Gene decay in Shigella as an incipient stage of host-adaptation

Background

Many facultative bacterial pathogens have undergone extensive gene decay processes, possibly due to lack of selection pressure during evolutionary conversion from free-living to intracellular lifestyle. Shigella, the causative agents of human shigellosis, have arisen from different E. coli-like ancestors independently by convergent paths. As these bacteria all have lost large numbers of genes by mutation or deletion, they can be used as ideal models for systematically studying the process of gene function loss in different bacteria living under similar selection pressures.

Methodologies/Principal Findings

We compared the sequenced Shigella genomes and re-defined decayed genes (pseudogenes plus deleted genes) in these bacteria. Altogether, 85 genes are commonly decayed in the five analyzed Shigella strains and 1456 genes are decayed in at least one Shigella strain. Genes coding for carbon utilization, cell motility, transporter or membrane proteins are prone to be inactivated. Decayed genes tend to concentrate in certain operons rather than distribute averagely across the whole genome. Genes in the decayed operon accumulated more non-synonymous mutations than the rest genes and meanwhile have lower expression levels.

Conclusions

Different Shigella lineages underwent convergent gene decay processes, and inactivation of one gene would lead to a lesser selection pressure for the other genes in the same operon. The pool of superfluous genes for Shigella may contain at least two thousand genes and the gene decay processes may still continue in Shigella until a minimum genome harboring only essential genes is reached.     

Depth of burial,an important factor in controlling bacterial decay of waterlogged archaeological poles

Wood discs from two waterlogged softwood poles were investigated for variations in bacterial decay. Exterior and interior degradation was observed using light, transmission and scanning electron microscopy. Maximum water content (U_max) was measured and extent of decay from the surface towards the wood interior was investigated. Despite a well preserved appearance, the majority of the tracheids were heavily degraded. Erosion bacteria were identified as the main degraders and a significant difference in degree of decay was found between the upper and lower parts of each pole. Small differences in oxygen concentration, derived from depth of burial, are suggested as the controlling factor. Active erosion bacterial decay was found in the inner parts of the 1200-year old wooden poles.     

Brown rot decay of copper-chromated-phosphorus impregnated fence poles: Characterization by molecular analyses and microscopy

At one location in central Sweden, agricultural pine (Pinus sylvestris L.) fence poles treated with a commercial copper–chromium–phosphorus preservative (CCP) formulation according to use class 4 at retention of 30 kg m⁻³ were prematurely degraded by fungi after only two years in-service. Light- and electron microscopy analyses showed decay to result from primarily brown rot attack. Culture studies produced on different agar and copper-containing media using small wood slivers removed from infected poles allowed establishment of a number of pure cultures of Phycomycetes, Ascomycetes, Fungi Imperfecti and Basidiomycete fungi. Using morphological characters, PCR and sequencing of isolated strains, Antrodia vaillantii was determined as the most abundant basidiomycete present and as the major causal agent of decay. Compatibility tests and comparison of the ITS nrDNA sequences of our putative A. vaillantii isolate with other A. vaillantii strains and with Antrodia radiculosa showed differences suggesting a hybrid strain. A combination of site characteristics (e.g. hot spots of A. vaillantii), the use of juvenile poles, copper tolerance and overall ineffectivity of CCP against A. vaillantii is suggested as reasons for premature decay.     

Diversity of fungi in creosote-treated crosstie wastes and their resistance to polycyclic aromatic hydrocarbons

This study was conducted to generate information regarding the diversity of fungi inhabiting creosote-treated wood in a storage yard for crosstie wastes in Gwangmyeong, Korea. Additionally, the resistance to polycyclic aromatic hydrocarbons (PAHs) of indigenous fungi that mainly occupy creosote-treated wood was evaluated. We isolated fungi from the surface and inner area of crosstie wastes and identified them using a combination of traditional methods and molecular techniques. Overall, 179 isolates including 47 different species were isolated from 240 sampling sites. The identified fungal species included 23 ascomycetes, 19 basidiomycetes, and 5 zygomycetes. Three species, Alternaria alternata, Irpex lacteus, and Rhizomucor variabilis, were the most frequently isolated ascomycetes, basidiomycetes, and zygomycetes, respectively. The results of this study showed that there was a large difference in the fungal diversity between the surface and the inner area. Additionally, zygomycetes and ascomycetes were found to have a greater tolerance to PAHs than basidiomycetes. However, two basidiomycetes, Heterobasidion annosum and Schizophyllum commune, showed very high resistance to PAHs, even in response to the highest concentration (1,000 ppm), which indicates that these species may play a role in the degradation of PAHs.     

A new method specifically designed to expose cells isolated in vitro to radon and its decay products

A system was set up to provide direct exposure of cells cultured in vitro to radon and its decay products. Radon gas emanating from a uranium source was introduced at a measured concentration in a closed 10-m(3) exposure chamber. Cells were cultured on the microporous membrane of an insert that was floating over the culture medium in a six-well cluster plate. Plates with cells were placed in an open thermoregulated bath within the chamber. Under these conditions, cells were irradiated by direct deposition of radon and radon decay products. During exposure, all parameters, including radon gas concentrations, decay product activities, and potential alpha-particle energy concentrations, were determined by periodic air-grab samplings inside the chamber. The energy spectrum of deposited decay products was characterized. An estimation of alpha-particle flux density on the area containing cells was performed using CR-39 detector films that were exposed in cell-free wells during the cell exposure. The number of alpha-particle traversals per cell was deduced both from the mean number of CR-39 tracks per surface unit and from measurements of entire cells or nuclear surfaces. This paper describes the design of experiment, the dosimetry of radon and radon decay product, and the procedures for aerosol measurements. Our preliminary data show the usefulness of the in vitro cell culture approach to the study of the early cellular effects of radon and its decay products.     

Localisation and characterisation of incipient brown-rot decay within spruce wood cell walls using FT-IR imaging microscopy

Spruce wood that had been degraded by brown-rot fungi (Gloeophyllum trabeum or Poria placenta) exhibiting mass losses up to 16% was investigated by transmission Fourier transform infrared (FT-IR) imaging microscopy. Here the first work on the application of FT-IR imaging microscopy and multivariate image analysis of fungal degraded wood is presented and the first report on the spatial distribution of polysaccharide degradation during incipient brown-rot of wood. Brown-rot starts to become significant in the outer cell wall regions (middle lamellae, primary cell walls, and the outer layer of the secondary cell wall S1). This pattern was detected even in a sample with non-detectable mass loss. Most significant during incipient decay was the cleavage of glycosidic bonds, i.e. depolymerisation of wood polysaccharides and the degradation of pectic substances. Accordingly, intramolecular hydrogen bonding within cellulose was reduced, while the presence of phenolic groups increased.     

Ostracod reactions to non-toxic and toxic algae

Summary When fed algae continuously, laboratory ostracods had a life span of 21–28 days; without food, they were able to survive about 7 days. When exposed to thick suspensions of gas-vacuolate blue-green algae, survival rates were generally low. Twenty five % of our euplanktonic strains killed entire ostracod populations within 24–48 hrs; about 30% of other waterbloom strains were dangerous to ostracods causing either death or coordination loss. Some amphibious non-gas-vacuolated strains were also toxic to ostracods. Toxins from broken cells were not persistent in effect; ostracods surviving the initial shock often appeared recovered within 2–4 days. In di-algal systems, ostracods generally fed on a single species and did not always choose green algae over blue-green. Unicellular green algal strains (Ankistrodesmus, Scenedesmus, Kirchneriella) were generally preferred. Some chlorophycean forms (Zygnema, Hormidium, Trentepholia) were shunned in favor of bluegreens such as Tolypothrix and Westiella. Erect and branched strains (Fischerella, Westiella, Tolypothrix) were eaten before Anabaena and Nostoc with the latter genus being least preferred. Intact Nostoc colonies were usually not ingested, but some loosely growing, non-toxic strains of both Nostoc and Anabaena provided adequate food for ostracod populations indefinitely.     

A curvature-mediated mechanism for localization of lipids to bacterial poles

Subcellular protein localization is a universal feature of eukaryotic cells, and the ubiquity of protein localization in prokaryotic species is now acquiring greater appreciation. Though some targeting anchors are known, the origin of polar and division-site localization remains mysterious for a large fraction of bacterial proteins. Ultimately, the molecular components responsible for such symmetry breaking must employ a high degree of self-organization. Here we propose a novel physical mechanism, based on the two-dimensional curvature of the membrane, for spontaneous lipid targeting to the poles and division site of rod-shaped bacterial cells. If one of the membrane components has a large intrinsic curvature, the geometrical constraint of the plasma membrane by the more rigid bacterial cell wall naturally leads to lipid microphase separation. We find that the resulting clusters of high-curvature lipids are large enough to spontaneously and stably localize to the two cell poles. Recent evidence of localization of the phospholipid cardiolipin to the poles of bacterial cells suggests that polar targeting of some proteins may rely on the membrane's differential lipid content. More generally, aggregates of lipids, proteins, or lipid-protein complexes may localize in response to features of cell geometry incapable of localizing individual molecules.     

Application of method of moments analysis to fluorescence decay lifetime distributions

In fluorescence decay work, distributions of exponential decay lifetimes are anticipated where complex systems are examined. We describe here methods of gaining information on such distributions using the method of moments analysis approach. The information obtained may be as simple as the average and deviation of the lifetime distribution, quantities which we show may be estimated directly from the results of a multiexponential analysis. An approximation to the actual distribution shape may also be obtained using a procedure we call the variable filter analysis (VFA) method without making any assumptions about the shape of the distribution. Tests of VFA using both simulated and experimental data are described. Limitations of this method and of distribution analysis methods in general are discussed. Results of analyses on experimental decays for ethidium intercalated in core particles and in free DNA are reported.     

A Fourier method for the analysis of exponential decay curves.

A method based on the Fourier convolution theorem is developed for the analysis of data composed of random noise, plus an unknown constant "base line," plus a sum of (or an integral over a continuous spectrum of) exponential decay functions. The Fourier method's usual serious practical limitation of needing high accuracy data over a very wide range is eliminated by the introduction of convergence parameters and a Gaussian taper window. A computer program is described for the analysis of discrete spectra, where the data involves only a sum of exponentials. The program is completely automatic in that the only necessary inputs are the raw data (not necessarily in equal intervals of time); no potentially biased initial guesses concerning either the number or the values of the components are needed. The outputs include the number of components, the amplitudes and time constants together with their estimated errors, and a spectral plot of the solution. The limiting resolving power of the method is studied by analyzing a wide range of simulated two-, three-, and four-component data. The results seem to indicate that the method is applicable over a considerably wider range of conditions than nonlinear least squares or the method of moments.     

A review of global instruments to combat invasive alien species in forestry

Although impacts of biological invasions may be local, at least at first, the causes of introduction are mostly international. Through trade and transport pathways, countries both send and receive non-native species. There are numerous international and regional instruments, binding and nonbinding, which have been developed to deal with the problem of the movement of alien invasive species, however there are gaps in the current international framework. Global goals in the management of forestry-related threats from invasive alien species should include making best use of existing regulatory frameworks, investing more into global research initiatives, and targeting existing tools and resources more effectively. Given the lack of resources for many developing countries to undertake research, conduct risk assessments and implement quarantine measures, there is a need for regional and global support for countries that lack sufficient resources to implement effective phytosanitary systems.     

A new method for the analysis of sums of exponential decay curves

A method based on Fourier Transform is presented for the representation of data by an arbitrary sum of exponentials or Gaussian functions. The method has been successfully applied to the type of data sets which arise in pharmacokinetic studies. Two techniques for error ripple elinination are discussed.     

Pooling and PCR as a method to combat low frequency gene targeting in mouse embryonic stem cells

The introduction of germ line modifications by gene targeting in mouse embryonic stem (ES) cells has proven a fundamental technology to relate genes to mammalian biology. Critical aspects required for successful gene targeting have traditionally been experimental enhancements that increase the frequency or detection of homologous recombination within ES cells; however, the utilization of such methods may still result in the failed isolation of a positively targeted ES cell clone. In this study, we discuss the current enhancement methods and describe an ES cell pooling strategy that maximizes the ability to detect properly targeted ES cells regardless of an inherent low targeting efficiency. The sensitivity required to detect correctly targeted events out of a pool of ES cell clones is provided by polymerase chain reaction (PCR), and only those pools containing positives need to be expanded and screened to find individually targeted clones. This method made it possible to identify targeted clones from a screen of approximately 2,300 ES cell colonies by performing only 123 PCR reactions. This technically streamlined approach bypasses the need to troubleshoot and re-engineer an existing targeting construct that is functionally suitable despite its low targeting frequency.     

A simplified model to predict stress fracture in young elite combat recruits

The purpose of the study was to develop a simple prediction model for stress fractures (SFs) in young male recruits to identify risk factors for SF. Data were collected from 57 young (18.5 ± 0.5 years) male athletes before elite combat basic training (BT). Measurements included anthropometric variables, blood samples, fitness tests, bone quality (peripheral quantitative computed tomography [pQCT]), psychological assessment, nutritional habits, and history of physical activity. A medical evaluation was done periodically. The SFs were clinically diagnosed during the 1-year training and thereafter confirmed by bone scintigraphy. Three "simple to monitor" variables were found to be significantly (p < 0.05) related to SF occurrence during basic and advanced training: aerobic training frequency, aerobic training duration, and waist circumference. From these 3 variables, a new model was constructed that successfully predicted 85% of the soldiers with (n = 23) and without (n = 34) SF as follows:(Equation is included in full-text article.)where PSF is the stress fracture prediction according to the Log Odds (SF), Odds(SF) is the ratio between the probability of SF existence and nonexistence, ATn is the aerobic training (times per week), ATt is the aerobic training duration (minutes per week), and waist is the circumference (centimeters). This model was validated on a different database taken from another 59 elite combat recruits before BT and successfully predicted 76.5% of the soldiers with SF (n = 22) and without SF (n = 37). A young male recruit for elite combat unit is at a greater risk of developing SF if, before entering BT, he trained aerobically <2 times per week with each training >40 minutes and has a waist circumference of <75 cm. However, further evaluation is required for different combat recruits, ages, and training programs to validate these results.     

细菌耐药性应对策略研究进展

细菌耐药性(Antimicrobial resistance,AMR)持续增长,但新上市抗生素数量却持续下降。抗生素耐药基因(Antimicrobial resistance gene,ARG)和抗生素耐药菌感染已严重威胁人类健康。因此,需要多方面联合采取措施来应对AMR所带来的各种挑战,包括创新生物医药、改善抗生素使用和抗生素耐药监测系统、减少抗生素耐药基因产生速度、阻止健康护理相关感染和多重抗生素耐药菌传播与扩散、开发微生物学快速诊断方法与设备、减少临床和兽医抗生素滥用等。庆幸的是,AMR已受到各国政要、科学家和企业家等的高度重视与支持,相信随着新技术、新产品的不断问世和管理新措施的不断出台,AMR问题一定会得到控制和缓解。     

Horizontal distribution of Daphnia pulex in response to toxic and non-toxic algal extracts

We studied the horizontal distribution of Daphnia pulex as aresponse to gradients of toxic extracts of two cyanobacteria,Microcystis aeruginosa and Oscillatoria agardhii and non-toxicextracts of the green alga Scenedesmus obtusiusculus. The experimentwas performed in the dark using a flow through system with fivechambers. Daphnia pulex aggregated at the inlet of Scenedesmusextract, but showed similar responses to extracts of toxic cyanobactenaand food-free medium. Chemical cues seem to affect food search,but do not effect Daphnia pulex's avoidance of toxic algae.     

A simple and efficient method for analysis of plant growth regulators: a new tool in the chest to combat recalcitrance in plant tissue culture

This report presents a simple, rapid and accessible validated method for quantification of eight major plant growth regulators (PGR): cytokinins (6-(γ,γ-dimethylallylamino)purine (2-iP), benzylaminopurine (BA) and zeatin), auxin (indole-3-acetic acid; IAA), jasmonic acid (JA), salicylic acid (SA), gibberellic acid (GA3) and abscisic acid (ABA) by liquid chromatography mass spectrometry. This method was tested in eight species including agricultural, ornamental and medicinal species: St. John’s wort, African violet, banana, American elm, tobacco, potato, sweet wormwood, and fennel. The method has good reproducibility and good sensitivity with %RSD (percent relative standard deviation) between 1 and 10% for all matrices and recovery values of 89 to 118% for all analytes. Method detection limits were 50.65 ng/g, 203.4 ng/g, 50.65, ng/g, 50.65 ng/g, 203.4 ng/g, 12.7 ng/g, 193 pg/g and 3.08 ng/g, for SA, IAA, zeatin, JA, GA3, ABA, 2-iP, and BA, respectively. Our results with a range of plant species show that this method represents a simple, low-cost method for analysis of PGRs, and may also serve as an useful starting point for the analysis of other related PGRs, as demonstrated by inclusion of the SA derivative, acetylsalicylic acid, and the JA derivatives: 12-oxo-phytodienoic acid and JA-isoleucine. The efficiency of this method will enable its incorporation into the plant tissue culture work flow and through characterization of endogenous PGR levels, will allow for improved method development for recalcitrant species facilitating fundamental and applied studies in plant morphogenesis, propagation and conservation.     

The contribution of post-copulatory mechanisms to incipient ecological speciation in sticklebacks

Ecology can play a major role in species diversification. As individuals are adapting to contrasting habitats, reproductive barriers may evolve at multiple levels. While pre-mating barriers have been extensively studied, the evolution of post-mating reproductive isolation during early stages of ecological speciation remains poorly understood. In diverging three-spined stickleback ecotypes from two lakes and two rivers, we observed differences in sperm traits between lake and river males. Interestingly, these differences did not translate into ecotype-specific gamete precedence for sympatric males in competitive in vitro fertilization experiments, potentially owing to antagonistic compensatory effects. However, we observed indirect evidence for impeded development of inter-ecotype zygotes, possibly suggesting an early stage of genetic incompatibility between ecotypes. Our results show that pre-zygotic post-copulatory mechanisms play a minor role during this first stage of ecotype divergence, but suggest that genetic incompatibilities may arise at early stages of ecological speciation.