Info

Bacterial population in the upper small intestine. The counts of bacteria increase 1-2 logs or more higher than in healthy humans. Anatomical defects (diverticulitis) or physiological abnormalities (e.g., lack of acid secretion in the stomach or stasis) will encourage overgrowth. Pathophysiological consequences include malabsorption and nutritional deficiencies resulting directly from bacterial activity (mucosal damage by bacterial products) and indirectly by competing for nutrients (vitamin...

Detection Of Restriction Systems

This is exemplified by the original detection of the R-M systems of E. coli K-12 and E. coli B by Bertani and Weigle in 1953. Phage A grown on E. coli strain C (A . C), where E. coli C is a strain that apparently lacks an R-M system, forms plaques with poor efficiency efficiency of plating (EOP) of 2 X 104 on E. coli K-12 because the phage DNA is attacked by a restriction endonuclease (Fig. 29.1). Phage A grown on E. coli K-12 (A K) forms plaques with equal efficiency on E. coli K-12 and E....

Function Of Symbiotic Microorganisms

Symbiotic microorganisms as a source of novel metabolic capabilities Symbiotic microorganisms are widely believed to contribute to the nutrition of insects. This was first deduced from the distribution of the associations among insects. In general, the microorganims are restricted to insects living on nutritionally poor or unbalanced diets. They are widespread or universal among insects feeding through the lifecycle on the phloem and xylem sap of plants, deficient in essential amino acids...

Dimorphic Life Cycle Of Caulobacter Crescentus

A distinguishing feature of the development of stalked bacteria is that it is an integral part of the growth of the cell and not an alternative to it, as are the other bacterial developmental processes that occur in response to stress. The molecular mechanisms that control the developmental cycle of stalked bacteria have been studied most extensively in Caulobacter crescentus. Each division of Caulobacter cells gives rise to a swarmer cell and a stalked cell (Fig. 25.7). The swarmer cell is...

Nucleotide Excision Repair

The ideal repair system is one that is somewhat indiscriminate and which can respond to virtually any kind of damage. Such a repair system has been characterized in E. coli in which it consists of at least six gene products of the uvr system. This ensemble of proteins consists of the UvrA protein that binds as a dimer to DNA in the presence of ATP, followed by the UvrB protein which cannot bind DNA by itself. Translocation of the UvrA2B complex from initial undamaged DNA sites to damaged sites...

Generation Of Identification Matrices

One of three approaches can be used to generate identification matrices. Cluster analysis. A cluster analysis of fresh isolates and reference strains (taxa) is carried out. Phena (clusters of taxa) are selected from a dendrogram and their properties are summarised to create a starting or frequency matrix containing all characters used in the study. The identification matrix is developed by including the most useful characters and rejecting those that do not distinguish between phena. Some...

Characteristics Of Bacillus Subtilis

The genus Bacillus consists of gram-positive, endospore-forming, rod-shaped bacteria. There are more than 70 species, which display wide morphological and physiological diversity. Only 2 (B. anthracis and B. cereus) are known to be human pathogens. The defining feature of the genus is endospore formation. The genus is subdivided into six groups using a variety of morphological (particularly sporangial) and metabolic criteria. Bacillus subtilis belongs to group II, whose distinguishing features...

Denitrification

When oxygen becomes limiting, some microorganisms, mainly aerobic bacteria, have the ability to switch to the use of the nitrogen oxides NOi, NOi, NO, and N2O as terminal acceptors of electrons in their metabolism. This process is known as denitrifi-cation, and it permits organisms to continue what is essentially a form of aerobic respiration in which the end product is dinitrogen. However, intermediates sometimes accumulate. Denitrification is of major importance because it closes the global...

Lps

MAP kinases p38, & other proteins FIGURE 56.6 The pathway involved in the stimulation of macrophages and other myeloid cell lines by LPS. The LPS binding protein (LBP) delivers LPS to the GPI anchored form of CD14 (mCD14). LPS is transferred to TLR4 in complex with MD-2 and, perhaps, other proteins. This complex participates in intracellular signal generation. Once stimulated, a phosphorylation signal trans-duction cascade leads to transcription of genes encoding cytokines and inflammatory...

Federations Sponsoring Databases That Identify Collection Resources

The World Federation for Culture Collections (WFCC) is a Commission of the International Union of Biological Sciences (IUBS) and a federation within the International Union of Microbiological Societies (IUMS) and www.wfcc.info). Its purpose is to support and promote establishment of culture collections. In collaboration with the Microbial Resources Centres (MIRCEN) and other organizations described below, it sponsors a database that is a directory of culture collections, the World Data Centre...

Export of outermembrane proteins

Outer-membrane proteins are synthesized as precursor proteins with classic signal sequences and are exported to the periplasm by the Sec system for polypeptide secretion. The signal sequence is removed by the leader peptidase (or, in the case of lipoproteins, by a specific prolipoprotein signal peptidase), located at the periplasmic face of the inner membrane. The interaction of soluble porin monomers in the periplasm with (presumably nascent) lipopolysaccharide is thought to promote a...

Base Excision Repair

Base excision repair by glycosylases and apyrimidmic or apurinic endonucleases Bases modified by deamination can be repaired by a group of enzymes called DNA glycosylases, which specifically hydrolyze the N-glycosyl bond of that base and the deoxyribose of the DNA backbone generating an apyrimidinic or an apurinic site (AP site) (Fig. 27.7). These are small, highly specific enzymes that require no cofactor for functioning. They are the most highly conserved proteins, attesting to the...

Chaperones

Chaperones, or proteins that help other proteins fold, are a major class of the proteins produced after heat stress. In the test-tube, under very dilute conditions, small proteins fold by themselves, demonstrating that the polypeptide chain itself encodes the information necessary for proper folding. However, in the cell, proteins are present at very high concentrations, and the nascent, unfolded protein has a very high potential to aggregate with other nascent chains via hydrophobic...

Production Of Germfree Animals

Germ-free animals are obtained via cesarean section. In one approach, a specially constructed steel autoclave-type unit (as has been described) is used, which is divided into two compartments by a horizontal separator with a circular opening that is closed with a sheet of plastic. After autoclaving the units with the surgical equipment in the upper part, the lower part is opened to the environment. This (now nonsterile) part contains a small platform on which the anesthetized pregnant female...

The boy in the bubble

In general, most controlled studies have been carried out with GF and GN rats and mice. The GF animal technique has the potential for selective association of the originally GF animal with a specific microflora element, including parasites. Mentioned earlier is the potential of bringing its distended cecum back within acceptable limits by association with a well-defined cocktail of microbial species. These are introduced by bringing monocultures grown in test tube into the main unit after...

Ki

Note B vitamins (in mg) thiamine HCl, 1.23 pyridoxine HCl, 1.54 biotin, 0.25 folic acid, 0.37 vitamin B12 (pure), 1.44 riboflavin, 1.85 niacinamide, 9.2 i-inositol, 61.6 Ca pantothenate, 12.3 choline HCl, 310. Amounts of lipid nutrients in one measured daily adult dose of 0.25 mL purified soy triglycerides, 0.22 g retinyl palmitate, 4.3 g (7.8 IU) cholecalciferol, 0.0192 g (0.77 IU) 2-ambo-a-tocopherol, 2.2 mg 2-ambo-a-tocopheryl acetate, 4.4 mg phylloquinone, 48.0 g. The fatty acid content is...

Psychrophiles

Over 80 of the total biosphere of Earth is at a temperature permanently below 5 C, and it is therefore not surprising that a large number and variety of organisms have adapted to cold environments. These natural environments include cold soils water (fresh and saline, still and flowing) in and on ice in polar or alpine regions polar and alpine lakes, and sediments caves plants, and cold-blooded animals (e.g. Antarctic fish). Artificial sources include many refrigerated appliances and equipment....

Introduction

As early as 1885, Louis Pasteur had mentioned to his students the desirability of being able to study metabolism without the interference of an actively metabolizing intestinal microflora, mentioning at the same time that, in his opinion, life under those conditions would be impossible (Pasteur, 1885). However, before the end of that century, Nutthal and Thierfelder (1895) had built equipment that eventually enabled a newborn cesarean-derived guinea pig to survive (Fig. 46.1). Thus, the study...

Germfree Isolators

1950 Incubator Microbiology

Soon, the above contraption was replaced by simpler two-compartment steel autoclave-type equipment, in which one compartment served as a two-way entry port for sterilizing food and bedding, the other being the sterile compartment fitted with (nowadays) neo-prene gloves, long enough for handling animals, cages, and equipment (Fig. 46.2). Gloves were often fitted with thin latex hand gloves to make necessary manipulations easier. Equipment was sterilized beforehand either by steam or, later, by...

Biostimulation

The earliest system of enhanced or engineered in situ bioremediation of groundwater was designed by R. L. Raymond and co-workers with Sun Research and Development Company in Philadelphia and described in a 1978 American Petroleum Institute report titled Field Application of Subsurface Biodegradation of Gasoline in a Sand Formation. The Raymond process was a patented system U.S. Patent No. 3,846,290 (1974) in which biodegradation of petroleum hydrocarbons (namely, gasoline constituents) in...

Habitats and microorganisms

An extreme acidophile has a pH optimum for growth at or below pH 3.0. This definition excludes microorganisms that are tolerant to pH below 3, but that have pH optima closer to neutrality, including many fungi, yeast, and bacteria (e.g., the ulcer- and gastric-cancer causing gut bacterium Helicobacter pylori). Extremely acidic environments occur naturally and artificially. The hyperthermophilic extreme acido-philes Sulfolobus, Sulfurococcus, Desulfurolobus, and Acidianus produce sulfuric acid...

Assimilation And Ammonification

Most microbes in nature can not fix N2 and must obtain their nitrogen supply in the form of ammonia (NH 4), nitrate (NOi), or free amino acids. Ammonia is assimilated by the glutamate dehydrogenase or (in N-deficiency) the glutamine synthetase-glutamate synthase (GS-GOGAT) system. Nitrate is reduced by assimilatory nitrate and nitrite reductases to NH4 (Fig. 59.1), a system that is repressed by NH+, but is unaffected by O2. Growth may be limited by C or N availability, and in agricultural soils...

The Conjugative Process

Unlike the other processes contributing to horizontal gene transfer, transformation, and transduction, conjugation can be characterized by two important criteria. There must be close cell-to-cell contact between the donor and recipient cells and DNA transfer must begin from a specific point on the transferred DNA molecule, be it a plasmid, transposon, or chromosome (Fig. 22.1). This point is encoded within the origin of transfer (oriT) called nic. The proteins which act on these sites are...

International Treaties

The 1925 Geneva Protocol was the first international treaty to place restrictions on BW. The Geneva Protocol followed a series of international agreements that were designed to prohibit the use in war of weapons that inflict or prolong unnecessary suffering of combatants or civilians. The St. Petersburg Declaration of 1868 and the International Declarations Concerning the Laws and Customs of War, which was signed in Brussels in 1874, condemned the use of weapons that caused useless suffering....

Liquid versus solid support

The ability of some conjugative systems to mate equally well in liquid media or on a solid support is one of the hallmarks of conjugation. Although all con-jugative elements can mate well on a solid support, usually a filter placed on the surface of a pre-warmed nutrient agar plate, many transfer systems, including those of the IncF group and the pheromone-responsive plasmids of Enterococcus, mate very efficiently in liquid media. This difference can be traced to the nature of the mating pair...

The echinocandins

The echinocandins include echinocandins, pneumo-candins, aculeacins, mulundo- and deoxymulundo-candin, sporiofungin, vWF 11899 A-C, and FR 901379. The echinocandins have better in vitro and in vivo anti-fungal activity than the papulocandins. Pharmaceutical development has resulted in several semisynthetic echinocandins with an improved antifungal activity compared to those of the naturally occurring molecules described previously. Cilofungin is a biosemisynthetic analog of the naturally...

Bacteria

Significance Dormancy Microbiology

Occurrence, habitats, species, and functions In the ocean luminous bacteria occur ubiquitously and can be isolated from most seawater samples from the surface to depths of 1000 m, and they appear as bright colonies on plates (Fig. 14.2). They are very often found in some kind of symbiotic association with higher organisms (e.g. fish or squid), in which the light emission is evidently of functional importance to the host. In parasitic or saprophytic associations the advantage of light...

Tdna

The T-DNA is delimited by 25-bp direct, imperfect repeats termed border sequences (Fig. 2.2). Flanking one border is a sequence termed overdrive that functions to stimulate the T-DNA processing reaction. All DNA between the border sequences can be excised and replaced with genes of interest, and A. tumefaciens will still efficiently transfer the engineered T-DNA to plant cells. This shows that the border sequences are the only cis elements required for T-DNA transfer to plant cells and that...

Sporulation In Streptomyces Coelicolor

Life Cycle Streptomyces Coelicolor

The aerial mycelium of Streptomyces coelicolor forms by directed cell growth and differentiates into a series of spores (Fig. 25.3). The vegetative mycelium grows in the nutrient substratum by the linear growth of cell wall close to the hyphal tip (Fig. 25.4). Branching of the vegetative mycelium allows close-to-exponential increase of the mycelial mass. Septation is infrequent in the vegetative mycelium and the vegetative septa do not allow cell separation. With time, the vegetative mycelium...

Regulation of termination at an intrinsic terminator

Many operons regulated by transcriptional attenuation contain a DNA region that specifies a RNA sequence that can fold to form a hairpin structure followed by a run of U's, a structure called an intrinsic terminator. Intrinsic terminators instruct RNA poly-merase to terminate transcription. The region encoding the intrinsic terminator is located immediately preceding the gene or genes that are being regulated. The transcript segment before and including part of the terminator often contains a...

Extracellular Nucleationprecipitation Pathway

Many strains of E. coli and Salmonella enteritidis produce a class of thin (< 2nm), irregular, and highly aggregated surface fibers known as curli (Fig. 38.1E). These distinct organelles mediate binding to a variety of host proteins, including plasminogen, fibronectin, and human contact-phase proteins. They are also involved in bacterial colonization of inert surfaces and have been implicated in biofilm formation. Curli are highly stable structures and extreme chemical treatment is required...

Fruitingbody Formation In Myxobacteria

Fruiting-body formation in myxobacteria is only one example of bacterial social behavior. The entire life cycle of myxobacteria is pervaded by social behavior. Myxobacterial cells move together and feed cooperatively to maximize the efficiency of extracellular degradation. The enclosure of myxospores in the fruiting body allows then to be dispersed together and ensures that a sufficiently large population of cells will be present after germination to facilitate social interactions. The...

Eps And The Glycocalyx

EPS and glycocalyx are terms used to describe the polysaccharide produced by bacterial cells. EPS refers to one of the major components of biofilms, and gly-cocalyx refers to the polysaccharide matrix surrounding individual cells. EPS has an important role in biofilm structure and function and has a complex physical and chemical nature. Its functions are mostly protective in nature and this is one of the benefits for bacteria in the sessile state. Because the glycocalyx is the outermost...

Mode Of Action

Considering the heterogeneity of chemicals used as biocides, and the fact that they have been considered general cell poisons for a long time, one can understand the lack of detailed information on mode of action of industrial biocides. For most of the biocides, mode of action seems to be a concentration-dependent phenomenon by which individual effects can be identified and studied. Since biocides will act on organisms in an outside to inside direction, many have classified the target regions...

Biofilms in medical systems

Biofilms affecting human health can be divided into the following categories 1. Biofilms formed on human tissue. These biofilms occur in the healthy body, for example, on teeth, in the digestive tract, and in the female genital tract. They may have a role in prevention of certain infections but can be overgrown by pathogenic microorganisms. 2. Biofilms formed on medical implants within the body. 3. Biofilms formed on surfaces outside the body that may harbor harmful pathogens. Examples of these...

Alternate Chaperone Pathway

A variation of the chaperone-usher pilus assembly pathway has been identified in strains of ETEC. These bacteria are major pathogens associated with diar-rheal diseases of travelers, infants, and young children. ETEC strains produce several types of uniquely assembled adhesive pili that are considered to be important mediators of bacterial colonization of the intestine. The best studied of these pili is CS1, which appears to be composed predominantly of a major subunit, CooA, with a distally...

Table Of Stock Collections

To facilitate look-up of specific kinds of collections and especially to facilitate locating the Web address of a collection, a tabular rather than text format is used to present collections by type and country, to provide brief descriptions of the collections, and to cite the Web addresses. Clearly a totally comprehensive listing of such diverse and widespread resources is not possible, and regrettable oversights have no doubt occurred. Widely used and Web-accessible sites have been...

Classification Of Biocides

Classifying industrial biocides based on their chemical structures is not an easy task. Many review articles present group classifications and include a miscellaneous group whose members do not fit in any major class. Table 11.5 is a representation of this type of classification. Biocides are sometimes also grouped based on their mode of action. This can be organized based on the target region of the microorganism affected by biocide action. Terms and categories such as membrane-active biocides...

Assembly Of Lipopolysaccharides

In E. coli, the minimal LPS molecule required for viablity consists of Kdo2-lipid A (sometimes known as Re-LPS Fig. 56.2, Panel B). Since E. coli can efficiently insert Re-LPS and larger LPS molecules on their cell surfaces, the later steps in LPS assembly pathways have generally been amenable to dissection by genetic approaches (e.g. structural analyses of mutant LPSs), FIGURE 56.4 Visualization of LPS molecules in silver-stained sodium dodecyl sulfate polyacrylamide gel electrophoresis...

Overview Of Infection Process

Agrobacterium Tumefaciensinfection

Agrobacterium species are commonly found in a variety of environments including cultivated and non-agricultural soils, plant roots, and even plant vascular systems. Despite the ubiquity of Agrobacterium species in soil and plant environments, only a small percentage of isolates are pathogenic. Two species are known to infect plants by delivering DNA to susceptible plant cells. Agrobacterium tumefaciens is the causative agent of crown gall disease, a neoplastic disease characterized by...

Chemical detoxification of bacterial exotoxins

Shortly after the determination that toxic components were associated with bacterial pathogens, several studies showed that cell extracts or cell cultures of a pathogen could be treated with chemical denaturants, such as formalin, to produce nontoxic immunogenic material that could prevent the disease associated with that pathogen. In the case of diphtheria toxin and tetanus toxin, chemical modification with formalin produced toxoids that were used as acellular vaccines in large-scale...

Current Research Programs

Biological weapons research in the United States is under the direction of the BDRP, headquartered at Fort Detrick, Maryland. In accordance with official U.S. policy, the BDRP is solely defensive in nature, with the goal of providing methods of detection for, and protective measures against, biological agents that could be used as weapons against U.S. forces by hostile states or individuals. Current U.S. policy stems from the 1969 declaration made by President Nixon that confined the U.S. BW...

Bacterial Identification Software

Several probabilistic identification programs have been published, some are available as interactive web pages although whether these pages offer any advantage over software installed on a user's machine is questionable. A list of resources is presented below. In many instances the software can be used with various identification matrices. Examples from one program, PIBWin (a Windows version of Bacterial Identifier) are shown in Figs 52.1-52.3. BBACTID Bryant, T. N., Capey, A. G., and Berkeley,...

Osmoregulation Model

A model for bacterial osmoregulation based in large part on that presented by Csonka and Epstein (1996) for E. coli and S. typhimurium is shown in Fig. 64.2. The initial signal for a change in osmolality is proposed to FIGURE 64.2 Model of osmoregulation in Escherichia coli. The outer box represents the outer membrane and the inner box the inner membrane. The lower left portion of the schematic indicates the K+ uptake systems, which are activated by decreased turgor pressure resulting from...

Chemistry Of Bacterial Cell Walls

The structural principle that glycan strands are cross-linked by peptides in order to form a strong latticework for a bacterial exoskeleton has been invented in nature twice, in Archaea and in Eubacteria. Archaea contain a compound called pseudomurein. Although the architectural style is the same in pseudomurein and in murein, the building materials are different. The murein of Eubacteria consists of glycan strands that are cross-linked by peptides (Figs 19.3 and 19.7). The amino sugars...

Bibliography

Bacterial S -layers. Curr. Opin. Struct. Biol. 4, 204-212. Beveridge, T. J., and Graham, L. L. (1991). Surface layers of bacteria. Microbiol. Rev. 55, 684-705. Boot, H. J., and Pouwels, P. H. (1996). Expression, secretion and antigenic variation of bacterial S-layer proteins. Mol. Microbiol. 21, 1117-1123. Kneidinger, B., Graninger, M., Puchberger, M., Kosma, P., and Messner, P. (2001). Biosynthesis of nucleotide-activated D-glycero-D-manno-heptose. J. Biol. Chem. 276,...

Endospore Formation In Bacillus Subtilis

Sporulation Sigma Factors

Endospore formation has been found exclusively in gram-positive bacteria and is best understood in Bacillus subtilis. The primary signal for the initiaton of sporulation is nutrient starvation. Cell density is also important for efficient sporulation, presumably to ensure that cells are sufficiently abundant. It may be that if starving cells are at a high density, it is better to sporulate rather than compete for nutrients. However, if cells are at a low density, the chances of finding...

Nutritional categories of organisms

Based on their principal carbon and energy sources, (micro)organisms are classified into four nutritional categories (Table 62.1). Most microorganisms using light as their principal source of energy are photo-autotrophs (sometimes also referred to as photolitho-autotrophs), whereas photoheterotrophs are a small group of specialists (certain purple and green bacteria). The ability to grow chemoautotrophically (i.e. in the dark in a medium containing only inorganic nutrients, including a reduced...

Cestodes And Worms

Taenia saginata, the beef tapeworm, is highly endemic in certain areas of the world, such as parts of South America, Africa, South Asia, and Japan. Humans are the definitive host for the adult tapeworm, which is one of the largest human parasites. They may live as long as 20 years and grow up to 25 meters in length. Consumption of undercooked or raw beef containing living larval forms is how it is acquired. Cattle are the intermediate hosts, in which the hexa-canth embryos emerge from the eggs...

Viral Diversity

No matter whether it is more correct to consider viruses as living organisms or as renegade genome fragments, the viruses have very important impacts on other types of organisms and should not be neglected in discussions of microbial diversity. These obligately parasitic entities have no independent physiological activities and require a suitable host for reproduction, which damages or destroys host cells. The importance and success of viruses as parasites in higher organisms is well known....

SoxR and SoxS

The SoxR protein is a redox-sensing transcriptional activator that belongs to the MerR family of DNA-binding proteins. SoxR is a homodimer of 17-kDa sub-units, each one containing a redoxactive 2Fe-2S center. The DNA-binding activity of SoxR does not depend on the iron-sulfur clusters, but only SoxR with oxidized 2Fe-2S centers activates transcription. The activation of SoxR through the one-electron oxidation of its 2Fe-2S centers therefore corresponds to an allosteric transition in the...

Iron Uptake

Bacteria can obtain iron from a variety of sources but, regardless of its origin, iron must be transported The Desk Encyclopedia of Microbiology ISBN 0-12-621361-5 Copyright 2003 Elsevier Ltd All rights of reproduction in any form reserved through the several microbial surface layers to reach the cytoplasm. For gram-negative bacteria, these layers minimally include an outer membrane, a monolayer of peptidoglycan, and an innermost cytoplasmic membrane. The peptidoglycan cell wall is located in...

D vir genes

The Ti plasmid carries an 35-kb region that harbors at least six operons involved in T-DNA transfer. Two of these operons have a single open reading frame, whereas the remaining operons code for 2-11 open reading frames. The products of the vir region direct events within the bacterium that must precede export of a copy of the T-DNA to plant cells. These events include (i) elaboration of the VirA VirG sensory transduction system for perception of plant-derived signals and tran-scriptional...

Mechanisms Of Infection

Rhizobia can infect their hosts and induce root- or stem-nodule formation by several mechanisms, the most common of which are 1. Root hair penetration and infection-thread formation as occurs in clovers, beans and soybeans (Hirsch, 1992). 2. Entry via wounds or sites of lateral-root emergence (Boogerd and van Rossum, 1997), as occurs in peanut and Stylosanthes. Rhizobia spread intercellularly or cause infected cells to collapse, colonizing the space. 3. Infection via cavities surrounding...

Early Germplasm And Type Culture Collections

The Collection of the Bacterial Strains of Institut Pasteur (CIP) traces its origins to Dr. Binot, who began to collect strains in 1891. It is a private, nonprofit collection that has become enlarged primarily by collaboration with the research laboratories of the Pasteur Institute. It maintains, preserves (by lyophilization since 1952), distributes, and provides information about strains. The CIP joined the World Federation of Culture Collections (WFCC) and the European Culture Collections...

Evaluation

There are numerous methods that have been and can be employed to evaluate biocide efficacy, including a variety of basic microbiological tests, simulation tests in the laboratory, practical tests, and field tests to demonstrate the effectiveness of a biocide. First, it has to be demonstrated that the chemical or preparation being evaluated has antimicrobial activity. In this stage, the spectrum of activity is determined against bacteria (gram-positive, gram-negative, Mycobacteria, etc.), fungi...

Conjugation In Natural Environments

Although the process of conjugation is thought to be relevant to the adaptation of organisms to environmental conditions such as the acquisition of antibiotic resistance under continuous pressure for selection, there is much to be learned about the process in nature (Davison, 1999 Paul, 1999). Conjugation can be demonstrated in the gut of animals, biofilms, soil, aquatic environments including wastewater, on the surface of plants and animals, etc. However, the level of transfer is usually very...

Genetic detoxification of bacterial exotoxins

Developments in genetic engineering have provided an opportunity to produce recombinant forms of bacterial exotoxins that possess greatly reduced toxic-ity, but retain immunogenicity. The use of genetic engineering to develop a toxoid of pertussis toxin has been successful. The whole-cell pertussis vaccine is composed of a chemically treated preparation of Bordetella pertussis, which is effective in the elicitation of a protective immune response after mass immunization. However, the whole-cell...

The Biological Nitrogen Fixation Process

Dinitrogen gas is both chemically inert and very stable, requiring much energy to break the triple bond and reduce the N N to ammonia in an endothermic reaction 3H2 + N2 2 NH3. This can be accomplished chemically by the Haber-Bosch process or biologically by prokaryotic organisms using adenosine triphosphate (ATP) energy to initiate the bond-breaking reaction. The prokaryotes able to fix nitrogen are extremely heterogeneous, with representatives that are autotrophic, heterotrophic, aerobic,...

Therapeutic Applications Of Exotoxins

One of the most exciting areas of bacterial exotoxin research has been the development of strategies to use exotoxins in therapeutic disciplines. Some therapies use the native cytotoxic form of the exotoxin. Other therapies use either the A or B domain, which is conjugated to a heterologous binding component or to effector elements, respectively, to produce a chimeric molecule with directed properties. Botulinum toxin and tetanus toxin (BT TT) are each a single protein that is organized as an...

Archaeal Diversity

The Archaea, like the Bacteria, are prokaryotic in terms of their cellular architecture. They reproduce asexually and depend on dissolved substances for carbon and energy. There, however, the similarity between the two domains ends. The Archaea are quite different from the Bacteria in the cell wall polymers they produce, their unusual lipids, resistance to broad spectrum antibiotics that inhibit most bacteria, and numerous details of their information processing machinery. The discovery by Carl...

Effects Of Increased Osmolality On Proteins

During exposure to hyperosmotic stress conditions, solutes will increase in concentration inside cells. Many of the deleterious effects of hyperosmotic stress can be interpreted in the context of solute effects on macromolecules. Increased osmolality tends to promote the dehydration of proteins. In a sense, proteins can be considered as behaving similar to a semipermeable membrane. The exposure of a protein to an environment in which the aw is lower than that of the water bound up to the...

Diets For Germfree Animals

Diets for GF animals are nowadays well established. They fall into three categories natural ingredient diets fortified for the losses that occur during sterilization (Table 46.1) diets with minimal antigenicity, used mainly for immunological studies and the chemically defined antigen-free diets, used for immunological and other studies where absolute definition of environment and dietary intake is required, again used mainly in immunology. For more defined work in the first category, diets...

Historical Introduction

Bacterial chromosomes were discovered much later than their eukaryotic counterparts because they do not exhibit the striking condensation at metaphase that makes eukaryotic chromosomes so easy to visualize. By the 1940s evidence that bacteria undergo spontaneous mutation finally emerged, and this established that bacteria must have mutable genes, the functional elements of chromosomes. At about the same time, Avery and associates uncovered the chemical nature of genetic material with a...

J

No cognate MTase e.g. mcrBC outside recognition sequence e.g. Fokl One polypeptide is both an ENase and MTase Heterodimeric Enase and MTase A Type II R M system comprises two separate enzymes one is the restriction ENase and the other the modification MTase. The nuclease activity requires Mg2+, and DNA methylatieon requires S-adenosylmethionine (AdoMet) as methyl donor. The target sequence of both enzymes is the same the modification enzyme ensures that a specific base within the target...

O

Chemistry, mechanism of action, and antiviral activity Didanosine (2',3'-dideoxyinosine ddl and Videx) is a purine nuceloside with inhibitory activity against both HIV-1 and HIV-2. Didanosine is activated by intracellular phosphorylation. The conversion of 2',3'-dideoxyinsine-5'-monophosphate to its triphosphate derivative is more complicated than that with other nucleoside analogs because it requires additional enzymes, including a 5' nucleotidase and subsequently, adenylosuccinate...

Targeting Adhesins For Antimicrobial Therapy

Bacterial adhesin-receptor binding events are critical in the pathogenesis of virtually every bacterial disease. In some cases, the knockout of a specific adhesin can greatly attenuate bacterial virulence. Uropathogenic E. coli strains, for example, which have been engineered to express type 1 pili lacking the FimH adhesin, are unable to effectively colonize the bladder. Similarly, a P-piliated pyelonephritic strain of E. coli lacking a functional PapG adhesin is unable to infect the kidney....

Bacterial Genetic Stock Centers

Sexuality and the ability to make genetic crosses between bacteria was discovered in E. coli in the 1940s. The use of microorganisms to explore the relationship between genes and biochemical pathways also became established in that decade. Individual laboratories accumulated large numbers of E. coli mutants, primarily derivatives of the wild-type isolate E. coli K-12. In the 1960s, it became apparent that a national repository would greatly aid the free exchange of strains and the advance of...

Transformation of monocots

In the past 5 years, dramatic progress has been made toward the development of protocols for stably transforming agriculturally important monocotyledonous plant species. The first indication of gene transfer involved the introduction of a plant viral genome into a plant host via A. tumefaciens-mediated transfer of T-DNA carrying the viral genome. Once inside the plant host, the viral DNA excises from the T-DNA and infects the host, inciting disease symptoms that are characteristic of the virus....

Energy generation

Group Translocation Bacteria

Energy generation refers to the trapping in a metaboli-cally useful form of the energy absorbed from sunlight or released by reduction of some inorganic molecule or the oxidation or breakdown of an organic molecule serving as energy source. Bacteria can generate energy by many different processes. In simple fermentative pathways, such as the glycolytic breakdown of glucose to lactate, ATP can be formed during several enzymatic steps by the process of substrate level phosphorylation. Important...

Sigma S

The alternative sigma factor, sigma S (as), encoded by the rpoS gene, is expressed during starvation or in the stationary phase in a variety of bacterial species. RNA polymerase containing as activates the expression of several genes that counteract oxidative stress, and bacteria that are starved or in stationary phase are more resistant to oxidative stress than are cells growing exponentially. The a s-activated genes include katE (catalase-hydroperoxidase HPII), dps (protective DNA-binding...

Genetics Of Bacterial Behavior

The most common strategy that has been used to isolate mutants that are defective in chemotaxis has involved selecting for cells that cannot swarm from a colony inoculated into the center of a dish filled with semisolid nutrient agar. Chemotactic cells form a colony at the point where they are initially inoculated, and the growing cells consume nutrients in the culture media creating attractant gradients that cause them to swarm outward from the center. Mutant cells that are deficient in...

Osmotic Downshift

Because the cytoplasmic membrane is highly permeable to water, maintaining appropriate internal osmolality as well as turgor pressure in dilute environments necessitates a series of adaptive steps that in some instances are the converse of those undertaken during high osmolality conditions and that in some cases are unique. Most of what is known about adaptation to osmotic downshifts has come from studies of bacteria. After exposure to a low osmolality environment (one that is hypoosmotic to...

Taxonomy and classification

By its morphology, genetic structure, nucleotide sequence, the virus belongs to the second subfamily of retrovirus, the lentiviruses, which includes viruses causing slow pathologies in animals, such as Visna, equine infectious anemia (EIA) and feline immunodeficiency virus. Retrolentiviruses of primates (SIVs, HIVs) are characterized by a tropism to CD4+ lymphocytes, a property not shared by lentiviruses of ungulates. Mature virions (diameter 100-120 nm) have a characteristic spherical...

C DNA bending

Associated with the E. coli chromosome are five small proteins that either bend DNA or bind to bends and stabilize them. The most abundant is HU, a protein with long flexible arms that reach around DNA and force it to make a U-turn. HU does not recognize a specific nucleotide sequence therefore, it is considered to provide a general bending activity. Several examples have been found in which HU serves as an architectural protein, assisting in the formation of DNA-protein complexes that carry...

Anaerobic Methylotrophs

All extant methanotrophs are obligate aerobes. However, there is now good biogeochemical and biological evidence that methane oxidation occurs in marine environments, such as sulfate-rich sediments, alkaline soda lakes, and some freshwater lakes. However, to date, no anaerobic bacteria that will grow on or oxidize methane have been isolated from these environments and cultivated in the laboratory. It is not known if such bacteria are true methanotrophs or if a consortium of bacteria is involved...

Cell Structure Of The Archaea

Archaea, like Bacteria, are prokaryotes (Table 7.1). They lack membrane-bound organelles such as a nucleus, or mitochondria, and are devoid of a cytoskeleton. Their chromosomal DNA is typically a single circular molecule and their ribosomes are of the 70S type. Their cell membranes and surface layers TABLE 7.1 Major features distinguishing archaea and bacteria (b) Hydrocarbon glycerol linkage (a) Cell wall inhibitors No (b) Protein synthesis inhibitors No' (c) Transcription inhibitors No Some...

Genetic engineering

There has been considerable controversy regarding the potential for genetically engineered organisms to serve as effective BW agents. Recombinant DNA technology has been cited as a method for creating novel, pathogenic microorganisms. Theoretically, organisms could be developed that would possess predictable characteristics, including antibiotic resistance, altered modes of transmission, and altered pathogenic and immuno-genic capabilities. This potential for genetic engineering to...

The Tcomplex transporter

Type IV transporters DNA conjugation systems adapted for export of virulence factors DNA sequence studies within the past 4 years have identified extensive similarities between products of the virB genes and components of two types of transporters dedicated to movement of macromolecules from or between cells (Fig. 2.4). The first type, encoded by tra operons of conjugative plasmids, functions to deliver conjugative plasmids to bacterial recipient cells. The IncN plasmid, pKM101, and the IncW...

Transovarial transmission

Microorganisms located in insect tissues and cells are generally transmitted from mother to offspring via the unfertilized egg in the female ovary. As a result, the symbiotic microorganisms are present even before fertilization and, potentially, for the entire lifespan of the insect. The timing and anatomical details of transovarial transmission vary widely among insect groups, consistent with these associations having evolved independently on multiple occasions. In some insects (e.g., aphids),...

Biased random walk

In a constant environment, motile bacteria generally move in a random walk of straight runs punctuated by brief periods of reversal that serve to randomize the direction of the next run. The chemotaxis system functions by controlling the probability of a reversal. If, during a run, the system determines that conditions are improving, then it sends a signal to the motor that suppresses reversals so that the cell tends to keep moving in the preferred direction. If, on the other hand, the system...

Principle Of Biosensors

A biosensor is a detection system composed of biological sensing elements, such as enzymes, antibodies, microorganisms, and DNA, and an electronic signal-transducing element (Fig. 17. 1) (Buerk, 1993). Atrans-ducer can convert a change in the concentration of a product of a biological reaction into an electronic signal. For example, an oxygen electrode converts a change in the oxygen concentration of a sample caused by enzymes or biodegradation into a change in electric current. The transducers...

Diversity Of Symbiotic Microorganisms In Insects

Distribution of symbiotic microorganisms across the microbial kingdoms Symbiotic microorganisms include members of all microbial kingdoms (Table 54.1) various Eubacteria, methanogens (Archaea), and protists and fungi (Eukaryota). The Eubacteria, especially members of the y-Protobacteria, are widely represented both in the guts and cells of insects, but methanogens and protists occur in the strictly anaerobic portions of the guts of certain insects. Yeasts have been reported in the gut lumen,...

Aspergillosis

Systemic aspergillosis is caused by Aspergillus species (sp.) of which the most common are A. fumigatus and A. flavus. Most cases of human aspergillosis are believed to occur after inhalation of airborne conidia. However, infection following surgery can also follow the deposition of airborne spores in exposed tissues. Aspergillus sp. are very common in the environment and can be found in soil, plants, and decaying vegetation. Conidia germinate in the lung and can invade host tissue if not...

Conjugative Pilus Assembly Pathway

In gram-negative bacteria, certain pili, collectively known as conjugative pili, facilitate the interbacterial transfer of DNA. These pili allow donor and recipient bacteria to make specific and stable intercellular contacts before DNA transfer is initiated. In some cases, conjugative pili may also form the conduits for intercellular DNA transfer. Horizontal gene transfer, or conjugation, mediated by conjugative pili is inextricably associated with the spread of antibiotic resistance among...

Gut microbes and host nutrition

The importance of gut microbes to the host's nutrition is well documented in ruminants with foregut fermentation and in herbivorous nonruminants with hind gut fermentation. Because of microbial activity, ruminants and herbivorous nonruminants are able to utilize cell wall polysaccharides of plants as sources of energy. Another feature that makes ruminants unique is their ability to convert nonprotein nitrogen into protein. In monogastrics, the products of microbial energy-yielding metabolism,...

Enteropathogenic E coli

Enteropathogenic E. coli (EPEC) is an important cause of diarrhea in infants less than 2 years of age. EPEC is transmitted by the fecal-oral route by person-to-person contact. The infection occurs more frequently during the warm seasons. Infection with EPEC is often severe and leads to a high mortality rate in developing countries. The symptoms of the disease include watery diarrhea, vomiting, and fever. All EPEC strains induce a characteristic attaching and effacing (A E) lesion on the brush...

Genetics

Flagellar genetics has been most extensively studied in S. typhimurium, especially using the enormous number of strains that Dr. Shigeru Yamaguchi (Meiji University) has collected for more than 30 years. The discussion in this section is, unless otherwise indicated, based on results obtained from these strains. There are more than 50 flagellar genes, which are divided into three types, according to the null mutant phenotype. Defects in the majority of the flagellar genes result in flagellar...

Electrochemical Gradient Other Than By Electron Transport

Organisms that are incapable of any form of respiration still require an ion electrochemical gradient across the cytoplasmic membrane for purposes such as nutrient uptake. One way in which this requirement can be met is for some of the ATP synthesized by fermentation to be used for ATP hydrolysis by the FoF1 ATPase. This means that this enzyme works in the reverse of its usual direction and pumps protons out of the cell. Thus there are many organisms that can prosper in the absence of any...

Type Ii Secretion Pathway For Type 4 Pilus Assembly

Type 4 pili are multifunctional structures expressed by a wide diversity of bacterial pathogens. These include Pseudomonas aeruginosa, Neisseria gonorrhoeae and N. meningitidis, Moraxella species, Azoarcus species, Dichelobactor nodus, and many other species classified in these and other genera. Type 4 pili are significant colonization factors and have been shown to mediate bacterial interactions with animal, plant, and fungal cells. In addition, these pili can modulate target-cell specificity,...

Computer Identification Systems

The main approach to the identification of an unknown bacterium involves determination of its relevant characters and the matching of these with an appropriate database that defines known taxa. This database may be known as a probability matrix, or identification matrix. The ideal objective is to assign a name to the unknown that is not only correct but also predictive of some or all its natural characters. Computerized identification schemes provide a more flexible system than those of...

Bacterial Foodborne Pathogens

There are many different bacterial pathogens that have been associated with food-borne disease, as shown in Table 40.2. Despite this large number of bacterial pathogens, they generally cause disease by a limited number of mechanisms, such as via a preformed toxin, the production of a toxin in the intestine, invasion of the intestinal epithelial cells, or some other process. The various organisms are broken down into these mechanistic groups and will be described in more detail. A. Bacteria...

Filament

The flagellum is a complex structure composed of many different kinds of proteins. However, the term flagellum, especially in earlier studies, often indicates the flagellar filament only, because the filament is the major portion of the entire flagellum. In this section, I describe the filament and occasionally call the filament just flagellum. The number and location of flagella on a cell are readily discernible traits for the classification of bacterial species. The number ranges from one to...

Bacterial Agents Of Gastritis

Helicobacter pylori is a spiral, microaerophilic gramnegative bacterium with two to six polar sheathed flagellae that endow the bacterium with a corkscrew mode of motility. It has a relatively small genome of 1.7 X 106bp which is highly AT-rich, similar to that of Campylobacters. The complete sequence of the genome has been determined for two strains. This organism is extremely prevalent, residing in large numbers (108-1010 organisms per stomach) in the stomachs of at least half of the human...

Propagation and maintenance 1 Propagation

On solid media, phages produce clear, lysed areas in bacterial lawns or, if sufficiently diluted, small holes called plaques, each of them corresponding to a single viable phage. In liquid media, phages sometimes cause complete clearing of bacterial cultures. Phages are grown on young bacteria in their logarithmic phase of growth, usually in conditions that are optimal for their host. Some phases require divalent cations (Ca2+, Mg2+) or other cofactors. Phages are propagated by three types of...

The esophagus and the stomach

The esophageal and gastric ecosystems generally are not conducive to microbial growth. In the case of the esophagus, the flow of solids, fluids, and oral secretions washes away the microbes. The gastric stomach is inhospitable for most microbes because of the acidic environment. Yet the esophagus and stomach do host many different microbes, more in some animals than others. Lactic acid bacteria (Bifidobacterium, Lactobacillus, and Streptococcus) and yeasts are the most common isolates from the...

Normal oral flora

Any description of the resident flora of the oral cavity must take into consideration the variety of small ecosystems in the various oral habitats. The normal flora of such ecosystems describes those bacteria which are regularly present in all healthy members of the host population. The qualitative assessment of oral bacterial communities indicates that they are comprised of a relatively stable collection of species and strains can be found in similar habitats in the mouths of different members...

Historical Perspective And Classification Of Pili

Pili were first noted in early electron microscopic investigations as nonflagellar, filamentous appendages of bacteria. In 1955, Duguid designated these appendages fimbriae (plural, from Latin for thread or fiber) and correlated their presence with the ability of E. coli to agglutinate red blood cells. Ten years later Brinton introduced the term pilus (singular, from Latin for hair) to describe the fibrous structures (the F pilus) associated with the conjugative transfer of genetic material...

Process Development And Scaleup

Process development usually overlaps culture development. The purpose of process development is the formulation of media, optimization of culture conditions, and determination of the biochemical engineering parameters used to design the full-scale bioreactors. The early stages of process development are usually performed in shake flasks, where the nutritional requirements of the culture are determined and potential media components are screened. Initial growth and production studies can be...

Description Of The Diseases

These infections are limited to the most superficial layers of the epidermis and or its keratinized appendages, such as the hair and nails. The major cutaneous structures are shown in Fig. 41.1 and the most common pathogens causing superficial mycoses are listed in Table 41.1. Cutaneous candidiasis is an infection of the skin that is generally caused by the yeast-like fungus C. albicans and which can be either acute or chronic in nature. C. albicans is part of the normal flora of the...