Role of the cell-wall structure in the retention of bacteria by microfiltration membranes

This experimental study investigates the retention of bacteria by porous membranes. The transfer of bacteria larger than the nominal pore size of microfiltration track-etched membranes has been studied for several kinds of bacterial strains. This unexpected transfer does not correlate to the hydrophobicity, neither to the surface charge of the microorganism, as suggested in previous reports. We conclude that, in our conditions, the kind of bacteria (Gram-positive or Gram-negative) is finally the most important parameter. As the distinction between those two types of bacteria is related to the cell-wall structure, we provide an experimental evidence, via the action of an antibiotic, that the cell-wall flexibility triggers the transfer of the bacteria through artificial membranes, when the pores are smaller in size than the cell.     

Characterization of fungal spores by laser desorption/ionization time-of-flight mass spectrometry

A considerable volume of research has now been completed on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to the analysis of bacteria; however, to date no definitive studies have been made using this technique on fungi. Preliminary studies on the application of the MALDI-MS methodology, previously developed for the analysis of bacteria, to the analysis of intact fungal spores are described here. MALDI-MS and electrospray mass spectrometry enable the high molecular weight analysis of proteins, glycoproteins, oligosaccharides and oligonucleotides. Using MALDI-MS with bacteria has demonstrated the ability to produce 'fingerprints' of the intact cells with the ions observed being associated with the proteinaceous components of the cell wall. This paper reports the adaptation of this technique to the direct analysis of fungal cells. The high percentage of carbohydrate in the fungal cell wall indicates that the ions observed in the mass spectrometric experiments may be of carbohydrate origin. Penicillium spp., Scytalidium dimidiatum and Trichophyton rubrum have been studied in this preliminary investigation and all show individually distinctive spectra which would appear to provide a profile of the cellular material with discrete peaks being observed over the mass range 2 to 13 kDa. The spectra obtained are reproducible within the method used but, as shown in our previous studies on bacteria, washing may selectively release components from the fungal cell wall.     

Detection of bacterial quorum sensing <Emphasis Type="Italic">N</Emphasis>-acyl homoserine lactones in clinical samples

Bacteria communicate among themselves using certain chemical signaling molecules. These signaling molecules generally are N-acyl homoserine lactones (AHLs) in Gram-negative bacteria and oligopeptides in Gram-positive bacteria. In addition, both Gram-positive and Gram-negative bacteria produce a family of signaling molecules known as autoinducer-2 that they employ for their communications. Bacteria coordinate their behavior by releasing and responding to the chemical signaling molecules present in proportion to their population density. This phenomenon is known as quorum sensing. The role of bacteria in the pathogenesis of several diseases, including gastrointestinal (GI) disorders, is well established. Moreover, rather recently bacterial quorum sensing has been implicated in the onset of bacterial pathogenicity. Thus, we hypothesized that the signaling molecules involved in bacterial communication may serve as potential biomarkers for the diagnosis and management of several bacteria-related diseases. For that, we previously developed a method based on genetically engineered whole-cell sensing systems for the rapid, sensitive, cost-effective and quantitative detection of AHLs in biological samples, such as saliva and stool, from both healthy and diseased individuals with GI disorders. Although various analytical methods, based on physical-chemical techniques and bacterial whole-cell biosensors, have been developed for the detection of AHLs in the supernatants of bacterial cultures, only a few of them have been applied to AHL monitoring in real samples. In this paper, we report work performed in our laboratory and review that from others that describes the detection of AHLs in biological, clinical samples, and report some of our recent experimental results.     

Electrochemical reduction of oxygen catalyzed by a wide range of bacteria including Gram-positive

Most bacteria known to be electrochemically active have been harvested in the anodic compartments of microbial fuel cells (MFCs) and are able to use electrodes as electron acceptors. The reverse phenomenon, i.e. using solid electrodes as electron donors, is not so widely studied. To our knowledge, most of the electrochemically active bacteria are Gram-negative. The present study implements a transitory electrochemical technique (cyclic voltammetry) to study the microbial catalysis of the electrochemical reduction of oxygen. It is demonstrated that a wide range of aerobic and facultative anaerobic bacteria are able to catalyze oxygen reduction. Among these electroactive bacteria, several were Gram-positive. The transfer of electrons was direct since no activity was obtained with the filtrate. These findings, showing a widespread property among bacteria including Gram-positive ones, open new and interesting routes in the field of electroactive bacteria research.     

Bacterial transport in porous media: New aspects of the mathematical model

Transport of bacteria is an important aspect from scientific, industrial and environmental point of view. In this work, a one-dimensional mathematical model based on linear equilibrium adsorption of bacteria has been developed to predict bacterial transport through porous media. This model is more realistic than existing models because of its coupling both physicochemical and biological phenomena. Two important biological phenomena, the growth and decay of bacterial cells and chemotactic/chemotaxis of bacteria along with physicochemical properties have been adequately incorporated which are quite new aspects in our model. In agreement with experimental study by [D.K. Powelson, R.J. Simpson, C.P. Gerba, J. Environ. Qual. 19 (1990) 396], model simulations indicated that enhancement of breakthrough occurs due to increase in flow velocity, cell concentration, substrate concentration, respectively. It has also been found that chemo tactic has a significant effect on bacterial transport, especially under conditions of considerable substrate gradient and at low pore velocity. The importance of threshold concentration of captured cells (σ₀) on bacterial transport has also been identified which is also a new aspect in our model.     

Cutting boards in Salmonella cross-contamination

Cutting boards are commonly perceived as important fomites in cross-contamination of foods with agents such as Salmonella spp., despite the lack of supporting epidemiological data. A variety of woods and plastics have been used to make work surfaces for cutting. In general, wood is said to dull knives less than plastic, and plastic is seen as less porous than wood. Research to model the hypothetical cross-contamination has been done in a variety of ways and has yielded a variety of results. At least some of the work with knife-scarred plastic indicates that the surface is very difficult to clean and disinfect, although this may vary among the polymers used. High-density polyethylene, which is most used in commercial applications, has been shown to delaminate in response to knife scarring. Wood is intrinsically porous, which allows food juices and bacteria to enter the body of the wood unless a highly hydrophobic residue covers the surface. The moisture is drawn in by capillary action until there is no more free fluid on the surface, at which point immigration ceases. Bacteria in the wood pores are not killed instantly, but neither do they return to the surface. Destructive sampling reveals infectious bacteria for hours, but resurrection of these bacteria via knife edges has not been demonstrated. Small plastic cutting boards can be cleaned in a dishwasher (as can some specially treated wooden boards), but the dishwasher may distribute the bacteria onto other food-contact surfaces. Most small wooden boards (i.e., those with no metal joiners in them) can be sterilized in a microwave oven, but this should be unnecessary if accumulation of food residues is prevented. However, 2 epidemiological studies seem to show that cutting board cleaning habits have little influence on the incidence of sporadic salmonellosis. Further, one of these studies indicated that use of plastic cutting boards in home kitchens is hazardous, whereas use of wooden cutting boards is not.     

Evolution of antibodies for environmental monitoring: from mice to plants

Immunoassays are one of the most convenient methods for environmental monitoring, but have been limited so far by low yield and low affinity antibodies (Abs). With the advent of recombinant Ab (rAb) technology and the expression of these Abs in organisms such as yeast, bacteria, insects and plants, widespread monitoring of our food and environment for organic contaminants using immunoassays has become feasible. A multitude of immunoassays have been developed to detect pesticides in soils, ground and river water, foods and biological samples, such as urine and semen. In this paper, we describe advances in Ab production, the move away from using animals, phage-display technologies and the advent of plant-derived Ab expression systems. Finally, we describe future possibilities in Ab technology for environmental monitoring.     

An unexpected switch in the modulation of AI-2-based quorum sensing discovered through synthetic 4,5-dihydroxy-2,3-pentanedione analogues

Quorum sensing (QS) has traditionally referred to a mechanism of communication within a species of bacteria. However, emerging research implicates QS in interspecies communication and competition, and such systems have been proposed in a wide variety of bacteria. The AI-2-based QS system represents the most studied of these proposed interspecies systems, and has been proposed to regulate diverse functions such as bioluminescence, expression of virulence factors, and biofilm formation. As such, the development of modulatory compounds, both agonists and antagonists, is of great interest for the treatment of bacterial infections and the study of unknown AI-2-based QS systems. Toward this end, we have designed and synthesized a panel of 4,5-dihydroxy-2,3-pentanedione/AI-2 analogues and evaluated their effects on the AI-2 QS of various bacteria. The panel of compounds exhibited differential effects in the bacterial cell lines examined, providing a platform for the development of broad-spectrum modulators of AI-2-based QS.     

Glycosylation of the Arg-gingipains of Porphyromonas gingivalis and comparison with glycoconjugate structure and synthesis in other bacteria

Post-translational modification of proteins by covalent attachment of sugars to the protein backbone (protein glycosylation) is the most common post-translational modification in the eucaryotic cell. However, the addition of carbohydrates to proteins of Eubacteria and Archaea has been demonstrated and accepted only recently. There is now a rapidly expanding list of bacterial glycoproteins that have been characterised from a variety of different organisms including many important pathogens. The Arg-gingipains of Porphyromonas gingivalis are recent additions to this list. In this review we present a summary of our investigations on the structure of the glycan additions to these proteolytic enzymes, the genetics of the glycosylation process and some of the effects on enzyme function and recognition. These findings are placed in the context of the current status of understanding of glycoconjugate structure and synthesis in other bacteria. Given the importance of glycosylation of eucaryotic proteins to their stability, structure, resistance to proteolysis and recognition, the modifications to the proteases described in the present report are likely to have a functional role in the properties of these enzymes in periodontal disease.     

具有“杀菌-释菌”功能转换的智能抗菌表面

细菌在生物材料表面的黏附和后续生物被膜的形成会引起一系列严重后果,因此赋予生物材料表面抗菌性能成为国内外科研工作者们的研究热点.然而目前常见的抗菌策略主要集中在杀死表面黏附的细菌,而忽略了死细菌在表面的积累所引起的如抗菌效率下降、二次污染等诸多问题.针对此,研究者们提出了"杀菌-释菌"功能转换的智能抗菌策略并以此发展了一系列智能抗菌表面.本专论基于我们课题组的研究成果,根据杀菌剂与材料表面结合方式的不同(永久固定杀菌剂、可重复负载杀菌剂和不需要杀菌剂),对近年来智能抗菌表面领域的研究进展进行了评述.这些智能抗菌表面能够在杀灭细菌后及时清除表面残留的死细菌,从而保持了长效抗菌功能.最后对该领域未来的研究方向进行了展望.     

DNA replication in the third domain (of life)

DNA replication is the process underlying evolution and the propagation of living organisms. Since the discovery of DNA-dependent DNA polymerases more than 40 years ago, the mechanisms governing DNA replication have been extensively studied in bacteria and eukarya. During the last several years, these studies have been extended to the third domain of life, the archaea. Although archaea are prokaryotes, their replication machinery and the proteins participating in the initiation of DNA replication are more similar to those found in eukarya than bacteria. It appears, however, that replication in archaea is a simpler version of the eukaryotic one as fewer polypeptides participate in each phase of the replication process. The archaeal replication apparatus also has several unique features not found in eukaryotic organisms. Furthermore, like bacteria, members of this domain thrive under a broad range of environmental conditions including extreme temperature, high salt, pH, etc. Thus, the replication machinery had to adapt to these extreme conditions. This article summarizes our current understanding of the mechanisms governing DNA replication in archaea and highlights similarities and differences between archaeal replication and that of bacteria and eukarya.     

Microbial Degradation of Halogenated Hydrocarbons: A Biological Solution to Pollution Problems?

Chlorinated hydrocarbons are widely used because of their chemical and thermal stability as well as their fungicidal, herbicidal, and insecticidal properties. Unfortunately, it is just this stability that makes the compounds persistent in nature; half-lives of more than 15 years are not uncommon. In many countries the use of some chlorinated compounds has been prohibited, even though many such compounds (e.g., DDT) exhibit exactly the desired spectrum of effects. Surprisingly, microbiol systems that can degrade most chlorinated hydrocarbons have been found in nature. Indeed, it is possible, in many cases, to isolate pure cultures of bacteria that can utilize these compounds as the sole source of carbon and energy. Even polychlorinated compounds, such as the wood preservative and herbicide pentachlorophenol, can be utilized as a source of carbon by some bacteria. The study of the biodegradation of halogenated hydrocarbons has led to the discovery of novel catabolic pathways in which unusual and previously undescribed enzymatic activities have been detected. Bacterial enzymes have even been isolated that can replace halogen substituents in aliphatic and aromatic compounds with hydroxyl groups or hydrogen atoms. Improved understanding of the biodegradation of halogenated hydrocarbons, as described in this article, will almost certainly result in new biotechnological applications, especially in the area of waste-water treatment.     

The yin and yang of amyloid: insights from α-synuclein and repeat domain of Pmel17

Amyloid has been traditionally viewed in the context of disease. However, the emerging concept of 'functional amyloid' has taken a new direction into how we view amyloid. Recent studies have identified amyloid fibrils ranging from bacteria to humans that have a beneficial role, instead of being associated with a misfolded state that has been implicated in diseases such as Alzheimer's, Parkinson's and prion diseases. Here, we review our work on two human amyloidogenic polypeptides, one associated with Parkinson's disease, α-synuclein (α-syn), and the other important for melanin synthesis, the repeat domain (RPT) from Pmel17. Particularly, we focused our attention on spectroscopic studies of protein conformation and dynamics and their impact on α-syn amyloid formation and for RPT, we discussed the strict pH dependence of amyloid formation and its role in melanin biosynthesis.     

Bacterial lantibiotics: strategies to improve therapeutic potential

Lantibiotics are ribosomally-synthesised antimicrobial peptides produced by Gram-positive bacteria that are characterised by the presence of lanthionine and/or methyllanthionine residues. Other unusual post-translationally modified amino acids, most frequently dehydroalanine and dehydrobutyrine, can also be present. While it has been frequently suggested that these peptides have the potential to be utilised in a wide range of medical applications, to date no actual therapeutic applications have been convincingly described. More recently, however, they have been the focus of much attention as a consequence of improved biotechnological capabilities, an improved understanding of lantibiotic biosynthesis and mode of action, and their high specific activity against multi-drug resistant bacteria. This review concerns the fundamental analyses that have revealed the importance of individual amino acids in these peptides and has permitted the implementation of rational mutagenesis strategies ('intelligenetics') to alter individual residues with a view to ultimately widening the active pH range, improve stability, and enhance binding to cell wall targets with the ultimate aim of optimising their antimicrobial activity. It is hoped that as a consequence of this improved knowledge the most suitable application of individual lantibiotics will become apparent. It should also prove possible, in the near future, to generate tailor-made lantibiotics and utilise biosynthetic enzymes to incorporate modified amino acids into non-lantibiotic peptides. In the shorter term, the extensive characterisation of lantibiotics will be instrumental in reassuring drug industry regulators of their safety and facilitate the widespread application of these novel antimicrobial agents in medicine.     

Bacterial membranes as predictors of antimicrobial potency

A wide range of chemical structures having antimicrobial activity have been studied in an effort to treat the increasing emergence of bacteria that are resistant to traditional antibiotics. These agents have varying degrees of toxicity against different bacterial species. We demonstrate, using members of a novel class of antimicrobial agents, the oligomers of acyllysine, that one cause for the difference in species selectivity is the ability to induce the clustering of anionic lipids, resulting in their segregation into domains. This phenomenon occurs only in bacterial membranes composed of both anionic and zwitterionic lipids and not with bacteria whose membrane lipids are largely anionic. As a consequence it can be predicted which bacterial species will be most affected by antimicrobial agents that function principally by this mechanism. This finding allows for the design of new antibiotics with selective toxicity against different groups of bacteria.     

What Do We Know About Nuclear Fission?

Nuclear fission, although a physical phenomenon, is also of interest to the chemist. It was discovered by chemists, and chemists have made a material contribution to our present knowledge in this field. A comprehensive theory of nuclear fission has not, as yet, been developed, despite the volume of experimental data that has amassed in the 35 years since its discovery. In the past few years discoveries have been made which cannot be explained with conventional theoretical models of nuclear fission. The most important discovery was that of shape isomerism, a novel type of nuclear isomerism. It would appear that an accurate calculation of fission barriers is a prerequsite for precise explanation of many experimental findings. Recent results in this connection and an outline of the present state of our knowledge of nuclear fission constitute the main theme of this paper.     

Theoretical analysis of bacterial efflux pumps inhibitors: Strategies in-search of competent molecules and develop next

Multi-drug resistance (MDR) bacteria pose a significant threat to our ability to effectively treat infections due to the development of several antibiotic resistant mechanisms. A major component in the development of the MDR phenotype in MDR bacteria is over expression of different-type of efflux pumps, which actively pump out antibacterial agents and biocides from the periplasm to the outside of the cell. Consequently, bacterial efflux pumps are an important target for developing novel antibacterial treatments. Potent efflux pump inhibitors (EPIs) could be used as adjunctive therapies that would increase the potency of existing antibiotics and decrease the emergence of MDR bacteria. Several potent inhibitors of efflux pumps have been reported which has been summarized here. All the natural and synthetic EPIs were optimized with Gaussian and Avogadro software. The optimized structures were docked with each class of efflux pumps and their bonding parameters were computed. The theoretical analyses were performed with density functional theory (DFT). Overall, computational study revealed a good trend of electrophilicity and ionization potential of the EPIs, the obtained average values are within in the range of 0.001414 AU ± 0.00032 and 0.208821 AU ± 0.015545, respectively. Interestingly, cathinone interacts with most of the efflux pumps among the tested inhibitors. The electrophilicity and ionization potential of cathinone are 0.00198 and 0.2388 AU, respectively. The study opens a new road for designing future-generation target-specific efflux pump inhibitors, as well as one molecule with multiple inhibition abilities.     

甲烷氧化菌的高密度培养及其在生物柴油炼制中的应用

天然气是储量最丰富的能源之一,但限于勘探、运输、配置等问题,一直以来人们对它的利用都不是很合理.能源危机和环境问题推动了生物质能源的开发利用,甲烷氧化菌是以甲烷为唯一碳源和能源进行生长的一类细菌,具有炼制生物柴油的潜力.综述了近几年甲烷氧化菌在高密度培养及深加工炼制生物柴油的研究进展,着重分析了高密度培养和生物柴油炼制过程中在传质与反应器设计、菌种培养、脂质提取、加氢脱氧四个过程中面临的技术难点,给出了解决方法并展望了其在未来的发展.     

Viruses More Friends than Foes

Viruses are normally defined as pathogens and have a bad reputation because of pandemics such as Influenza, HIV/AIDS, Ebola, and SARS. Most viruses are, however, not enemies or killers but play important roles in the origin, development and maintenance of life of all species on our planet. This is new information we learnt by new technologies such as sequencing. Viruses are the most successful species on Earth, they are ubiquitous, in the oceans, in our environment, in animals, plants, bacteria, up in the air, perhaps even in the universe, within our body and even as part of our genomes. They influence our health, our well‐being, mental properties, our gut microbiota including obesity, and may help to cope with multi‐drug‐resistant bacteria. There the phages, viruses of bacteria, raise hopes. Viruses built our immunity: viruses protect against viruses. We do not have to lay eggs – thanks to viruses! They are the drivers of evolution and adaptation to environmental changes, also e. g. in plankton. The success story of viruses started about 3.5 billion years ago when life began. Newly discovered giant viruses are almost bacteria in their composition, suggesting that the borderline between dead matter and life is continuous. There are many open questions – how did life begin, is there life on exoplanets, how to find it? Are virus‐like elements, viroids, important for the origin of life? Will viruses eliminate mankind [1]?     

Peptide AS-48: prototype of a new class of cyclic bacteriocins

After the discovery of bacteriocin AS-48, a 70-residue cyclic peptide produced by Enterococcus faecalis subsp. liquefaciens, some naturally-occurring cyclic proteins from bacteria have been reported. AS-48 is encoded by the 68-kb pheromone-responsive plasmid pMB2, and the gene cluster involved in production and immunity has been identified and sequenced. This peptide exerts a bactericidal action on sensitive cells (most of the Gram-positive and some Gram-negative bacteria). Its target is the cytoplasmic membrane, in which it opens pores, leading to the dissipation of the proton motive force and cell death, a mechanism similar to that proposed for the action of defensins or, most generally, cationic antibacterial peptides. This fact, together with its remarkable stability and solubility over a wide pH range, suggest that this bacteriocin could be a good candidate as a natural food preservative. The amino acid composition of purified AS-48 shows the absence of modified or dehydrated residues, making it clearly different from lantibiotics. Bacteriocin AS-48 also differs from defensins in that it does not contain cysteines and consequently no disulfide bridges, which makes is high stability even more remarkable. Composition analysis of AS-48 shows a high proportion of basic to acidic amino acids, conferring to this peptide a strong basic character, with an isoelectric point close to 10.5. Determination of the AS-48 structural gene DNA sequence, together with the sequences of AS-48 protease digestion fragments and mass spectrometry determinations, allowed us to determine unambiguously the cyclic structure of the molecule, being the first example of a posttranslational modification in which a cyclic structure arises from a "head-to-tail" linkage. We have solved the three-dimensional structure of AS-48 in solution, and it consists of a globular arrangement of five alpha-helices enclosing a compact hydrophobic core. Interestingly, the head-to-tail peptide link between Trp-70 and Met-1 lies in the middle of alpha-helix 5, which is shown to have a pronounced effect on the stability of the three-dimensional structure. Analysis of structure-function relationship allowed us to propose models to understand the aspects of the molecular function of AS-48. The purpose of this work is to review recent developments in our understanding about the biochemical and biological characteristics and structure of this unusual type of bacteriocin.