River forcing at work: ecological modeling of prograding and regressive deltas

Two explicit landscape simulation models were used to investigate habitat shifts in coastal Louisiana due to varying river forcing and sea level rise scenarios. Wetland conversion to open water and yearly shifts of marsh habitats in two contrasting estuarine regions were examined; the Atchafalaya delta which is a prograding delta area with strong riverine input, and the Barataria Basin is a regressive delta with high wetland loss which is isolated from riverine input. The models linked several modules dynamically across spatial and temporal scales. Both models consisted of a vertically integrated hydrodynamic model coupled with process-based biological modules of above and below ground primary productivity and soil dynamics. The models explored future effects of possible sea level rise and river diversion plans for 30 and 70-year projections starting in 1988. Results showed that increased river forcing had large land preservation impacts, and indicated that healthy functioning of the Mississippi Delta depends largely on inputs of freshwater, nutrients, and sediments in river water. These types of models are useful for research and as management tools for predicting the effects of regional impacts on structural landscape level changes.     

NMR and homology modeling studies of copper(II)-halocyanin from Natronobacterium pharaonis bacteria

Halocyanin from the haloalkaliphilic archaean Natronobacterium pharaonis is a peripheral membrane type 1 blue copper protein with a single polypeptide chain of 163 amino acid residues. Halocyanin participates as putative electron carrier protein associated to an electron acceptor role for a terminal oxidase and has the lowest redox potential value reported to date for a BCP. NMR studies and homology modeling calculations were performed to evaluate the electronic properties of Cu(II)-halocyanin from Natronobacterium pharaonis. The copper coordination site properties of Cu(II)-halocyanin are discussed. The ¹H NMR spectra, isotropic chemical shifts and relaxation times for halocyanin are compared with those of other BCPs such as azurin, amicyanin, plastocyanin and stellacyanin. The wild-type Cu(II)-halocyanin presents almost the same ¹H NMR spectra in comparison with Cu(II)-plastocyanin as expected from a similar coordination symmetry. However, minor differences were found. In order to get some insight on these differences, a computational model for Cu(II)-halocyanin from N. pharaonis was built. Model is based on sequential homology of halocyanin with two different families of proteins: plastocyanins and pseudoazurins. Homology modeling was performed using two different structural templates and copper ion was added for further refinement of the coordination site. Proposed structure was in good agreement with NMR experimental information and is the first three-dimensional model reported to date of an halocyanin. Small differences were found in the copper coordination site with respect to other BCP with known structure. This work is also an interesting example of expertise-driven homology modeling across different protein families.     

海南石梅湾青皮林最小取样面积与物种多样性研究

石梅湾海岸青皮(Vatica hainanensis)林是海南独特的雨林群落之一。本文选用8种“种-面积渐近线”对该群落的最小取样面积进行了拟合研究。结果表明,其中5条曲线的R^2大于0．97,拟合状况很好,但所得出的最小取样面积各不相同。进一步经过“重要值-面积曲线”的群落特征分析,确认群落的最小取样面积只有800m^2。石梅湾青皮林最小取样面积比海南其他类型雨林、滇南热带雨林、东南亚热带雨林以及非洲雨林都要小。通过对1000m^2样地的物种多样性分析,结果表明：在垂直结构上,石梅湾青皮林B层乔木的Gleason指数大于A层乔木,和海南山地雨林的情况不同。海岸青皮林为物种多样性不高的单优林,群落的物种多样性、均匀度远小于海南其他类型的山地雨林与混合青皮林;在海岸青皮林群落内,青皮的相对密度、相对优势度、重要值大大高于其他物种。此研究表明：海南热带雨林同样存在物种多样性不高、单优特征显著的顶极群落;海南海岸青皮林是迄今为止热带雨林取样面积最小的森林类型。     

青枯病生防菌ANTI-8098A菌株发酵过程氨基酸变化动态的研究

青枯病生防菌ANTI- 80 98A发酵过程的氨基酸测定结果表明 :ANTI - 80 98A的氨基酸代谢消耗发生在 0～ 2 4h ,消耗了 87.0 7%的总氨基酸 ;代谢累积发生在 2 4～ 4 8h ,4 8h的总氨基酸为 0h的 1 .6 7倍。在 1 7种测定的氨基酸中 ,1 6种氨基酸都表现出与总氨基酸类似的变化趋势 ,丝氨酸在 32h有最大值 ;根据含量大小可分为 3类 ,根据变异系数大小也可分为 3类 ,其中谷氨酸含量 ,丝氨酸变异系数最大。氨基酸种类特性的聚类分析结果表明 :当λ =1 7.5 0时 ,氨基酸变化可分为 4大类。发酵时间的聚类分析结果表明 :当λ=2 5 .36时 ,可分为 3大类 ,与总氨基酸的变化相关     

Female mate assessment and choice behavior affect the frequency of alternative male mating tactics

Explanations for the existence of alternative male mating tacticsfocus primarily on male–male competition. Mating systems,however, are composed of interactions both within and betweenthe sexes, and the role of female behavior in shaping male matingtactics should not be overlooked. By using a dynamic state variablegame model, I examine how female mate assessment and choicebehavior affect the frequency of alternative male mating tactics.When females can accurately assess the quality of males, onlymales with high quality are likely to be chosen as mates, andthus, lower-quality males gain little fitness from courtingfemales. This leads lower-quality males to switch to an alternativemating tactic that attempts to circumvent female mate choice.In contrast, if the abilities of females to accurately assessmales are constrained by assessment costs, imperfect information,or time constraints, or if the pool of available males is smaller,then lower-quality males are increasingly chosen as mates andthey less often use alternative mating tactics. Thus, femalebehavior shapes the frequency of alternative male mating tactics.A consequence of this game between the sexes is that male behavior(i.e., increased alternative mating tactics) decreases the benefitsfemales might otherwise gain from lower assessment costs, clearersignals of male quality, more time to choose a male, and moremales from which to choose a mate.     

柠檬形克勒克酵母对温州蜜柑“国庆一号”采后贮藏的防腐效果

Citrus unshiu “Guoqing No.1” was used as material for elucidating the effect of Kloeckera apiculata suspension post-harvest treatment on preventing fruit decay during storage period. The result showed that K. apiculata preparation of 2×106CFU/mL (CFU, cloning forming unit) significantly reduced the development of decay caused by green mold, blue mold and stem rot, showing the same effect of carbendazim treatment after storage period of 100 days, and the disease incidence was controlled under 1%. The antagonist population was between 3.5×105CFU/mL and 1.7×107CFU/mL in citrus fruit, and increased 1.7×107CFU/mL after 40 days storage, and then stabilized for the remaining storage period. After storage at 5℃ for 100 days, K. apiculata strain 34-9 did not alter any quality parameters of fruit. During storage, the change of relative electrical conductivity (REC) showed a coordinate tendency with malondlaldehyde (MDA) content, which kept continuously growing from the beginning to the end of the storage. In the storage period of 25 days, the REC value and MDA content of the treatments were all significantly lower than those of water treatment, but had no obvious difference from those of carbendazim treatment. K. apiculata strain 34-9 had no effect on the enzyme activity of super oxide dismutase (SOD), but significantly improved peroxidase (POD) activity after 100 day storage.     

Cooperativity of cytochrome P450 1A2: interactions of 1,4-phenylene diisocyanide and 1-isopropoxy-4-nitrobenzene

Homotropic cooperativity of 1-alkoxy-4-nitrobenzene substrates and also their heterotropic cooperative binding interactions with the iron ligand 1,4-phenylene diisocyanide (Ph(NC)₂) had been demonstrated previously with rabbit cytochrome P450 (P450) 1A2 [G.P. Miller, F.P. Guengerich, Biochemistry 40 (2001) 7262-7272]. Multiphasic kinetics were observed for the binding of Ph(NC)₂ to both ferric and ferrous P450 1A2, including relatively slow steps. Ph(NC)₂ induced an apparently rapid change in the circular dichroism spectrum, consistent with a structural change, but had no effect on tryptophan fluorescence. Ph(NC)₂ binds the P450 iron in both the ferric and ferrous forms; ferric P450 1A2 was reduced rapidly in the absence of added ligands, and the rate was attenuated when Ph(NC)₂ was bound. No oxidation products of Ph(NC)₂ were detected. Docking studies with a rabbit P450 1A2 homology model based on the published structure of a human P450 1A2·α-naphthoflavone (αNF) complex indicated adequate room for a complex with either two 1-isopropoxy-4-nitrobenzene molecules or a combination of one 1-isopropoxy-4-nitrobenzene and one Ph(NC)₂; in the case of αNF no space for an extra ligand was available. The patterns of homotropic cooperativity seen with 1-alkoxy-4-nitrobenzenes (biphasic plots of v vs. S) differ from those seen with polycyclic hydrocarbons (positive cooperativity), suggesting that only with the latter does the ligand interaction produce improved catalysis. Consistent with this view, Ph(NC)₂ inhibited the oxidation of 1-isopropoxy-4-nitrobenzene and other substrates.     

Residues Arg114 and Arg337 are critical for the proper function of Escherichia coli gamma-glutamyltranspeptidase

To evaluate the importance of conserved Arg114 and Arg337 residues of Escherichia coli γ-glutamyltranspeptidase (EcGGT), Lys, Leu, or Asp-substituted mutants were constructed by site-directed mutagenesis. The wild-type and mutant enzymes were overexpressed in the recombinant E. coli M15 and purified by nickel-chelate chromatography to near homogeneity. With the exception of R114K, all the other mutants significantly lost GGT activity, confirming the importance of these two residues in EcGGT. Kinetic analysis of R114L, R114D, R337K, and R337L revealed a significant increase in K_m with a minor change in k_cat, leading to more than an 8-fold decrease in k_cat/K_m values. Mutations of Arg337 impaired the capability of autocatalytic processing of the enzyme. In vitro maturation experiments revealed that EcGGT precursor mutants, pro-R337K and pro-R337L, could precede a time-dependent autocatalytic process to generate the small and large subunits, while no autocatalytic processing was observed in pro-R337D. Computer modeling showed that the critical bonding distance of Gln390 O-Thr391 HG1 and Gln390 C-Thr391 OG1 are significantly increased in Arg337 replacements, implying that these distance changes might be responsible for the lack of enzyme maturation.     

Reciprocal allostery arising from a bienzyme assembly controls aromatic amino acid biosynthesis in Prevotella nigrescens

Modular protein assembly has been widely reported as a mechanism for constructing allosteric machinery. Recently, a distinctive allosteric system has been identified in a bienzyme assembly comprising a 3-deoxy-d-arabino heptulosonate-7-phosphate synthase (DAH7PS) and chorismate mutase (CM). These enzymes catalyze the first and branch point reactions of aromatic amino acid biosynthesis in the bacterium Prevotella nigrescens (PniDAH7PS), respectively. The interactions between these two distinct catalytic domains support functional interreliance within this bifunctional enzyme. The binding of prephenate, the product of CM-catalyzed reaction, to the CM domain is associated with a striking rearrangement of overall protein conformation that alters the interdomain interactions and allosterically inhibits the DAH7PS activity. Here, we have further investigated the complex allosteric communication demonstrated by this bifunctional enzyme. We observed allosteric activation of CM activity in the presence of all DAH7PS substrates. Using small-angle X-ray scattering (SAXS) experiments, we show that changes in overall protein conformations and dynamics are associated with the presence of different DAH7PS substrates and the allosteric inhibitor prephenate. Furthermore, we have identified an extended interhelix loop located in CM domain, loop_C320-F333, as a crucial segment for the interdomain structural and catalytic communications. Our results suggest that the dual-function enzyme PniDAH7PS contains a reciprocal allosteric system between the two enzymatic moieties as a result of this bidirectional interdomain communication. This arrangement allows for a complex feedback and feedforward system for control of pathway flux by connecting the initiation and branch point of aromatic amino acid biosynthesis.     

Molecular-genetic systems of development: Functional dynamics and molecular evolution

This work for the first time compares results obtained with studies of parametric robustness of the Hh- and Dpp/BMP signal cascades responsible for morphogenesis and molecular evolution of the Hh- and Dpp/BMP cascade genes. There is a link between adaptive evolution of genes and those changes in kinetic parameters of the signal cascade models, which are critical for normal functioning of these cascades. Special attention is paid to events of the molecular evolution of the Hh- and Dpp/BMP cascade genes that matched with the emergence of the major taxonomic types and classes of Bilateria.