Highveld biology

Legionella publications

noreply@blogger.com (Blog owner) — Wed, 17 Jun 2009 15:52:00 +0000

A collection of open access publications on Legionella

Legionella: Molecular Microbiology
The main focus is the current state of many of the most critical features of Legionella. Internationally renowned authors have contributed chapters describing and discussing the latest research findings with an emphasis on molecular aspects.

Legionella Papers
The topics covered range from the history of the identification of Legionella and clinical disease treatment, to the microbe's gene expression and secretion ...

Dictyostelium, a Tractable Model Host Organism for Legionella
In this review we describe both Legionella and Dictyostelium factors and processes that are relevant to infection. Moreover, we summarize the results of the ...

The Flagellar Regulon of Legionella pneumophila
Legionella is a ubiquitious inhabitant of aquatic habitats, and it is believed that motility is an important feature in the life cycle of L. pneumophila in ...

The Dot/Icm Type IVB Secretion System of Legionella
The major virulence system of Legionella pneumophila is a specialized secretion system encoded by twenty-six dot/icm genes. This secretion machine is ...

Secretion and Export in Legionella
L. pneumophila secretes many factors that promote its growth and persistence within the environment, various types of host cells, and the mammalian lung.

Diagnostics and Clinical Disease Treatment
The methods currently available to diagnose Legionnaires disease are culture, urinary antigen detection, direct fluorescent antibody testing, detection of ...

Legionnaires Disease: History and Clinical Findings
The history of Legionnaires disease began at least 33 years before the 1976 Philadelphia epidemic, when Legionella micdadei was isolated from human blood.

Further reading: Legionella: Molecular Microbiology

Gene chip

noreply@blogger.com (Blog owner) — Tue, 16 Jun 2009 11:08:00 +0000

In microarrays, the DNA oligonucleotides are attached to a solid surface such as glass or a silicon chip, in which case they are commonly known as gene chips.

Gene chips can be used to measure changes in expression levels, to detect single nucleotide polymorphisms (SNPs, in genotyping or in resequencing mutant genomes, and for many other purposes.

The applications of gene chips in the areas of molecular biology, biotechnology, medicine and bioscience are discussed in a new two-volume book published recently:

Volume 1: Lab-on-a-Chip Technology: Fabrication and Microfluidics
Volume 2: Lab-on-a-Chip Technology: Biomolecular Separation and Analysis

Biochip

noreply@blogger.com (Blog owner) — Tue, 16 Jun 2009 11:00:00 +0000

A biochip is a collection of miniaturized test sites (microarrays) arranged on a solid substrate that permits many tests to be performed at the same time in order to achieve higher output and speed. Biochips can also be used to perform techniques such as electrophoresis or PCR using microfluidics technology

Further reading: A new two-volume book Lab-on-a-Chip Technology was published recently. The book describes the recent innovations in the biochip field and the applications of biochips in the areas of molecular biology, biotechnology, medicine and bioscience.

Volume 1: Lab-on-a-Chip Technology: Fabrication and Microfluidics
Volume 2: Lab-on-a-Chip Technology: Biomolecular Separation and Analysis

Microbiology online

noreply@blogger.com (Blog owner) — Tue, 26 May 2009 13:24:00 +0000

Microbiology Journal
Descriptions, aims and scope of a wide range of journals in all areas of microbiology to help the microbiologist make decisions on the best microbiology journal for the submission of manuscripts and for research.

Microbiology Conferences
Current microbiology conferences, meetings, symposia, workshops and advanced courses.

Microbiology Books
Current and forthcoming high-level reference books on all aspects of microbiology.

Microbiology Blog
Current microbiology news and views to help the busy scientist keep up-to-date on research, forthcoming conferences, hot research topics, high impact publications, and much more.

Miniaturized PCR-based biosensors

noreply@blogger.com (Blog owner) — Fri, 22 May 2009 12:52:00 +0000

Within the last ten years there have been significant efforts to take PCR out of the laboratory and into the field. This is partially due to an increased demand for rapid and accurate methods of detecting pathogenic bacteria, viruses and other disease-causing agents. Due to its relative accuracy and sensitivity, the polymerase chain reaction (PCR) is well suited to these needs. Miniaturized PCR-based biosensors have been developed utilizing a variety of manufacturing technologies. At least four commercial entities have developed miniaturized PCR-based detection systems with corresponding detection assays targeting DNA from tissue, blood, environmental, or food samples (Herold and Rasooly, 2009. Lab-on-a-Chip Technology. ISBN: 978-1-904455-47-9). These PCR-based systems are both sensitive and robust, but a variety of contaminants can inhibit successful amplification and diminish their sensitivity.

In order to circumvent this problem, DNA is typically extracted and purified from a sample through a variety of lysis protocols and purification techniques. One of the most common methods is chemical lysis followed by DNA purification using silica-based resins. DNA in chaotropic salt containing buffers, such as those containing guanidinium or sodium iodide salts, preferentially binds to silica surfaces, while other macromolecules, such as protein and lipids, remain free in solution. These unwanted components can be removed by various methods, including centrifugation and subsequent alcohol based washing steps. The relatively pure DNA is then eluted in low-ionic strength buffer or water. Simple kits are commercially available based upon particulate matrices with problematic flow rates and no direct integration into chip-based devices. At least one group has reported the incorporation of silica-based resins into a micro-flow device while others have used microfabricated silica pillar structures for the same purpose.

Integrating DNA purification and subsequent reactions on the same chip reduces sample size, conserves sample volume and eliminates complicated steps for the technician. Once DNA has been extracted and purified from a given sample, PCR can be employed to amplify target DNA sequences. For pathogen detection, specific PCR primers can be designed to amplify known pathogenesis genes or other identifying sequences within the chromosome or associated DNA. Various strategies have been used to cyclically heat and cool the chip to the required temperatures using infrared light, thermoelectric coolers, and resistive electrodes (Herold and Rasooly, 2009. Lab-on-a-Chip Technology. ISBN: 978-1-904455-47-9). In addition to changing the temperature of the entire reaction chamber, other methods have used so-called 'flow-through' PCR in which the sample is passed through different thermal regions on the chip. Another approach employs a thermoelectric cooler (TEC) that can alternately heat and cool, depending on the direction of electrical current. These miniature heat pumps are easily controlled with electronic feedback controllers and have relatively low power requirements (5��10 watts).

A method for performing microchip-based PCR with an external heat source such as a TEC or resistive heater has been described. Although flow-through PCR and other novel methods of microchip-based thermocycling have been described, external heating of the microchip is still one of the simplest and most reliable methods of performing PCR in lab-on-a-chip systems. Additionally, external heating of the microchip allows for seamless integration of the PCR amplification component with existing microchip designs. Fabrication steps and amplification methods have been successfully used for chip-based PCR amplification (Herold and Rasooly, 2009. Lab-on-a-Chip Technology. ISBN: 978-1-904455-47-9).

Lab-on-a-chip Technology

noreply@blogger.com (Blog owner) — Wed, 20 May 2009 16:32:00 +0000

The term 'laboratory' can be defined as a facility which provides controlled conditions for scientific research, experiments or measurements. In recent years, many lab-on-a-chip (LOC) devices, which provide controlled conditions for scientific measurements without a formal laboratory, have been developed and used in a wide array of biomedical and other analytical settings. LOC devices integrate and scale down laboratory functions and processes to a miniaturized chip format. In this context the term 'chip' is used loosely, unlike the 'traditional' silicon chip from electronics. LOC devices, or chips, can be fabricated from many types of material including various polymers (e.g. acrylic, polyester, and polycarbonate), glass, or silicon, as well as combinations of these materials.

In this context the term 'chip' is used loosely, unlike the 'traditional' silicon chip from electronics. LOC devices, or chips, can be fabricated from many types of material including various polymers (e.g. acrylic, polyester, and polycarbonate), glass, or silicon, as well as combinations of these materials. Unlike the 'traditional' silicon integrated circuit (IC) fabrication technologies, a broad variety of fabrication technologies are used for LOC device fabrication.

Almost all LOC systems have several common features including microfluidics and sensing capabilities. Microfluidics deals with fluid flow in small channels (e.g. sub-millimetre diameter) with flow control devices (e.g. channels, pumps, mixers and valves). Sensing capabilities including usually optical or electrochemical sensors are often integrated into the chip. Closely related fields to LOC systems are micro total analysis systems (μTAS), which focus primarily on the integration and miniaturization of analytical chemistry assays, and microelectromechanical systems (MEMS), which are the integration of mechanical and electrical elements (e.g. logical circuits, sensors, or actuators), can integrate decision-making capability with sensing and control elements on a chip. All of these technologies are based on the rapidly evolving field of microfabrication technology. LOC, μTAS and MEMS are overlapping technologies that often share the same elements (e.g. microfabrication, material, controls, and sensors).

It is a challenge to fully describe the fast-moving field of LOC in one publication. However, the two-volume work Lab-on-a-Chip Technology achieves this aim. It presents descriptions of some of the many types of LOC, including fabrication and application details, to give the reader a sense of the range of LOC technologies and the enormous potential that these devices possess.

A history of lab-on-a-chip technology

In the early 1960s, several research groups started working on miniaturized silicon sensors. An early integrated LOC device was a complete gas chromatograph on a single 'chip' developed at Stanford University and published in 1979. This new tool was 'expected to find application in the areas of portable ambient air quality monitors, implanted biological experiments, and planetary probes'. The expectations for LOC have been realized repeatedly in the laboratory and commercial applications are beginning to be realized (Herold and Rasooly 2009. Lab-on-a-Chip Technology. Caister Academic Press ISBN: 978-1-904455-47-9).

In the 1980s and 1990s the LOC field moved rapidly and in the last decade approximately 3500 LOC related publications are indexed in Pubmed describing numerous fabrication methods and new applications using a broad array of technologies. The trend is towards more complex integrated multi-analyte LOC systems capable of more comprehensive analyses, utilizing advances in electronics and microfabrication that enable miniaturization and broader capabilities. The newest generation of LOC systems includes a miniaturized chip for isolation of rare circulating tumour cells in cancer patients and complex LOC devices utilizing valving technologies that provide dense fabrication and parallel pneumatic actuation of hundreds of valves.

Bibliography:

Lactic Acid Bacteria

noreply@blogger.com (Blog owner) — Wed, 13 May 2009 10:54:00 +0000

Lactobacillus

Lactobacillus is a genus of Gram-positive facultative anaerobic or microaerophilic bacteria. In humans they are symbiotic and are found in the gut flora. Lactobacillus species are used for the production of yogurt, cheese, sauerkraut, pickles, beer, wine, cider, kimchi, chocolate and other fermented foods, as well as animal feeds such as silage. In recent years much interest has been shown in the use of lactobacilli as probiotic organisms and their potential for disease prevention in humans and animals read more ...

Lactic Acid Bacteria with Anti-Cancer Activities

Beneficial bacteria include Lactobacillus and Bifidobacterium spp. and other lactic acid bacteria (LAB) commonly known as probiotics. LAB possesses numerous potential therapeutic properties including anti-inflammatory and anti-cancer activities and other features of interest. In recent years, studies with in vitro cell culture and animal models that clearly demonstrated protective effects of LAB for anti-tumor and anti-cancer effects. Dietary administration of LAB alleviated the risks of certain types of cancers and suppressed colonic tumor incidence, volume and multiplicity induced by various carcinogens in different animal models. Oral administration of LAB effectively reduced DNA adduct formation, ameliorated DNA damage and prevented putative preneoplastic lesions such as aberrant crypt foci induced by chemical carcinogens in the gastrointestinal (GI) tract of various animal models. LAB also increased the latency period and survival rates in test animals when challenged with carcinogenic agents. Reports also indicated that LAB cultures administered to animals inhibited liver, colon, bladder and mammary tumors, highlighting potential systemic effects of probiotics with anti-neoplastic activities read more ...

Medicinal Uses of Lactic Acid Bacteria

Most probiotic strains belong to the genus Lactobacillus. The promising results of a first generation of probiotic microbes, evaluated in animal models as well as natural infections in animals and humans indicate a promising future for coming generations of probiotics. Antibiotic-associated, travellers' and pediatric diarrhea have been most studied, and more recently, inflammatory bowel disease and irritable bowel syndrome. Probably future probiotics will contain mixes of strains with complementary characteristics, tailormade for different gastrointestinal diseases, vaginosis or as delivery systems for vaccines, immunoglobulins and other protein based therapies read more ...

Exopolysaccharide Formation by Lactic Acid Bacteria

Lactic acid bacteria (LAB) synthesise a wide variety of exopolysaccharides (EPS); these polysaccharides are synthesised extracellularly from sucrose by glycansucrases, or intracellularly by glycosyltransferases from sugar nucleotide precursors. Biofilm formation, stress resistance and sucrose utilisation are clearly linked to the formation of EPS in individual species of LAB. The high frequency of homopolysacharide (HoPS) and heteropolysaccharide (HePS) producing LAB in the oral cavity and intestinal ecosystems argues in favour for an important role of EPS formation for the persistence of LAB in these habitats. The intricate regulatory network controlling the expression of glycansucrases in oral streptococci is in keeping with the contribution of HoPS and extracellular glycansucrases to biofilm formation and persistence in the oral cavity. EPS production by intestinal lactobacilli may play a comparable role. Glycansucrases in Lb. reuteri of HoPS and FOS production are regulated in response to stress sensed by the cytoplasmic membrane. The products of glycansucrases improve survival of lactobacilli in a scenario characterised by strong fluctuations in water activity, temperature, pH, and nutrient supply, and the presence of natural inhibitors. Because the expression of glycansucrases in many strains of lactobacilli and Leuconostoc species is induced by sucrose, the contribution of glycansucrases to sucrose catabolism may be their main ecological role in some strains read more ...

Biosynthesis of Exopolysaccharides Produced by Lactic Acid Bacteria

Exopolysaccharides (EPS) produced by lactic acid bacteria (LAB) can be classified according to the chemical composition and biosynthesis mechanism as homopolysaccharides (HoPS) and heteropolysaccharides (HePS). HoPS are composed of a single monosaccharide type, either glucose or fructose, and they are polymerised extracellularly by means of glycansucrases, sucrose being the donor of the corresponding sugar moiety. These α- or β-D-glucans and β-fructans are polymers of high molar mass (≥ 1 x106 Da) which can have different degrees of branching and they are usually produced in amounts higher than 1 g/L, although this value varies according to the strain and the production conditions. The glucansucrase and fructansucrase enzymes present a conserved functional structure in which four domains can be recognized, although enzymes produced by different strains do not share similar sequences. The HePS are built up of repeating unit structures of two or more types of monosaccharides, substituted monosaccharides and other organic and inorganic molecules. To date, around 42 different unique structures comprising from di- to octasaccharides have been described. Galactose, glucose, rhamnose and to a lower extent N-acetyl-glucosamine and N-acetyl-galactosamine are present in their composition. The HePS biosynthesis is a complex process not fully understood, that involves the activity of several specific, as well as housekeeping, enzymes which also participate in the metabolism of carbohydrates and in the synthesis of some components of the cell-wall. The genes involved in HePS synthesis are organised in eps clusters that share a common structural organization in which genes involved in regulation, export, polymerisation and chain length determination, as well as glycosyltransferases responsible for the intracellular assembly of the repeated units, can be recognised read more ...

Commercial Exploitation of Exopolysaccharides from Lactic Acid Bacteria

Lactic acid bacteria play a crucial role in various food fermentations. Several strains can produce long chain sugar polymers called exopolysaccharides (EPS). These can be classified due to different criteria e.g. the composition of different or just one kind of sugar monomer in hetero- and homopolysaccharides. While heteropolysaccharides are intensively used as additives in milk products, homopolysaccharides can be introduced in sourdough products influencing structural quality, baking ability and reducing bread staling factors. Additionally, beneficial effects on enteral health are possible. An example for industrial use of EPS in bakery products is the application of dextran in panettone and other breads. Also the addition of non-bacterial hydrocolloids is well established in industrial baking. Several investigations concerning the replacement of these additives by bacterial EPS have been made and provide data of dough and bread parameters such as textural factors, water retention and moisture and specific bread volume. Practically no information is available on the effects of bacterial EPS in other fermented foods such as fermented meat products, sauerkraut or vinegar. EPSs can be as defined additives or alternatively via in situ production by starter cultures. The addition of purified EPS has to be labelled on the end product, which is a disadvantage since consumers demand for fewer additives in foods. On the other hand, in situ production appears to be less effective in traditional wheat and rye dough systems due to strain-dependent acid formation, which may be required but counteracts positive EPS effects. Forthcoming chances of EPS applications may therefore lie within special applications as in gluten free breads where both, reduced pH and EPS should have synergistic positive effects on structure read more ...

Nutritional and Functional Benefits of Exopolysaccharides from Lactic Acid Bacteria

The quest to find food ingredients with valuable bioactive properties has encouraged interest in exopolysaccharides (EPSs) from lactic acid bacteria (LAB). Functional food products that offer health and sensory benefits beyond their nutritional composition are becoming progressively more important in the food supply chain. Informed consumers are becoming increasingly more health conscious and more aware that disease prevention can be effected through dietary means and, more specifically, by particular components of foods. Although the sensory benefits of EPSs are now well established, more knowledge to fully understand how these polysaccharides can impact on human health and nutrition is needed. Because of the wide variation in molecular structures of EPSs, and the complexity of the mechanisms by which physical changes in foods and bioactive effects are elicited, the future commercial development of EPS-producing cultures and ingredients will depend heavily upon this platform of knowledge read more ... Further reading:

Plant Genomics

noreply@blogger.com (Blog owner) — Wed, 25 Mar 2009 16:32:00 +0000

Plant genomics is an increasingly important area of science that has expanded in recent years due to the development of advanced technologies and methods. An understanding of plant genomics is a prerequisite for advanced plant breeding and crop improvement. An in-depth knowledge of plant genomics helps researchers to enhance production, confer resistance or tolerance to adverse conditions and improve crops. The recent advances in plant genomics and bioinformatics has had a significant impact on plant science and genetics. New methods and technology have led to a greater understanding of both structural genomics and functional genomics. Plant genomics generates opportunities to create crops with improved traits.

Gene Silencing with Green Fluorescent Protein

The green fluorescent protein (GFP) of jellyfish (Aequorea victoria ) has significant advantages over other reporter genes, because expression can be detected in living cells without any substrates. Epigenetic phenomena are important to consider in plant biotechnology experiments for elucidate unknown mechanism. In a recent study, soybean immature cotyledons were generated embryogenesis cells and engineered with two different gene constructs (pHV and pHVS) using gene gun method. It was demonstrated that using sGFP(S65T ) as a reporter gene in vector system may be useful for transgenic evaluation and avoid gene silencing in plants for the benefit of plant transformation system.

Antisense Phenotypes in Transgenic Rice

OsARF1 is the first full-length member of auxin response factor (ARF) gene family to be cloned from monocot plant. Using quantitative RT-PCR a recent study found that the transcript abundance of OsARF1 was significantly higher in embryonic tissues than in vegetative tissues. To investigate the effect of OsARF1 on the phenotype of rice, a cDNA fragment of OsARF1 was inserted in inverse orientation to the 35S promoter in vector pBin438 to produce an antisense (AS) construction. The AS-OsARF1 construct was transferred into rice (Oryza sativa L. japonica ) calli via Agrobacterium tumefaciens -mediated transformation. Molecular analysis of transgenic plants showed that the functional expression of OsARF1 was inhibited at mRNA level efficiently. The AS-OsARF1 plants showed extremely low growth, poor vigor, short curled leaves and tillered but were sterile. Therefore, the OsARF1 was shown to be essential for growth in vegetative organs and seed development. Further reading: Plant Genomics

Clostridium

noreply@blogger.com (Blog owner) — Thu, 22 Jan 2009 11:58:00 +0000

The genus Clostridium represents a heterogeneous group of anaerobic spore-forming bacteria, comprising prominent toxin-producing species, such as Clostridium difficile, Clostridium botulinum, Clostridium tetani and Clostridium perfringens, in addition to well-known non-pathogens like solventogenic Clostridium acetobutylicum. In the last decade several clostridial genomes have been deciphered and post-genomic studies are currently underway. Genetic manipulation tools have permitted functional-based and systems biology analyses of several clostridial strains.

Toxins of Clostridium

Botulinum neurotoxins (BoNTs) are the most potent natural toxins known. The family of BoNTs comprises of seven antigenically distinct serotypes (A to G) that are produced by various toxigenic strains of spore-forming anaerobic Clostridium botulinum. They act as metalloproteinases that enter peripheral cholinergic nerve terminals and cleave proteins that are crucial components of the neuroexocytosis apparatus, causing a persistent but reversible inhibition of neurotransmitter release resulting in flaccid muscle paralysis.

Apart from being the sole causative agent of the deadly food poisoning disease, botulism, BoNTs pose a major biological warfare threat due to their extreme toxicity and easy production. They are used as powerful tools to treat an ever expanding list of medical conditions (Proft, T. 2009). A better understanding of the structure-function relationship of clostridial neurotoxins will help decipher their molecular mode of action and also provide a greater understanding of the potential use of their individual domains in answering more fundamental questions of neuroexocytosis. It is also critical for designing effective specific inhibitors to counter botulism biothreat and for the development of new therapeutics (Proft, T. 2009).

Clostridium Food Poisoning

Clostridium botulinum produces extremely potent neurotoxins that result in the severe neuroparalytic disease, botulism. Although of lower lethality, the enterotoxin produced by Clostridium perfringens, during sporulation of vegetative cells in the host intestine, still results in debilitating acute diarrhea and abdominal pain. Sales of refrigerated, processed foods of extended durability including sous-vide foods, chilled ready-to-eat meals, and cook-chill foods have increased over recent years. As a result of conditions accommodating growth, anaerobic spore-formers have been identified as the primary microbiological concerns in these foods. Heightened awareness over intentional food source tampering with botulinum neurotoxin has arisen with respect to genes encoding the toxins that are capable of transfer to nontoxigenic clostridia. Similarly, enterotoxin produced by Clostridium perfringens and the genomic location of the cpe gene has epidemiologic significance for understanding the capability to cause foodborne disease in humans. Unique characteristics and virulence factors of Clostridium botulinum and Clostridium perfringens make them foodborne hazards in the food supply (Fratamico et al 2008))

Spores of Clostridium

Bacteria of the genera Bacillus and Clostridium can be found in two distinct states. In the vegetative state, the bacterium is metabolically active and uses available nutrients to grow and divide by binary fission, a process that generates two identical daughter cells. By contrast, when nutrients are scarce, a developmental program of endospore formation (sporulation) is initiated, resulting in the production of a highly resistant spore (Graumann, P. 2007). In the spore state, the bacterium is metabolically dormant, and its genetic material, protected in the core of the spore, can endure a variety of challenges, including radiation, heat and chemicals. Sporulation is a complex process, which requires the generation of two distinct cell types: a forespore and a larger mother cell. The progression of the developmental program is controlled by two exquisitely regulated cell type-specific lines of gene expression that run in parallel and are connected at the post-transcriptional level. Various genetic screens and genome-wide transcriptional analyses have identified more than 600 genes that are expressed in the course of sporulation. The function of several of these genes has been characterized in detail and subcellular localization data are available for more than 70 sporulation proteins (Graumann, P. 2007). Sporulation constitutes one of the best characterized developmental programs at the molecular and cellular levels.

Legionella

noreply@blogger.com (Blog owner) — Thu, 22 Jan 2009 11:00:00 +0000

Legionella pneumophila is a Gram-negative facultative intracellular pathogen, which in its natural environment multiplies in protozoa. This bacterium can also cause a severe pneumonia in man, better known as Legionnaires' disease, following infection of alveolar macrophages. L. pneumophila enters its host cell by phagocytosis, creating a phagosome that does not fuse with lysosomes wherein bacteria can multiply. See also: Legionella

Protein Secretion and Virulence in Legionella

When nutrients are depleted, Legionella enters the transmissive phase and expresss virulence proteins, resulting in lysis of host cells and the initiation of a new infection round. In each of these different stages of infection of host cells, virulence proteins need to be transported to their specific place of action. Several protein secretion systems have been identified in L. pneumophila and most of them play an important role in the virulence of this pathogen. Read more at Bacterial Secreted Proteins.

Legionella infect Amoeba

The Legionella bacterium infects free-living amoebae, such as Acanthamoeba, which is abundant in the water supplies and are know to support bacterial growth. In addition, Acanthamoeba cysts are resistant to many disinfectants, which would allow bacteria to survive in the water supplies and they can be air-borne. Acanthamoeba not only harbours Legionella pneumophila but the bacteria also multiply within Acanthamoeba suggesting that bacteria use amoeba both as a host and a reservoir.