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。     

己酮可可碱对肺纤维化大鼠MMP-2和TIMP-1表达的影响

目的观察己酮可可碱(pentoxifylline, PTX)对博来霉素致肺纤维化大鼠肺组织基质金属蛋白酶2(matrix metalloproteinase-2)和基质金属蛋白酶组织抑制剂1(tissue inhibitor of matrix metalloproteinase-1)表达的影响,初步探讨其抗肺纤维化的作用机制.方法 SD大鼠36只,随机分为模型组、治疗组和对照组.模型组和治疗组气管内注射博来霉素诱导肺纤维化,对照组在相同条件下给予生理盐水.第二天起治疗组大鼠腹腔给予己酮可可碱6mg/kg.d,其余两组相同条件下给予生理盐水.治疗的第7d和28d,处死动物取出肺组织,用RT-PCR和免疫组化ABC法观察各组鼠肺组织MMP-2和TIMP-1表达的变化. 结果与模型组比较,治疗组经PTX作用的第7d和28d肺组织中MMP-2和TIMP-1 mRNA的基因转录均有减少,MMP-2 mRNA表达分别降低33.4%和35.5%(P＜0.001),TIMP-1 mRNA表达分别降低25.3%和33.0%(P＜0.05).免疫组化结果则显示,PTX作用的第7d和28dMMP-2分别较模型组降低30.7%和41.7%(P＜0.05),TIMP-1分别降低13.1%和19.8%(P＜0.05).结论 PTX对肺纤维化不同时期肺组织中MMP-2和TIMP-1的表达均有一定程度的降低作用,其可能通过调整MMP-2和TIMP-1比值使其趋于平衡,从而延缓甚至抑制纤维化的进程.     

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.     

S-Allylcysteine reduces breast tumor cell adhesion and invasion

Previous studies show that aqueous garlic extract and its derivatives (e.g. S-allylcysteine [SAC]) prevent carcinogen-induced breast tumorigenesis. However, investigations testing the effect of SAC on later stages of breast tumorigenesis and/or metastasis have produced mixed results. Here we show that SAC significantly reduced anchorage-dependent and -independent growth of MDA-MB-231 breast tumor cells in a dose- and time-dependent fashion, and sub-lethal SAC-treatment altered mammary tumor cell adhesion and invasion through components of the extracellular matrix. We provide evidence to suggest increased expression of E-cadherin and reduced MMP-2 expression and activity are partially responsible for inhibition of mammary tumor cell invasion by SAC. Because E-cadherin and MMP-2 are important in cancer metastasis, these results suggest a link between SAC induction of E-cadherin and reduction of MMP2 activity with the inhibition of cell motility and invasion; thus providing evidence that events leading to breast cancer metastasis are repressed by sub-lethal SAC-treatment.     

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.     

Structural trees for proteins containing φ-motifs

In the present study, a novel structural motif of proteins referred to as the phi-motif is considered, and two novel structural trees in which the phi-motif is taken as the root structure have been constructed. The simplest phi-motif is formed by three adjacent beta-strands connected by loops and packed in one beta-sheet so that its overall fold resembles the Greek letter phi. Construction of the structural trees and modeling of folding pathways have shown that all structures of the protein superfamilies can be obtained by stepwise addition of alpha-helices and/or beta-strands to the root phi-motif taking into account a restricted set of rules inferred from known principles of protein structure. The structural trees are a good tool for structure comparison, structural classification of proteins, as well as for searching for all possible protein folds and folding pathways.     

Landscape-scale patterns of shrub-species abundance in California chaparral – The role of topographically mediated resource gradients

We examine the degree to which landscape-scale spatial patterns of shrub-species abundance in California chaparral reflect topographically mediated environmental conditions, and evaluate whether these patterns correspond to known ecophysiological plant processes. Regression tree models are developed to predict spatial patterns in the abundance of 12 chaparral shrub and tree species in three watersheds of the Santa Ynez Mountains, California. The species response models are driven by five variables: average annual soil moisture, seasonal variability in soil moisture, average annual photosynthetically active radiation, maximum air temperature over the dry season (May–October), and substrate rockiness. The energy and moisture variables are derived by integrating high resolution (10 m) digital terrain data and daily climate observations with a process-based hydro-ecological model (RHESSys). Field-sampled data on species abundance are spatially integrated with the distributed environmental variables for developing and evaluating the species response models.The species considered are differentially distributed along topographically-mediated environmental gradients in ways that are consistent with known ecophysiological processes. Spatial patterns in shrub abundance are most strongly associated with annual soil moisture and solar radiation. Substrate rockiness is also closely associated with the establishment of certain species, such as Adenostoma fasciculatum and Arctostaphylos glauca. In general, species that depend on fire for seedling recruitment (e.g., Ceanothous megacarpus) occur at high abundance in xeric environments, whereas species that do not depend on fire (e.g., Heteromeles arbutifolia) occur at higher abundance in mesic environments. Model performance varies between species and is related to life history strategies for regeneration. The scale of our analysis may be less effective at capturing the processes that underlie the establishment of species that do not depend on fire for recruitment. Analysis of predication errors in relation to environmental conditions and the abundance of potentially competing species suggest factors not explicitly considered in the species response models.