A genetic algorithm on multiple sequences alignment problems in biology

The study and comparison of sequences of characters from a finite alphabet is relevant to various areas of science, notably molecular biology. The measurement of sequence similarity involves the consideration of the possible sequence alignments in order to find an optimal one for which the “distance” between sequences is minimum. In biology informatics area, it is a more important and difficult problem due to the long length (100 at least) of sequence, this cause the compute complexity and large memory require. By associating a path in a lattice to each alignment, a geometric insight can be brought into the problem of finding an optimal alignment, this give an obvious encoding of each path. This problem can be solved by applying genetic algorithm, which is more efficient than dynamic programming and hidden Markov model using commomly now. Foundation item: Supported by Zi-qiang Foundation of Wuhan University and Open Foundation of the State Key-Laboratory of Software Engineering, Wuhan University Biography: Shi Feng(1966-), male, Associate professor, research direction: bioinformatics.     

Evidence for transmission of aphid-pathogenic fungi by migratory flight of Myzus persicae alates

The alates of the green peach aphid, Myzus persicae, were daily trapped from the air from late October through early January and carried to laboratory for determination of fungal infection by individually rearing them for 7 d on detached cabbage leaves in Petri dishes. Among 760 alates trapped, 266 (35%) were found carrying various fungal pathogens, 87.3% of them died due to mycosis during the first 3-day period of rearing and the rest died in the following two days. Most of the deaths of the alates were attributed to entomophthoralean fungi, taking 94.4%, and the rest were the hyphomycetous fungus Beauveria bassiana. Among the Entomophthorales-killed alates, P. neoaphidis took a proportion of 66.1%, Z. anhuiensis 22.6%, E. planchoniana 9.7%, and N. fresenii 1.6%, respectively. Two alates were found suffering from cross infection of two fungal species, i.e. P. neoaphidis with Z. anhuiensis and N. fresenii, respectively. The results represent the first report on transmission of aphid-pathogenic fungi by M. persicae alates through migratory flight.     

Palaeolake and palaeoenvironment between 42 and 18 kaBP in tengger desert, NW China

Comprehensive field investigations and laboratory analyses show that palaeolakes, including fresh- mesohaline water Megalake Tengger and other semi-con- nected, isolated water bodies, during late Pleistocene covered an area of more than 20000 km², which is more than half of the Tengger Desert in NW China. Stratigraphic correlation and chronological evidence indicate that before ca. 42000 aBP the area was more arid. The palaeolakes started to develop around 40000 uncal. ¹⁴C aBP but until 37000 ¹⁴C aBP their scope was limited. High water levels established from 35000 ¹⁴C aBP lasted until 22000 ¹⁴CaBP. Lake levels regressed between 22000 and 20000 ¹⁴C aBP but transgressed from 20000 to 18600 ¹⁴C aBP. Subsequently, water level declined further and the Megalake Tengger finally desiccated at around 18000 ¹⁴C aBP. Megalake Tengger possessed a fresh-mesohaline water property, implying that the regional precipitation increased significantly. During the period of Megalake Tengger, the climate was warmer-humid than present. The annual rainfall was 250 to 350 mm more than that of today and the temperature was 1.5 to 3.0℃ higher.     

Microelement analysis of source of raw materials of terracotta warriors and horses of Qin’s Mausoleum in pits No. 1 and No. 2

In order to search for sources of the raw material of the Qin’s terracotta warriors and horses, we selected 20 samples of pottery warriors and pottery horses of the Qin’s Mausoleum from pit No. 1, 19 samples of pottery warriors and brick from pit No. 2, 20 samples of clays near the Qin’s Mausoleum and 2 samples of Yaozhou porcelain bodies. The 32 kinds of element content of each sample were measured by neutron activation analysis (NAA). These data were analyzed by fuzzy cluster analysis, the trend cluster analysis diagram was obtained. The results showed that samples of terracotta warriors and horses from pits No.1 and No. 2 were closely related to the loam layer near Qin’s Mausoleum, but their relations with the loess layers were not so close, and they were out of all relation to Yaozhou porcelain bodies. Thus, it could be deduced that the Li Mountain clay may be considered as the original place of the raw materials of the terracotta warriors and horses, the kiln sites might be located nearby the Qin’s Mausoleum.     

Two closely linked rice U14 boxC/D snoRNAs

By analysis of the conserved elements in yeast U14 boxC/D snoRNA. the conserved elements in rice U14 boxC/D snoRNA have been speculated. Through computer search of the international rice genome database, two rice U14 snoRNA gene candidates are obtained. These two putative U14 snoRNA genes are closely linked on rice chromosome 2. The coding sequences of these two snoR-NAs exhibit the hallmark structure of boxC/D antisense snoRNA. They both have conserved boxC and boxD sequences and a 14nt-long complement to the sequence between 414nt and 427nt of rice 18S rRNA (according to GenBank accession no. X00755). The experimental evidence shows that these two snoRNAs are involved in the methylation of the complementary sequence of rice 18S rRNA. The existence and localization of these two snoRNAs are proved by RT-PCR and Northern blot. Further analysis shows that both of the newly found rice snoRNAs have high homology with maize U14 snoRNA. and they are named rice U14.1 snoRNA and U14.2 snoRNA respectively. The gene sequence encoding these two snoRNAs has been deposited in the GenBank database under accession number of AF332622.     

The reconstruction of fossil planation surface in China

On the basis of results of relative subjects, the fossil planation surface has been discussed by the authors from the point of geomorphologic view. The discussion contents included the characteristic information, research methods, paleotopography (gradient and altitude) and other problems about fossil planation surface. The recognition and reconstruction of fossil planation surface mainly rely on the following characteristic information: ( i ) the character of erosion unconformity surface; (ii) the paleo-weathering crust and residual deposits; (iii) the paleo-karst and filled deposit in the paleo-karst under the unconformity surface,and (iv) the character and environment of sediment above the unconformity surface. According to the above-mentioned characteristic information, the authors recognized and reconstructed two stages of fossil planation surface on Paleo-land of North China and Yangtze Paleo-land. These two fossil planation surfaces formed from Middle Ordovician to Lower Carboniferous and from Lower Permian to Upper Permian respectively. The paleo-gradient of fossil planation surface changed within 0.31‰-1.32‰, mostly less than 1.0‰. According to the developing depth of paleo-karst, the authors considered that in Suqiao buried-hill region of Paleo-land of North China, the paleo-altitude is 300 m or so above paleo-sea-level. The authors hope that the research is in favor of discussion about rising scale and process of the Tibetan Plateau. Besides, the research of fossil planation surface can provide a theoretical base for relative research,such as the reconstruction of paleoenvironment, the evolution and drift of paleo-continent, the formation and distribution of weathering ore deposits, the reservior and prospection of oil and gas, etc.     

Genistein inhibits human TNF-α-induced porcine endothelial cell adhesiveness for human monocytes and natural killer cells

Cellular immune response is a major barrier to xenotransplantation. Human tumor necrosis factor-α (hTNF-α) possesses cross-species activity and directly amplifies the immune rejection via the upregulation of adhesion molecules on porcine endothelium. We investigated the role of protein tyrosine phosphorylation in the induction of expression of E-sclectin and vascular cell adhesion molecule-1 (VCAM-1), and the augmentation of adhesion of human peripheral blood monocytes (PBMo) and natural killer cells (PBNK), after rhTNF-α-stimulation of porcine aortic endothelial cells (PAEC) in vitro, rhTNF-α-increased adhesiveness of PAEC for both PBMo and PBNK was dose-dependently reduced by pretreatment of PAEC with the selective protein tyrosine kinase (PTK) inhibitor genistein. The inhibitory effect occurred at the early time of PAEC activation triggered by rhTNF-α, and was completely reversible. PTK activity assay indicated that genistein also suppressed rhTNF-α stimulated activation of protein tyrosine kinases (PTKs) in PAEC in a dose-dependent manner. Flow cytometric analysis showed that genistein inhibited the upregulation of E-selectin and VCAM-1 by rhTNF-α. These results suggest that PTKs may regulate the expression of E-selectin and VCAM-1 on PAEC and the adherence of PBMo and PBNK induced by rhTNF-α. Moreover, dietary genistein, used as an adhesion antagonist, may contribute to managing the cell-mediated rejection in the clinical application.     

Adsorption of Xe in zeolite MCM-22

Adsorption of xenon in zeolite MCM-22, a zeolite containing two separate pore systems，has been investigated in detail by variable temperature (VT) ¹²⁹Xe NMR spectroscopy. NMR results suggest that Xe atoms are preferentially adsorbed in the supercages of the zeolite at low Xe pressure (less than a few atmosphere), while Xe atoms can penetrate into the two-dimensional sinusoidal channels at high Xe pressure. Exchange of xenon at the different adsorption sites in the same supercage, i.e. xenon atoms in the two pockets and those in the central part of the supercage, was confirmed at 145 K by two-dimensional (2D) ¹²⁹Xe NMR exchange spectroscopy. The time scale for the exchange is about several milliseconds.     

Analysis of EET on Ca increasing the melting point of Mg17Al12 phase

The present investigation showed that the additions of Ca to the alloy AZ91 were mainly dissolved into the Mg17Al12 phase and increased its melting point and thermal stability, which would have great effects on the high- temperature properties of AZ91 alloy. The empirical electron theory (EET) of solid and molecules was used to calculate the valence electron structures (VES) of Mg17Al12 intermetallic compound with and without Ca addition. The results showed that Ca dissolving in Mg17Al12 phase increased the strength of bonds that control the thermal stability of Mg17Al12 phase. Additions of Ca also made the distribution of the valence electrons on the dominant bond network more uniform in the whole unit cell of Mg17Al12. The theoretical conclusions well account for the experimental results.