalcogaster by next-generation sequencing. The mitochondrial genome of the sequenced species is circular molecules of 17,076?bp which have the typical mitochondrial genome complement of 13 protein-coding genes, 22 tRNAs, two ribosomal RNA genes and a control region. Rearrangements of gene positions are identical with the ancestral insect genome. Furthermore, phylogenetic relationships of the family Muscidae were evaluated in regard to mitochondrial protein coding genes. The inferred trees indicate that the Muscidae is a paraphyletic family. These data provide additional information for molecular identification of muscid species.     

POR C of Arabidopsis thaliana: a third light- and NADPH-dependent protochlorophyllide oxidoreductase that is differentially regulated by light

During the sequencing of the genome of Arabidopsis thaliana a gene has been identified that encodes a novel NADPH-protochlorophyllide oxidoreductase (POR)-like protein (accession number AC 002560). This protein has been named POR C. We have expressed the POR C protein in Escherichia coli and have determined its in vitro activity. POR C shows the characteristics of a light-dependent and NADPH-requiring POR similar to POR A and POR B. The expression of the POR C gene differs markedly from that of the POR A and POR B genes. In contrast to the POR A and POR B mRNAs, the POR C mRNA has been shown previously to accumulate only after the beginning of illumination. In light-adapted mature plants only POR B and POR C mRNAs were detectable. The amounts of both mRNAs show pronounced diurnal rhythmic fluctuations. While the oscillations of POR B mRNA are under the control of the circadian clock, those of POR C mRNA are not. Another difference between POR B and POR C was found in seedlings that were grown under continuous white light. The concentration of POR C mRNA rapidly declined and soon dropped beyond the limit of detection, after these seedlings were transferred to the dark. On the other hand, POR B mRNA was unaffected by this light/dark shift. When seedlings were exposed to different light intensities, the amounts of POR B mRNA remained the same, while POR A and POR C mRNAs were modulated in an inverse way by these light intensity changes. POR A mRNA was still detectable in seedlings grown under low light intensities but disappeared at higher light intensities, while the mRNA concentration of POR C rose with increasing light intensities. These different responses to light suggest that the functions of the three PORs of Arabidopsis are not completely redundant, but may allow the plant to adapt its needs for chlorophyll biosynthesis more selectively by using preferentially one of the three enzymes under a given light regime.     

Individualized medicine 2010

Molecular and cell biology have revolutionized not only diagnosis, therapy and prevention of human diseases but also greatly contributed to the understanding of their pathogenesis. Based on modern molecular and biochemical methods it is possible to identify on the one hand point mutations and single nucleotide polymorphisms. On the other hand, using high throughput array technologies, it is possible to analyse thousands of genes or gene products simultaneously, resulting in an individual gene or gene expression profile (signature). These data increasingly allow to define the individual risk for a given disease and to predict the individual prognosis of a disease as well as the efficacy of therapeutic strategies (individualized medicine). In the following sections some of the recent advances of predictive medicine and their clinical relevance will be addressed.     

Evolutionary Patterns of Gene Families Generated in the Early Stage of Vertebrates

In this paper we have analyzed 49 vertebrate gene families that were generated in the early stage of vertebrates and/or shortly before the origin of vertebrates, each of which consists of three or four member genes. We have dated the first (T₁) and second (T₂) gene duplications of 26 gene families with 3 member genes. The means of T₁ (594 mya) and T₂ (488 mya) are largely consistent to a well-cited version of two-round (2R) genome duplication theory. Moreover, in most cases, the time interval between two successive gene duplications is large enough that the fate of duplicate genes generated by the first gene duplication was likely to be determined before the second one took place. However, the phylogenetic pattern of 23 gene families with 4 members is complicated; only 5 of them are predicted by 2R model, but 11 families require an additional gene (or genome) duplication. For the rest (7 families), at least one gene duplication event had occurred before the divergence between vertebrate and Drosophila, indicating a possible misleading of the 4:1 rule (member gene ratio between vertebrates and invertebrates). Our results show that Ohno's 2R conjecture is valid as a working hypothesis for providing a most parsimonious explanation. Although for some gene families, additional gene duplication is needed, the credibility of the third genome duplication (3R) remains to be investigated. Received: 13 December 1999 / Accepted: 7 April 2000     

Oncogenic Notch Promotes Long-Range Regulatory Interactions within Hyperconnected 3D Cliques

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The Heterogeneity of Structural and Functional Photosynthetic Characteristics of Mesophyll Chloroplasts in Various Parts of Mature or Senescing Leaf Blade of Two Maize (Zea Mays L.) Genotypes

Differences in ultrastructural parameters of mesophyll cell (MC) chloroplasts, contents of photosynthetic pigments, and photochemical activities of isolated MC chloroplasts were studied in the basal, middle, and apical part of mature or senescing leaf blade of two maize genotypes. A distinct heterogeneity of leaf blade was observed both for structural and functional characteristics of chloroplasts. In both mature and senescing leaves the shape of MC chloroplasts changed from flat one in basal part of leaf to nearly spherical one in leaf apex. The volume density of granal thylakoids decreased from leaf base to apex in both types of leaves examined, while the amount of intergranal thylakoids increased in mature leaves but decreased in senescing leaves. The most striking heterogeneity was found for the quantity of plastoglobuli, which strongly increased with the increasing distance from leaf base. The differences in chloroplast ultrastructure were accompanied by differences in other photosynthetic characteristics. The Hill reaction activity and activity of photosystem 1 of isolated MC chloroplasts decreased from leaf base to apex in mature leaves. Apical part of senescing leaf blade was characterised by low contents of chlorophyll (Chl) a and Chl b, whereas in mature leaves, the content of Chls as well as the content of total carotenoids (Car) slightly increased from basal to apical leaf part. This was reflected also in the ratio Chl (a+b)/total Car; the ratio of Chl a/b did not significantly differ between individual parts of leaf blade. Both genotypes examined differed in the character of developmental gradient observed along whole length of leaf blade.     

Replication dynamics in fission and budding yeasts through DNA polymerase tracking

The dynamics of eukaryotic DNA polymerases has been difficult to establish because of the difficulty of tracking them along the chromosomes during DNA replication. Recent work has addressed this problem in the yeasts Schizosaccharomyces pombe and Saccharomyces cerevisiae through the engineering of replicative polymerases to render them prone to incorporating ribonucleotides at high rates. Their use as tracers of the passage of each polymerase has provided a picture of unprecedented resolution of the organization of replicons and replication origins in the two yeasts and has uncovered important differences between them. Additional studies have found an overlapping distribution of DNA polymorphisms and the junctions of Okazaki fragments along mononucleosomal DNA. This sequence instability is caused by the premature release of polymerase δ and the retention of non proof‐read DNA tracts replicated by polymerase α. The possible implementation of these new experimental approaches in multicellular organisms opens the door to the analysis of replication dynamics under a broad range of genetic backgrounds and physiological or pathological conditions.     

毛竹出笋后快速生长期内茎秆中光合色素和光合酶活性的变化

为了探讨毛竹(Phyllostachys pubescens)非同化器官茎秆的光合特性, 测定了毛竹出笋后快速生长期内(2011年4月13日到6月2日)的光合色素含量以及光合酶活性, 并通过激光共聚焦显微镜对其叶绿体分布进行了观察。结果表明: 毛竹茎秆中的叶绿体主要集中分布在表皮以下的基本组织中, 此外维管束鞘周围的细胞内也存在大量的叶绿体, 此特征类似于C₄植物的花环结构。在毛竹出笋后快速生长期内, 随着茎秆不断生长, 叶绿素a、叶绿素b和类胡萝卜素含量均极显著(p < 0.01)增加。在出笋10天时, 茎秆中核酮糖-1,5-二磷酸羧化酶/加氧酶(Rubisco)活性、磷酸烯醇式丙酮酸羧化酶(PEPC)活性和NADP-苹果酸酶(NADP-ME)活性最高, 之后随茎秆生长逐渐降低, 生长30天时酶活性与10天时相比分别降低了88.55% (p < 0.01)、77.46% (p < 0.01)和72.50% (p < 0.01), 而PEPC/Rubisco比值则随茎秆生长逐渐增加, 30天时比值达到12.83, 明显高于C₃植物。这表明毛竹茎秆内可能存在C₄光合途径, 此途径有利于毛竹提高光合效率, 进而促进其出笋后的快速生长。     

The full-length genome analysis of a street rabies virus strain isolated in Yunnan province of China

The epidemic of rabies has rapidly increased and expanded in Yunnan province in recent years.In order to further analyze and understand the etiological reasons for the rapid expansion of rabies in Yunn...     

The relation between the neutrality index for mitochondrial genes and the distribution of mutational effects on fitness

We explore factors affecting patterns of polymorphism and divergence (as captured by the neutrality index) at mammalian mitochondrial loci. To do this, we develop a population genetic model that incorporates a fraction of neutral amino acid sites, mutational bias, and a probability distribution of selection coefficients against new nonsynonymous mutations. We confirm, by reanalyzing publicly available datasets, that the mitochondrial cyt-b gene shows a broad range of neutrality indices across mammalian taxa, and explore the biological factors that can explain this observation. We find that observed patterns of differences in the neutrality index, polymorphism, and divergence are not caused by differences in mutational bias. They can, however, be explained by a combination of a small fraction of neutral amino acid sites, weak selection acting on most amino acid mutations, and differences in effective population size among taxa.