Aligning the proteome and genome of the silkworm, Bombyx mori

A technology of mass spectrometry (MS) was used in this study for the large-scale proteomic identification and verification of protein-encoding genes present in the silkworm (Bombyx mori) genome. Peptide sequences identified by MS were compared with those from an open reading frame (ORF) library of the B. mori genome and a cDNA library, to validate the coding attributes of ORFs. Two databases were created. The first was based on a 9× draft sequence of the silkworm genome and contained 14,632 putative proteins. The second was based on a B. mori pupal cDNA library containing 3,187 putative proteins of at least 30 amino acid residues in length. A total of 81,000 peptide sequences with a threshold score of 60% were generated by the MS/MS analysis, and 55,400 of these were chosen for a sequence alignment. By searching these two databases, 6,649 and 250 proteins were matched, which accounted for approximately 45.4% and 7.8% of the peptide sequences and putative proteins, respectively. Further analyses carried out by several bioinformatic tools suggested that the matches included proteins with predicted transmembrane domains (1,393) and preproteins with a signal peptide (976). These results provide a fundamental understanding of the expression and function of silkworm proteins.     

Seasonal variation of mixing depth and its influence on phytoplankton dynamics in the Zeya reservoir, China

In reservoirs or lakes, mixing depth affects growth and loss rates of phytoplankton populations. Based on 1-year data from the Zeya reservoir, China, we scaled the mixing depth throughout a whole year by utilizing cluster analysis, and then investigated its influence on phytoplankton dynamics and other physical and chemical parameters. Over the whole year, all physical and chemical parameters except TN and temperature had significant correlations with mixing depth, indicating that mixing depth is one of the important driving factors influencing water environment. According to mixing depth, a year can be divided into three different periods, including the thermally stratified period, isothermally mixed period, and transition period between them. When considering the former two different periods separately, mixing depth had no correlation with the phytoplankton biovolume. However, over the whole year a significant correlation was observed, which indicated that the influence of mixing depth on phytoplankton growth in the Zeya reservoir still followed Diehl’s theory. Furthermore, according to the steady-state assumption, a unimodal curve (mixing depth—phytoplankton biovolume) with a significant peak appearing at a mixing depth of 2 m was observed, closely agreeing with Diehl’ prediction.     

Function of SIRT1 in physiology

Sirtuins were originally defined as a family of oxidized nicotinamide adenine nucleotide (NAD⁺)-dependent enzymes that deacetylate lysine residues on various proteins. The sirtuins are remarkably conserved throughout evolution from archae to eukaryotes. They were named after their homology to the Saccharomyces cerevisiae gene silent information regulator 2 (Sir2). The mammalian sirtuins, SIRT1-7, are implicated in a variety of cellular functions ranging from gene silencing, control of the cell cycle and apoptosis, and energy homeostasis. As SIRT1 is a nuclear protein and is the mammalian homolog most highly related to Sir2, it has been the focus of a large number of recent studies. Here we review some of the current data related to SIRT1 and discuss its mode of action and biological role in cellular and organismal models. Published in Russian in Biokhimiya, 2009, Vol. 74, No. 7, pp. 869–876.     

Fusion protein of Δ27LFn and EFn has the potential as a novel anthrax toxin inhibitor

PA-binding domain of LF (LFn) or PA-binding domain of EF (EFn) is the anthrax protective antigen (PA) binding domain of anthrax lethal factor (LF) or edema factor (EF). Here we show the development of a novel anthrax toxin inhibitor, fusion protein of N-terminal 27 amino acids deletion of LFn (Δ27LFn) and EFn. In a cell model of intoxication, fusion protein of Δ27LFn and EFn (Δ27LFn-EFn) was a 62-fold more potent toxin inhibitor than LFn or EFn, and this increased activity corresponded to a 39-fold higher PA-binding affinity by Biacore analysis. More importantly, Δ27LFn-EFn could protect the highly susceptible Fischer 344 rats from anthrax lethal toxin challenge. This work suggested that Δ27LFn-EFn has the potential as a candidate therapeutic agent against anthrax.

Structured summary

MINT-7014735, MINT-7014747, MINT-7014761: PA63 (uniprotkb:P13423) and LF (uniprotkb:P15917) bind (MI:0407) by surface plasmon resonance (MI:0107)     

Divergence of exonic splicing elements after gene duplication and the impact on gene structures

Background  

The origin of new genes and their contribution to functional novelty has been the subject of considerable interest. There has been much progress in understanding the mechanisms by which new genes originate. Here we examine a novel way that new gene structures could originate, namely through the evolution of new alternative splicing isoforms after gene duplication.     

Impact of Pyrolysis Treatment on Heavy Metals in Sediment

This paper describes a laboratory study that examined the effect of pyrolysis treatment on the behavior of Hg, Cr, Zn, Pb, Cu and Cd in a stream sediment. The influences of pyrolysis on the evaporation, sequential extraction and leaching behavior of these metals were investigated. Cr, Zn, Pb and Cu were retained quantitively in the solid residue at temperatures up to 800°C while mercury and cadmium were completely or partially evaporated. The metal form distribution in the sludge samples was determined by the sequential extraction procedure. The procedure revealed that as a consequence of pyrolysis, the metals were more strongly fixed in the treated sediment, as could be seen by the decrease with temperature of the first two sequential-extracted fractions and increase of the residue fraction. The leaching results showed that the quantities of the studied metals leached in the two pyrolysis samples were lower than those in the untreated sediment. The amounts of metals leached from the pyrolysis residues correlated significantly with the first extracted fraction (exchangeable fraction).     

Transgene Expression Is Associated with Copy Number and Cytomegalovirus Promoter Methylation in Transgenic Pigs

Transgenic animals have been used for years to study gene function, produce important proteins, and generate models for the study of human diseases. However, inheritance and expression instability of the transgene in transgenic animals is a major limitation. Copy number and promoter methylation are known to regulate gene expression, but no report has systematically examined their effect on transgene expression. In the study, we generated two transgenic pigs by somatic cell nuclear transfer (SCNT) that express green fluorescent protein (GFP) driven by cytomegalovirus (CMV). Absolute quantitative real-time PCR and bisulfite sequencing were performed to determine transgene copy number and promoter methylation level. The correlation of transgene expression with copy number and promoter methylation was analyzed in individual development, fibroblast cells, various tissues, and offspring of the transgenic pigs. Our results demonstrate that transgene expression is associated with copy number and CMV promoter methylation in transgenic pigs.