Soliton-like and non-soliton regimes of interaction of taxis waves (illustrated with an example of bacterial population waves)

It has been shown in our previous studies that, during collision, bacterial population waves can penetrate each other or stop. In the present study, the mechanism of the two regimes of interaction is considered in detail. Based on the experimental and theoretical research, it has been shown that this interaction is a vivid example to confirm one of the characteristic properties of waves in cross-diffusion systems.     

Dynamics of bacterial population waves as dependent on the type of the chemotactic response function

A study was made of the time of formation and the rate of propagation of bacterial population waves as dependent on substrate concentration. Experimentally and theoretically it is shown that the time of bacterial wave formation grows with increasing concentration of the nutritive component. At the same time, the wave propagation rate drops at relatively high concentrations of the nutritive component. In numerical experiments with a mathematical model, comparative analysis has been made of the dynamics of the behavior of bacterial waves at different chemotactic responses.     

Formation of demarcation zones when bacterial population waves are drawn together

Many motile bacteria (for instance, Escherichia coli) inoculated at some point in a semisolid nutrient medium can form population waves: bands or rings. The formation of these motile structures is due to chemotaxis. The population waves when they are drawn together can form two types of non-motile structures. Firstly, the population waves can collide. Secondly, in certain conditions, the waves can slow down and stop without coming into contact directly with each other. In this way demarcation zones are formed. The mechanism of the occurrence of the demarcation zones has been unknown. In this paper we show that formation of these zones is due to lack of nutrients (which at the same time act as attractants) within the narrow gap between individual bacterial populations.     

Involvement of Ca2+ and cGMP in bacterial taxis

Abstract The level of cGMP in a suspension of Escherichia coli cells increased transiently upon the addition of chemoattractants. Ca²⁺ (1 mM), but not Mg²⁺, produced constant tumbling of cells in the presence of the ionophore A23187. The effect was observed either in stationary-state cells, or in a logarithmic culture treated with EDTA to increase permeability by A23187. Under the same conditions, Ca²⁺ decreased the cytoplasmic level of cGMP. In Phormidium uncinatum , rapid ⁴⁵Ca²⁺ accumulation followed a light-dark stimulus, or the addition of tetramethylquinone (TMQ), a chemorepellent. La³⁺, which increases the reversal rate, also enhanced the level of cytoplasmic Ca²⁺, presumably by blocking the outward Ca²⁺ flux. In both E. coli and P. uncinatum Ca²⁺ inhibited methylaccepting chemotaxis protein (MCP) methylation. It is concluded that cGMP and Ca²⁺ are secondary messengers in taxis information-processing.     

Critical manifolds,travelling waves,and an example from population genetics

A generalized Morse index theory is used to study travelling waves in a natural selection-migration model for a diploid organism when the selective strength is weak.     

Studies on Brachionus (Rotifera): an example of interaction between fundamental and applied research

The genus Brachionus has been the main subject of studies reported in about 1000 papers published since 1950. About three-fourths of these deal with Brachionus plicatilis and B. rotundiformis and are mainly related to their use as prey for aquatic organisms. Also abundant, but to a lesser extent, are studies on B. calyciflorus, many of which are concerned with aquatic ecotoxicology. These studies constitute an interesting interaction between fundamental and applied research. For example, advances in fundamental biology have been applied to improve the production of rotifer biomass. Alternatively, new perspectives in fundamental research on rotifers have emerged while solving technical and biological problems related to the rearing of aquatic animal larvae. This review describes some aspects that have shown a significant advance due to such interaction between fundamental and applied research on rotifers, e.g. growth conditions, biochemical composition and morphotypes.     

Fractionation of a bacterial cell population by adsorption to erythrocytes and yeast cells

Abstract Fluorochrome-labeled antibodies specific for either S or type-1 fimbriae of Escherichia coli were used to show that in broth culture the two fimbrial types of strain 3040 mostly occurred on different cells. 12% of the cells were nonfimbriated. A fractionation procedure that involved adsorption of bacterial cells onto erythrocytes and yeast cells was developed to isolate homogeneous subpopulations (S-fimbriated, type-1-fimbriated, and non-fimbriated) of. E. coli. The level of contamination in each isolated subpopulation was 4% at the highest. The method is useful in obtaining homogeneous bacterial populations for adherence studies and for purification of specific fimbrial antigens.     

Development of bacterial cytochrome P-450(cam) (cytochrome m) production

Cytochrome P-450(cam) monooxygenase is an important bacterial redox enzyme system with potential commercial value for detoxifying trace hydrocarbon contaminants, catalyzing regiospecific hydroxylations, and amperometric biosensing. The present study was undertaken to increase productivity of this enzyme, which is induced in its host, pseudomonas putida PpG 786, by D(+)-camphor. Culture processes were studied in batch, fed-batch, and continuous modes to evaluate metabolic behavior and develop constitutive equations for specific rate of growth (mu), camphor utilization (q(p)). Fed-batch culture was characterized by an extended linear growth phase which is often encountered in hydrocarbon fermentations. Inhibition by the camphor solvent, dimethylformamide, was assessed. Production of the terminal protein of the p-450(cam) enzyme system, cytochrome m, was shown to depend on growth medium iron content in fed-batch culture and was increased by 130% over previously protocols by eliminating iron deficiency. A continuous process that enables greater production rates was developed by using oxygen enrichment while simultaneously reducing gas throughput. Camphor and oxygen requirements were determined for fedbatch and continuous growth. (c) 1993 John Wiley & Sons, Inc.     

不同土壤细菌种群结构对氯嘧磺隆胁迫的响应及降解菌系的获得

应用PCR-DGGE、DNA测序等方法,在室内驯化条件下研究了8种来源于中国不同地区土壤样品细菌种群结构对氯嘧磺隆胁迫的响应。结果表明:在氯嘧磺隆100～500mg·L-1浓度梯度下,土壤细菌群落组成有明显的更迭现象,多样性发生明显变化,驯化至10周,绝大部分细菌种群消失,样品的细菌种群结构趋于简单并呈现趋同效应;DNA测序结果表明,在驯化第10周可培养Methylophilus sp.、Beta proteobacterium、uncultured bacterium成为优势菌属,所获细菌种群出现的16个优势种群中有10个与已知的具有有机污染物降解功能和有机污染环境修复功能细菌的相似性大于97%;其中5个与嗜甲基菌16S rDNA部分序列相似性达98%以上。获得了一组对氯嘧磺隆具有降解作用的细菌菌系,可在5d内将100mg·L-1氯嘧磺隆降解67%;其主要组成为嗜甲基菌属(Methylophilus sp.)、丛毛单胞菌属(Comamonas sp.)、鞘酯杆菌属(Sphingobacterium sp.)和嗜氢菌属(Hydrogenophi-lus sp.)。     

Tracing isolates of bacterial species by multilocus variable number of tandem repeat analysis (MLVA)

All bacterial genomes contain multiple loci of repetitive DNA. Repeat unit sizes and repeat sequences may vary when multiple loci are considered for different isolates of an individual microbial species. Moreover, it has been documented on many occasions that the number of repeat units per locus is a strain-defining parameter. Consequently, there is isolate-specificity in the number of repeats per locus when different strains of a given bacterial species are compared. The experimental assessment of this variability for a number of different loci has been called 'multilocus variable number of tandem repeat analysis' (MLVA). The approach can be supported or extended by locus-specific DNA sequencing for establishing mutations in the individual repeat units, which usually enhances the resolution of the approach considerably. Essentially, MLVA with or without supportive sequencing has been developed for all of the medically relevant bacterial species and can be used effectively for tracing outbreaks or other forms of bacterial dissemination. MLVA is a modern, timely and versatile bacterial typing methodology.     

Characterization of the bacterial community associated with the surface and mucus layer of whiting (Merlangius merlangus)

The bacterial community inhabiting the mucus layer and surface of whiting was examined to determine whether the bacteria present are a reflection of the surrounding water or an indigenous bacterial flora is present. The outer mucus, mouth mucus and gut of four whiting harvested from a site in the Irish Sea and the surrounding water were examined by terminal restriction fragment length polymorphism (tRFLP) analysis of the 16S rRNA gene and clone library construction. The water community was the most diverse, with only a small number of shared water-mucus phylotypes present. The bacterial flora associated with the outer mucus layer were more diverse than that of the mouth mucus and gut. All three mucus layers were characterized by the presence of a dominant phylotype, identified as clone wom-1, highly similar to Photobacterium iliopiscarium. In addition to other Photobacterium phylotypes, members of the CFB and Clostridia groups were also detected. Subsequently, whiting from 11 different sites along the east and south coast of Ireland were compared by tRFLP analysis. Strikingly, the mucus layer of whiting at all sites was characterized by the presence and dominance of a TRF corresponding to the clone wom-1 which was virtually absent from the water column.     

Disruption of a specific molecular interaction with a bound lipid affects the thermal stability of the purple bacterial reaction centre

Relatively little is known about the functions of specific molecular interactions between membrane proteins and membrane lipids. The structural and functional consequences of disrupting a previously identified interaction between a molecule of the diacidic lipid cardiolipin and the purple bacterial reaction centre were examined. Mutagenesis of a highly conserved arginine (M267) that is responsible for binding the head-group of the cardiolipin (to leucine) did not affect the rate of photosynthetic growth, the functional properties of the reaction centre, or the X-ray crystal structure of the complex (determined to a resolution of 2.8 Å). However, the thermal stability of the protein was compromised by this mutation, part of the reaction centre population showing an approximately 5 °C decrease in melting temperature in response to the arginine to leucine mutation. The crystallised mutant reaction centre also no longer bound detectable amounts of cardiolipin at this site. Taken together, these observations suggest that this particular protein-lipid interaction contributes to the thermal stability of the complex, at least when in detergent micelles. These findings are discussed in the light of proposals concerning the unfolding processes that occur when membrane proteins are heated, and we propose that one function of the cardiolipin is to stabilise the interaction between adjacent membrane-spanning α-helices in a region where there are no direct protein-protein interactions.     

Diverse bacterial groups are associated with corrosive lesions at a Granite Mountain Record Vault (GMRV)

Aims: This study applied culture‐dependent and molecular approaches to examine the bacterial communities at corrosion sites at Granite Mountain Record Vault (GMRV) in Utah, USA, with the goal of understanding the role of microbes in these unexpected corrosion events. Methods and Results: Samples from corroded steel chunks, rock particles and waters around the corrosion pits were collected for bacterial isolation and molecular analyses. Bacteria cultivated from these sites were identified as members of Alphaproteobacteria, Gammaproteobacteria, Firmicutes and Actinobacteria. In addition, molecular genetic characterization of the communities via nested‐polymerase chain reaction‐denaturing gradient gel electrophoresis (DGGE) indicated the presence of a broad spectrum of bacterial groups, including Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. However, neither cultivation nor molecular approaches identified sulfate‐reducing bacteria (SRB), the bacteria commonly implicated as causative organisms were found associated with corrosive lesions in a process referred to as microbially influenced corrosion (MIC). The high diversity of bacterial groups at the corrosion sites in comparison with that seen in the source waters suggested to us a role for the microbes in corrosion, perhaps being an expression of a redox‐active group of microbes transferring electrons, harvesting energy and producing biomass. Conclusions: The corrosion sites contained highly diverse microbial communities, consistent with the involvement of microbial activities along the redox gradient at corrosion interface. We hypothesize an electron transport model for MIC, involving diverse bacterial groups such as acid‐producing bacteria (APB), SRB, sulfur‐oxidizing bacteria (SOB), metal‐reducing bacteria (MRB) and metal‐oxidizing bacteria (MOB). Significance and Impact of the Study: The characterization of micro‐organisms that influence metal‐concrete corrosion at GMRV has significant implications for corrosion control in high‐altitude freshwater environments. MIC provides a potential opportunity to further our understandings of extracellular electron transfer and interspecies communications.     

日本弓背蚁肠道细菌群落的季节特征

[目的]在长期的进化过程中,蚂蚁和微生物之间建立了复杂的联系,尤其肠道微生物对蚂蚁的食性进化和物种分化产生了巨大的影响.弓背蚁属Camponotus蚂蚁消化道内普遍存在内共生菌Blochmannia及其他肠道细菌,这些细菌在寄主蚂蚁营养补充方面发挥了重要的作用,此外肠道微生物对食物类型的变化十分敏感,这些信息可能有助于调查寄主蚂蚁在不同季节的取食习性.本研究旨在揭示弓背蚁属蚂蚁肠道微生物是否存在季节特征.[方法]采用16S rRNA-RFLP方法分析比较了了2个日本弓背蚁蚁巢(巢1和2)的工蚁在4个月份时间点(2012年6月12日,8月15日和10月10日,2013年4月15日)的肠道茵群组成.[结果]在8个样品中共发现了17个属的细菌和1种未知细菌,弓背蚁属蚂蚁特有的内共生茵Blochmannia是优势细菌,出现在所有样品中,占67.1％～98.8％;假单胞菌属Pseudomonas和肠杆菌属Enterobacter在大多数的样本中都检测到,其他属的细菌则零星分布在个别样品中,只占较低的比例.两个蚁巢工蚁肠道茵群在4个月份没有呈现一致的变化趋势,都具有低的细菌多样性.在巢1中,4月和10月的肠道细菌多样性相对较高,在6月和8月较低;而在巢2中,8月的肠道细菌多样性明显高于4,6和10月.两个蚁巢6月和10月的肠道茵群组成相似,但是8月和4月差异较大.[结论]日本弓背蚁两个蚁巢的工蚁肠道菌群组成和多样性都随季节产生变化,但是没有呈现一致的变化趋势,没有表现出明显的季节特征.     

A novel approach for estimating growth phases and parameters of bacterial population in batch culture

Using mathematical analysis, a new method has been developed for studying the growth kinetics of bacterial populations in batch culture. First, sampling data were smoothed with the spline interpolation method. Second, the instantaneous rates were derived by numerical differential techniques and finally, the derived data were fitted with the Gaussian function to obtain growth parameters. We named this the Spline-Numerical-Gaussian or SNG method. This method yielded more accurate estimates of the growth rates of bacterial populations and new parameters. It was possible to divide the growth curve into four different but continuous phases based on changes in the instantaneous rates. The four phases are the accelerating growth phase, the constant growth phase, the decelerating growth phase and the declining phase. Total DNA content was measured by flow cytometry and varied depending on the growth phase. The SNG system provides a very powerful tool for describing the kinetics of bacterial population growth. The SNG method avoids the unrealistic assumptions generally used in the traditional growth equations.     

Construction of a full bacterial artificial chromosome （BAC） library of Oryza sativa genome

We have constructed a full BAC library for the superior early indica variety of Oryza sativa,Guang Lu Ai 4.The MAX Efficiency DH10B with increased stability of inserts was used as BAC host cells.The potent pBelo BACII with double selection markers was used as cloning vector.The cloning efficiency we have reached was as high as 98%,and the transformation efficiency was raised up to 10^6 transformants/μg of large fragment DNA.The BAC recombinant transformants were picked at random and analyzed for the size of inserts,which turned out to be of 120 kb in length on average.We have obtained more than 20,000 such BAC clones.According to conventional probability equation,they covered the entire rice genome of 420,000 kb in length.The entire length of inserts of the library obtained has the 5-to 6-fold coverage of the genome.To our knowledge,this is the first reported full BAC library for a complex genome.     

Detection of aerosolized bacterial spores (Bacillus atrophaeus) using free-flying honey bees (Hymenoptera: Apidae) as collectors

An aerosol cloud of Bacillus atrophaeus (previously B. subtilis variety niger) spores, an anthrax surrogate, was created in a large 0.4 ha (1 ac), bee-containing, open-mesh tent. Bees from a B. atrophaeus uncontaminated hive flying through the cloud adsorbed the spores in statistically significant quantities. After removal of the B. atrophaeus contaminated hive and introduction of another B. atrophaeus uncontaminated hive, the bees again were monitored for the next few days for B. atrophaeus spores. B. atrophaeus spores accumulated on the bees bodies following their exposure to the residual B. atrophaeus contamination in the tent. The spore loads on the bees quickly returned to background levels after the hives were removed from the contaminated tent area. It may therefore be practical to use honey bee colonies to monitor foraging areas for disease-causing spores.