Calculating spatial statistics for velocity jump processes with experimentally observed reorientation parameters

Mathematical modelling of the directed movement of animals, microorganisms and cells is of great relevance in the fields of biology and medicine. Simple diffusive models of movement assume a random walk in the position, while more realistic models include the direction of movement by assuming a random walk in the velocity. These velocity jump processes, although more realistic, are much harder to analyse and an equation that describes the underlying spatial distribution only exists in one dimension. In this communication we set up a realistic reorientation model in two dimensions, where the mean turning angle is dependent on the previous direction of movement and bias is implicitly introduced in the probability distribution for the direction of movement. This model, and the associated reorientation parameters, is based on data from experiments on swimming microorganisms. Assuming a transport equation to describe the motion of a population of random walkers using a velocity jump process, together with this realistic reorientation model, we use a moment closure method to derive and solve a system of equations for the spatial statistics. These asymptotic equations are a very good match to simulated random walks for realistic parameter values.     

A molecular systematic survey of cultured microbial associates of deep-water marine invertebrates

A taxonomic survey was conducted to determine the microbial diversity held within the Harbor Branch Oceanographic Marine Microbial Culture Collection (HBMMCC). The collection consists of approximately 17,000 microbial isolates, with 11,000 from a depth of greater than 150 ft seawater. A total of 2273 heterotrophic bacterial isolates were inventoried using the DNA fingerprinting technique amplified rDNA restriction analysis on approximately 750-800 base pairs (bp) encompassing hypervariable regions in the 5' portion of the small subunit (SSU) 16S rRNA gene. Restriction fragment length polymorphism patterns obtained from restriction digests with RsaI, HaeIII, and HhaI were used to infer taxonomic similarity. SSU 16S rDNA fragments were sequenced from a total of 356 isolates for more definitive taxonomic analysis. Sequence results show that this subset of the HBMMCC contains 224 different phylotypes from six major bacterial clades (Proteobacteria (Alpha, Beta, Gamma), Cytophaga, Flavobacteria, and Bacteroides (CFB), Gram + high GC content, Gram + low GC content). The 2273 microorganisms surveyed encompass 834 alpha-Proteobacteria (representing 60 different phylotypes), 25 beta-Proteobacteria (3 phylotypes), 767 gamma-Proteobacteria (77 phylotypes), 122 CFB (17 phylotypes), 327 Gram + high GC content (43 phylotypes), and 198 Gram + low GC content isolates (24 phylotypes). Notably, 11 phylotypes were < or =93% similar to the closest sequence match in the GenBank database even after sequencing a larger portion of the 16S rRNA gene (approximately 1400 bp), indicating the likely discovery of novel microbial taxa. Furthermore, previously reported "uncultured" microbes, such as sponge-specific isolates, are part of the HBMMCC. The results of this research will be available online as a searchable taxonomic database (www.hboi.edu/dbmr/dbmr_hbmmd.html).     

The new higher level classification of eukaryotes with emphasis on the taxonomy of protists

This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional "kingdoms." The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.     

Conceptualizing "suicidal genetically engineered microorganisms" for bioremediation applications

Use of genetically modified microorganisms (GEMs) for pollution abatement has been limited because of risks associated with their release in the environment. Recent developments in the area of recombinant DNA technologies have paved the way for conceptualizing "suicidal genetically engineered microorganisms" (S-GEMS) to minimize such anticipated hazards and to achieve efficient and safer bioremediation of contaminated sites. Our strategy of designing a novel S-GEM is based on the knowledge of killer-anti-killer gene(s) that would be susceptible to programmed cell death after detoxification of any given contaminated site(s).     

Role of inhibitors of proteolytic enzymes in plant defense against phytopathogenic microorganisms

This review analyzes the literature on various mechanisms of proteolytic enzyme inhibitors involved in plant defense against attack by phytopathogenic microorganisms. The action of proteinase inhibitors from plants upon the enzymes from pathogenic microorganisms and viruses is reviewed. Considerable attention is given to the induction of proteinase inhibitors in plants in response to the invasion of pathogens. Some aspects of application of proteinase inhibitors in biotechnology for production of transgenic plants with enhanced resistance to diseases are discussed.Translated from Biokhimiya, Vol. 69, No. 11, 2004, pp. 1600–1606.Original Russian Text Copyright © 2004 by Valueva, Mosolov.     

宏基因组学在微生物活性物质筛选中的应用

采用传统分离培养筛选微生物新活性物质的方法受到很大制约,自然界99%以上的微生物不能培养,其资源开发受到很大限制。环境微生物宏基因组技术应用避开了微生物分离纯培养问题,极大拓展了微生物资源的利用空间,增加获得新活性物质的机会和途径。本文着重介绍宏基因组的概念、研究策略包括DNA提取、文库构建与筛选等及在微生物活性物质筛选中的应用,并对宏基因组研究中存在的问题进行探讨。     

Organic and mineral fertilization, respectively, increase and decrease the development of external mycelium of arbuscular mycorrhizal fungi in a long-term field experiment

Effects of long-term mineral fertilization and manuring on the biomass of arbuscular mycorrhizal fungi (AMF) were studied in a field experiment. Mineral fertilization reduced the growth of AMF, as estimated using both measurements of hyphal length and the signature fatty acid 16:1ω5, whereas manuring alone increased the growth of AMF. The results of AMF root colonization followed the same pattern as AMF hyphal length in soil samples, but not AMF spore densities, which increased with increasing mineral and organic fertilization. AMF spore counts and concentration of 16:1ω5 in soil did not correlate positively, suggesting that a significant portion of spores found in soil samples was dead. AMF hyphal length was not correlated with whole cell fatty acid (WCFA) 18:2ω6,9 levels, a biomarker of saprotrophic fungi, indicating that visual measurements of the AMF mycelium were not distorted by erroneous involvement of hyphae of saprotrophs. Our observations indicate that the measurement of WCFAs in soil is a useful research tool for providing information in the characterization of soil microflora.     

Response of microbial communities of Lake Baikal to extreme temperatures

The survival rate, metabolic activity, and ability for growth of microbial communities of Lake Baikal have been first studied after exposure to extremely low temperatures (freeze-thawing) for different lengths of time. It has been shown that short-term freezing (1–3 days) inhibits the growth and activity of microbial communities. The quantity of microorganisms increased after 7-and 15-day freezing. In the periods of maximums, the total number of microorganisms in the test samples was twice as high as in the control. It was established that after more prolonged freezing the microorganisms required more time after thawing to adapt to new conditions. In the variants with 7-and 15-day freezing, the activities of defrosted microbial communities were three or more times higher than in the control. The survival rate and activity of Baikal microorganisms after freeze-thawing confirms the fact that the Baikal microbial communities are highly resistant to this type of stress impact.     

一株生物絮凝剂产生菌的筛选及絮凝活性研究

从活性污泥中筛选到一株产絮凝剂的菌株WJ-100。该菌株产絮凝剂的适宜pH塑6．5。适宜温度为25℃～40℃,摇床速度为80～240r／min;Na^＋、K^＋、Ca^2＋、Fe^3＋均有较好的促絮凝作用,Ca^2＋尤为显著;WJ-100以多种糖类为良好碳源,絮凝率达99.2％、99．8％甚至100％;该菌株在高岭土悬液pH2．0～10．0范围均有较好的絮凝效果。WJ-100在较大的pH、温度、碳源、摇床速度、搅拌速度等范围内均具有很高的絮凝活性,显示出重要的研究和应用价值。     

Rapid and efficient extraction of soluble proteins from Gram-negative microorganisms without disruption of cell walls

The ability of buffer solutions containing low concentrations of nonionic detergents (Triton X-100, Tween 20, Brij 58, and Lubrol PX) and the anionic detergent sodium deoxycholate, as well as mixtures of these detergents with chaeotropes (urea and guanidine hydrochloride), to extract intracellular proteins of Gram-negative microorganisms (Escherichia coli and Pseudomonas aeruginosa) was studied. It was established that the solutions containing Triton X-100 and sodium deoxycholate and the mixtures of these detergents with urea are the most effective. It was shown that the extraction of proteins from bacterial cells under the studied conditions is not accompanied by a release of DNA into solution but is associated with extraction of low-molecular RNAs. The level of protein extraction reaches 80%. No disruption of the bacterial cell wall occurs during the extraction, and proteins probably penetrate through meshes of the murein network. The efficiencies of our buffer mixtures are close to or higher than that of the commercial reagent CelLytic B (Sigma, United States). The practical uses of the chaeotropic mixtures developed are discussed.