Beyond the rotamer library: genetic algorithm combined with the disturbing mutation process for upbuilding protein side-chains

The disturbing genetic algorithm, incorporating the disturbing mutation process into the genetic algorithm flow, has been developed to extend the searching space of side-chain conformations and to improve the quality of the rotamer library. Moreover, the growing generation amount idea, simulating the real situation of the natural evolution, is introduced to improve the searching speed. In the calculations using the pseudo energy scoring function of the root mean squared deviation, the disturbing genetic algorithm method has been shown to be highly efficient. With the real energy function based on AMBER force field, the program has been applied to rebuilding side-chain conformations of 25 high-quality crystallographic structures of single-protein and protein-protein complexes. The averaged root mean standard deviation of atom coordinates in side-chains and veracities of the torsion angles of chi(1) and chi(1) + chi(2) are 1.165 A, 88.2 and 72.9% for the buried residues, respectively, and 1.493 A, 79.2 and 64.7% for all residues, showing that the method has equal precision to the program SCWRL, whereas it performs better in the prediction of buried residues and protein-protein interfaces. This method has been successfully used in redesigning the interface of the Basnase-Barstar complex, indicating that it will have extensive application in protein design, protein sequence and structure relationship studies, and research on protein-protein interaction.     

New approaches to direct gradient analysis using environmental scalars and statistical curve-fitting procedures

The conceptual framework of direct gradient analysis (DGA) is discussed in relation to the functional, factorial approach to vegetation. Both approaches use abstract simplified environment gradients with which to correlate vegetation response. Environmental scalars based on physical process models of environment and/or known biological growth processes can be incorporated to make analyses less location specific. An example of an environmental scalar (radiation index) for converting aspect and slope measurements to the more biologically relevant radiation input at a site is given. The problem of the shape of species response curves to environmental gradients is examined using a sample of 1 286 plots from eucalypt forest in southern New South Wales. An important conclusion is that skewed or bimodal response curves may be due to unsatisfactory distribution of observations and/or unrecognized environmental factors. The use of Generalized Linear Modelling (GLM) as a method for providing a statistical basis for DGA is presented. Analyses using GLM, and presence/absence data are presented for a range of eucalypt species (Eucalyptus rossii, E. dalrympleana, E. fastigata etc.). Successful prediction of species distributions (realized niches) can be achieved with mean annual temperature, mean annual rainfall, radiation index and geology. Quadratic terms are required in many cases, indicating bell-shaped response curves. The major variability associated with species niches is shown to be related to a limited number (4) of environmental factors. DGA with biologically relevant scalars and appropriate statistical methods is suitable for studying many problems of species' realized niches and plant community composition.     

Relationship between cytotoxicity and induction of sister-chromatid exchanges in mouse foetal cells exposed to several doses of carcinogenic and non-carcinogenic chemicals.

The increase in sister-chromatid exchanges induced by 5 chemicals, with different DNA damaging and carcinogenic activities, was studied in short-term foetal-mouse cultures. A significant increase in SCE was induced by N-methyl-N'-nitro-N-nitrosoguanidine, N-diazoacetylglycine-amide, azaserine and methotrexate. k-Strophantin, on the contrary, was totally inactive. On a molar basis, MNNG was the most active chemical followed by MTX, AZS and DGA, in that order. At equitoxic concentrations (D37), the order of SCE-inducing abilities was MNNG, DGA, AZS and MTX. Compared with previous data, at equitoxic concentrations, the most DNA-damaging agents were also the most effective in inducing SCE. The SCE increase seems to correlate not with unspecific cytotoxicity but more with DNA damage or other damage at the genome level. MTX, a non-mutagen, which induced SCE only at toxic levels, could be considered a false positive because this positivity may reflect an enhancement of incorporation of 5-BrdUrd into DNA. The positive results obtained with AZS suggest a sufficient sensitivity of the method for detecting relatively weak carcinogens.     

高杆野生稻PR2同源序列的分离与序列分析

根据已知植物病程相关蛋白基因β-1,3-葡聚糖酶基因（PR2）的保守结构域设计2对简并引物,从高杆野生稻基因组DNA中分离出3条防卫基因类似物（defense—genes analogues,DGAs）,其中2条具有通读的ORF,另一条提前出现终止密码子。对这3条序列在NCBI上进行同源性搜索发现,在核苷酸水平这3条序列均与水稻的β-1,3-葡聚糖酶基因具有90％～93％的同源性,与已知大麦、小麦、高梁、黑麦、燕麦、玉米等其它植物的β-1,3-葡聚糖酶基因具有69％-81％的同源性。在氨基酸水平与水稻、大麦、小麦、黑麦的β-1,3-葡聚糖酶具有60％～93％的同源性。对具有通读ORF的2条序列RD1-GG6和RD1-GG12进行表达分析,发现经水杨酸（SA）诱导后表达量明显提高。     

Characterisation and genetic mapping of resistance and defence gene analogs in cocoa (Theobroma cacao L.)

Disease resistance and defence gene analog (RGA/DGA) sequences were isolated in cocoa using a PCR approach with degenerate primers designed from conserved domains of plant resistance and defence genes: the NBS (nucleotide binding site) motif present in a number of resistance genes such as the tobacco N, sub-domains of plant serine/threonine kinases such as the Pto tomato gene, and conserved domains of two defence gene families: pathogenesis-related proteins (PR) of classes 2 and 5. Nucleotide identity between thirty six sequences isolated from cocoa and known resistance or defence genes varied from 58 to 80%. Amino acid sequences translated from corresponding coding sequences produced sequences without stop codons, except for one NBS –like sequence. Most of the RGAs could be mapped on the cocoa genome and three clusters of genes could be observed : NBS-like sequences clustered in two regions located on chromosomes 7 and 10, Pto-like sequences mapped in five genome regions of which one, located on chromosome 4, corresponded to a cluster of five different sequences. PR2-like sequences mapped in two regions located on chromosome 5 and 9 respectively. An enrichment of the genetic map with microsatellite markers allowed us to identify several co-localisations of RGAs, DGAs and QTL for resistance to Phytophthora detected in several progenies, particularly on chromosome 4 where a cluster of Pto-like sequences and 4 QTL for resistance to Phytophthora were observed. Many other serious diseases affect cocoa and the candidate genes, isolated in this study, could be of broader interest in cocoa disease management.     

Uptake, metabolism and mutagenic activity of aromatic glycidyl compounds

Aromatic diglycidyl compounds are very active mutagens when assayed in in vitro tests. In vivo, however, resorcinol diglycidyl ether provided no evidence for the clastogenic activity, while diglycidylaniline exhibited definite mutagenic activity in the micronucleus test. Since the only difference between these two compounds lies in the binding mode of the glycidyl groups to the aromatic nucleus (i.e. ether oxygen vs. aminic nitrogen), this apparent discrepancy in mutagenic activity led to the question of the mechanisms involved in such an activity difference. Although no clear signs of differential uptake or excretion could be detected in mice, differences could be seen in the spectrum of urinary metabolites; while resorcinol diglycidyl ether seemed to become fully converted to the genetically inactive bis-diol compound, a sizeable proportion of diglycidylaniline was converted only to the diol-epoxide. In vitro investigations and enzyme kinetic measurements with postmitochondrial supernatant of rat or mouse liver homogenate (S-9) finally yielded the biochemical explanation for this behaviour, as they showed a very low affinity of the diol-epoxide metabolite of diglycidylaniline for the epoxide hydrolase, normally involved in the degradation of such compounds. The diol-epoxide obtained from resorcinol diglycidyl ether, on the other hand, has an affinity to the degradation enzyme similar to, or even higher than, the one measured with the parent substance.     

The antagonistic effect and mechanisms of Bacillus amyloliquefaciens DGA14 against anthracnose in mango cv. ‘Carabao’

Bacillus amyloliquefaciens strain DGA14 was tested for in vitro antagonism towards Colletotrichum gloeosporioides, a causal pathogen of anthracnose in mango cv. ‘Carabao’. DGA14 produced extracellular metabolites in solid and liquid media that suppressed the growth of C. gloeosporioides. The cells of DGA14 were often observed adjacent to the pathogen so affecting its spore germination and mycelium development. DGA14 colonised mango fruit 48 h after artificial inoculation and persisted 14 days after storage at 18–20°C. On fruit surfaces, DGA14 attached and produced dents to spores of C. gloeosporioides. Dipping mangoes in aqueous cell suspension (10⁸ mL L^?1) of DGA14 significantly decreased the incidence of anthracnose as compared to untreated fruit.     

徐淮白山羊DGAT2基因内含子3多态性与生长性状关联分析

目的：探讨DGAT2基因内含子3的遗传多态性及其与山羊生长性状的关联。方法：采用PCR-SSCP、DNA序列分析及生物信息学技术研究徐淮白山羊DGAT2基因内含子3的多态性及其与山羊生长性状的关联情况。结果：徐淮白山羊DGAT2基因内含子3存在A、B2个等位基因,其基因频率依次为0.9550、0.0450,并且处于Hardy-Weinberg平衡状态;徐淮白山羊DGAT2基因不同基因型对徐淮白山羊体高有显著影响（P〈0.05）,而对其他体尺指标在统计学上无显著影响（P〉0.05）。结论：DGAT2基因内含子3的遗传多态性与徐淮白山羊生长性状存在相关。     

Relation between nitrogenase synthesis and activity in a marine unicellular diazotrophic strain, Gloeothece sp. 68DGA (Cyanophyte), grown under different light/dark regimens

The relationship between the abundance of nitrogenase and its activity was studied in the marine unicellular cyanobacterium Gloeothece sp. 68DGA cultured under different light/dark regimens. The Fe‐ and MoFe‐protein of nitrogenase and nitrogen (N₂)‐fixing (acetylene reduction) activity were detected only during the dark phase when the cells were grown under a 12 h light/12 h dark cycle (12L/12D). Nitrogenase activity appeared about 4 h after entering the dark phase. Maximum nitrogenase activity occurred at around the middle of the dark phase, and the activity rapidly decreased to zero before the start of the light phase. The rapid decrease of nitrogenase activity and the Fe‐protein of nitrogenase near the end of the dark phase in 12L/12D were partly recovered by the addition of l ‐methionine‐sulfoximine, an inhibitor of glutamine synthetase. Diurnal oscillation of the abundance of nitrogenase was maintained in the first subjective dark phase (i.e. the period corresponding to the dark phase) after the cells were transferred from 12L/12D to continuous illumination. However, enzyme activity was detected only when photosynthetic oxygen (O₂) evolution was completely suppressed by reducing the light intensity or by the addition of 3‐(3,4‐dichlorophenyl)‐1,1‐dimethylurea. Nitrogenase always appeared in the cells about 16 h after starting the light phase, even when the 12L/12D cycle was modified by the addition or subtraction of a single 6 h period of light or dark. These results suggest the following: (i) N₂‐fixation by Gloeothece sp. 68DGA is primarily regulated by an endogenous circadian oscillator at the level of nitrogenase synthesis. (ii) The endogenous circadian rhythm resets on a shift of the timing of the light phase. (iii) Nitrogenase activity is not always reflected in the presence of nitrogenase. (iv) The activity of nitrogenase is negatively regulated by fixed nitrogen and the concentration of ambient O₂.