Environmental distribution and persistence of Quahog Parasite Unknown (QPX)

Quahog Parasite Unknown (QPX) is the cause of mass mortality events of hard clams Mercenaria mercenaria from Virginia, USA, to New Brunswick, Canada. Aquaculture areas in Massachusetts, USA, have been particularly hard hit. The parasite has been shown to be a directly infective organism, but it is unclear whether it could exist or persist outside of its clam host. We used molecular methods to examine water, sediment, seaweeds, seagrass and various invertebrates for the presence of QPX. Sites in Virginia and Massachusetts were selected based upon the incidence of QPX-induced clam die-offs, and they were monitored seasonally. QPX was detectable in almost all of our different sample types from Massachusetts, indicating that the parasite was widely distributed in the environment. Significantly more samples from Massachusetts were positive than from Virginia, and there was a seasonal pattern to the types of samples positive from Massachusetts. The data suggest that, although it may be difficult to completely eradicate QPX from the environment, it may be possible to keep the incidence of disease under control through good plot husbandry and the removal of infected and dying clams.     

Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model

Predicting the phenotype of an organism from its genotype is a central question in genetics. Most importantly, we would like to find out if the perturbation of a single gene may be the cause of a disease. However, our current ability to predict the phenotypic effects of perturbations of individual genes is limited. Network models of genes are one tool for tackling this problem. In a recent study, (Lee et al.) it has been shown that network models covering the majority of genes of an organism can be used for accurately predicting phenotypic effects of gene perturbations in multicellular organisms. .     

Role of the parasporal body in causing toxicity of Bacillus thuringiensis toward Aedes aegypti larvae

A unique type of microorganism has been found causing an unusual disease in larvae of the clover cutworm, Scotogramma trifolii (Lepidoptera; Noctuidae). The organism contains DNA and reproduces exclusively by self-assembly forming enveloped reniform/bacilliform particles which measure 170 × 450 nm in negatively stained preparations. During initial stages of development, the organism apparently reproduces primarily within vesicles in the cytoplasm of a variety of cell types including hemocytes, and epidermal, fat body, and tracheal matrix cells. Most reproduction, however, occurs in vesicles that circulate in the hemolymph. These vesicles, most of which are derived from host cells, measure 2–10 μm in diameter, are highly refractile, reach populations as high as 10⁸/ml of hemolymph, and are diagnostic for the disease. The pathology caused by this organism, its shape and ultrastructure, and reproduction within vesicles indicate it is either a peculiar type of rickettsia, possibly related to those of the genus Rickettsiella, or a new type of invertebrate virus. Among its unusual features are its ability to induce the formation of reproductive vesicles from host cell components, and its apparent control of de novo ribosome and membrane synthesis within these vesicles as it develops. The possible relationship of this organism to baculoviruses and rickettsia is discussed.     

Malaria at the Hospital for Sick Children,Toronto.

The number of immigrants to Canada from countries where malaria is endemic increased sevenfold between 1964 and 1974. From January 1973 through July 1975, 15 cases of malaria were treated at the Hospital for Sick Children, Toronto. The only symptom common to all patients was fever, and it was not always cyclic. For any child with a fever of unknown cause who has been in a region where malaria is endemic within the previous 6 months, a blood smear should be examined for parasites. If the smear is negative even when stained with acridine orange, serologic testing should be performed. Acurrate species identification is important since therapy varies according to the causative organism.     

The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients

Bacterial infections of the lungs of cystic fibrosis (CF) patients cause major complications in the treatment of this common genetic disease. Burkholderia cenocepacia infection is particularly problematic since this organism has high levels of antibiotic resistance, making it difficult to eradicate; the resulting chronic infections are associated with severe declines in lung function and increased mortality rates. B. cenocepacia strain J2315 was isolated from a CF patient and is a member of the epidemic ET12 lineage that originated in Canada or the United Kingdom and spread to Europe. The 8.06-Mb genome of this highly transmissible pathogen comprises three circular chromosomes and a plasmid and encodes a broad array of functions typical of this metabolically versatile genus, as well as numerous virulence and drug resistance functions. Although B. cenocepacia strains can be isolated from soil and can be pathogenic to both plants and man, J2315 is representative of a lineage of B. cenocepacia rarely isolated from the environment and which spreads between CF patients. Comparative analysis revealed that ca. 21% of the genome is unique in comparison to other strains of B. cenocepacia, highlighting the genomic plasticity of this species. Pseudogenes in virulence determinants suggest that the pathogenic response of J2315 may have been recently selected to promote persistence in the CF lung. The J2315 genome contains evidence that its unique and highly adapted genetic content has played a significant role in its success as an epidemic CF pathogen.     

Myo-inositol-1-phosphate synthase from streptomyces griseus (Studies on the biosynthesis of cyclitols,XXXVIII1)

Summary It could be shown that Streptomyces griseus, the microorganism producing the antibiotic streptomycin and also mutant strains of this species that cannot synthesize streptomycin, possess myo-inositol-1-phosphate synthase (EC 5.5.1.4), the enzyme cyclizing D-glucose 6-phosphate. The enzyme isolated from that organism is extremely instable, its molecular weight is approximately 260,000, and it requires a divalent metal ion for its activity. This is the first instance that an enzyme of this specificity has been found in a prokaryotic organism.     

Biology of Pseudomonas stutzeri.

Pseudomonas stutzeri is a nonfluorescent denitrifying bacterium widely distributed in the environment, and it has also been isolated as an opportunistic pathogen from humans. Over the past 15 years, much progress has been made in elucidating the taxonomy of this diverse taxonomical group, demonstrating the clonality of its populations. The species has received much attention because of its particular metabolic properties: it has been proposed as a model organism for denitrification studies; many strains have natural transformation properties, making it relevant for study of the transfer of genes in the environment; several strains are able to fix dinitrogen; and others participate in the degradation of pollutants or interact with toxic metals. This review considers the history of the discovery, nomenclatural changes, and early studies, together with the relevant biological and ecological properties, of P. stutzeri.     

The Intelligent Egg, and How It Got That Way: from Genes to Genius in a Few Easy Lessons

A seed has no flowers or leaves, and an egg no fingers or lungs. Yet plants and animals not only have these things but they resemble their parents in detail throughout their bodies. Something is inherited, but what is it? Life is based on the activities of cells. An organism has large numbers of them—a human has trillions! Cells live as separate units, which enables them each to do its own thing within its particular organ, but to be an organism they must work together. A cell can only detect its immediate local environment, but that includes various kinds of signals or information from nearby or far away within the body—or even from the external environment. It is by being local but responding globally in this way that an egg becomes an organism, an organism manages its way through life, and organisms make up species and ecosystems that interact with each other. The evolution of these abilities has produced the glorious array of living forms that populate the world. In these ways, an egg may have no thoughts but is a highly intelligent being.     

Closure to efficient causation, computability and artificial life

The major insight in Robert Rosen's view of a living organism as an (M,R)-system was the realization that an organism must be “closed to efficient causation”, which means that the catalysts needed for its operation must be generated internally. This aspect is not controversial, but there has been confusion and misunderstanding about the logic Rosen used to achieve this closure. In addition, his corollary that an organism is not a mechanism and cannot have simulable models has led to much argument, most of it mathematical in nature and difficult to appreciate. Here we examine some of the mathematical arguments and clarify the conditions for closure.     

Biology of Pseudomonas stutzeri

Pseudomonas stutzeri is a nonfluorescent denitrifying bacterium widely distributed in the environment, and it has also been isolated as an opportunistic pathogen from humans. Over the past 15 years, much progress has been made in elucidating the taxonomy of this diverse taxonomical group, demonstrating the clonality of its populations. The species has received much attention because of its particular metabolic properties: it has been proposed as a model organism for denitrification studies; many strains have natural transformation properties, making it relevant for study of the transfer of genes in the environment; several strains are able to fix dinitrogen; and others participate in the degradation of pollutants or interact with toxic metals. This review considers the history of the discovery, nomenclatural changes, and early studies, together with the relevant biological and ecological properties, of P. stutzeri.     

Phenoptosis as genetically determined aging influenced by signals from the environment

Aging is a complex and not well understood process. Two opposite concepts try to explain its causes and mechanisms — programmed aging and aging of “wear and tear” (stochastic aging). To date, much evidence has been obtained that contradicts the theories of aging as being due to accumulation of various damages. For example, creation of adequate conditions for the functioning of the organism’s components (appropriate microenvironment, humoral background, etc.) has been shown to cause partial or complete reversibility of signs of its aging. Programmed aging and death of an organism can be termed phenoptosis by analogy to the term apoptosis for programmed cell death (this term was first suggested by V. P. Skulachev). The necessity of this phenomenon, since A. Weismann, has been justified by the need for population renewal according to ecological and evolutionary requirements. Species-specific lifespan, age-dependent changes in expression pattern of genes, etc. are compatible with the concept of phenoptosis. However, the intraspecific rate of aging was shown to vary over of a wide range depending on living conditions. This means that the “aging program” is not set rigidly; it sensitively adjusts an individual to the specific realities of its habitat. Moreover, there are indications that in rather severe conditions of natural habitat the aging program can be completely cancelled, as the need for it disappears because of the raised mortality from external causes (high extrinsic mortality), providing fast turnover of the population.     

Reaper-induced apoptosis in a vertebrate system.

The reaper protein of Drosophila melanogaster has been shown to be a central regulator of apoptosis in that organism. However, it has not been shown to function in any vertebrate nor have the cellular components required for its action been defined. In this report we show that reaper can induce rapid apoptosis in vitro using an apoptotic reconstitution system derived from Xenopus eggs. Moreover, we show that a subcellular fraction enriched in mitochondria is required for this process and that reaper, acting in conjunction with cytosolic factors, can trigger mitochondrial cytochrome c release. Bcl-2 antagonizes these effects, but high levels of reaper can overcome the Bcl-2 block. These results demonstrate that reaper can function in a vertebrate context, suggesting that reaper-responsive factors are conserved elements of the apoptotic program.     

Cloning and characterization of an ftsZ homologue from a bacterial symbiont of Drosophila melanogaster

A 1194 by open reading frame that codes for a 398 amino acid peptide was cloned from a λgt11 library of Drosophila melanogaster genomic DNA. The predicted peptide sequence is very similar to three previously characterized protein sequences that are encoded by the ftsZ genes in Escherichia coli, Bacillus subtilis and Rhizobium meliloti. The FtsZ protein has a major role in the initiation of cell division in prokaryotic cells. Using a tetracycline treatment that eradicates bacterial parasites from insects, the ftsZ homologue has been found to be derived from a bacterium that lives within the strain. However, polymerase chain reaction (PCR) amplification of the gene from treated embryos suggests that it is not derived from a gut bacterium. Nevertheless, by amplifying and characterizing part of the 16S rRNA from this bacterium we have been able to demonstrate that it is a member of the genus Wolbachia, a parasitic organism that infects, and disturbs the sexual cycle of various strains of Drosophila simulans. We suggest that this ftsZ homologue is implicated in the cell division of Wolbachia, an organism that fails to grow outside the host organism. Sequence and alignment analysis of this ftsZ homologue show the presence of a potential GTP-binding motif indicating that it may function as a GTPase. The consequences of this function particularly with respect to its role in cell division are discussed.     

Recognition of mucin components by Pseudomonas aeruginosa

Pseudomonas aeruginosa remains one of the most important bacterial pathogens in lung diseases and especially in Cystic fibrosis. This unusual predilection is best explained by the existence of defects in host defense mechanisms as resulting from the genetic lesion and the presence of a specific colonization niche within the lungs. The niche has been identified as the mucus layer wherein mucin glycoproteins provide a substrate for binding and allows the persistence of this organism in this milieu by a number of possible mechanisms. While this organism is capable of binding to non CF mucins, it is perhaps a combination of factors e.g. increased binding and decreased mucociliary clearance that is responsible for this marked state of colonization in CF. The organism uses chiefly proteins of its flagellar apparatus to initiate this binding and recognizes a variety of oligosaccharides that have been identified in mucins. Among these are both, neutral oligosaccharides and several forms of acidic oligosaccharides derived from the Lewis antigens. There are more than likely a larger repertoire of receptors than those identified and certainly more adhesins present than those currently known. However, the information gathered to date provides an excellent example of the specificity of bacterial interactions with mucins that will certainly be expanded as we study more pulmonary pathogens.     

Laboratory strains of Escherichia coli: model citizens or deceitful delinquents growing old disgracefully?

Escherichia coli stands unchallenged as biology's premier model organism. However, we propose, equipped with insights from the post-genomic era, a contrary view: that microbiology's chief idol has feet of clay. E. coli laboratory strains, particularly E. coli K-12, are far from model citizens, but instead degenerate and deceitful delinquents growing old disgracefully in our scientific institutions. E. coli K-12 is neither archetype nor ancestor. In addition, it has a far from optimal provenance for a model organism, with strong grounds for believing that current versions of the strain are quite distinct from any original wild-type free-living ancestor. In addition, it is usually studied under conditions far removed from its natural habitats and in ignorance of the selective pressures that have shaped its evolution. Fortunately, a flood of information from high-throughput genome sequencing, together with a new 'eco-evo' view of this model organism, promises to help put K-12 better into context.     

Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium thiebautii

Trichodesmium spp. are marine filamentous, nonheterocystous, nitrogen-fixing cyanobacteria which are an important component of marine ecosystems. This organism has never been maintained in axenic culture, and there has remained some doubt as to the identity of the organism responsible for nitrogen fixation in Trichodesmium aggregates. By using degenerate oligonucleotide primers, it has been possible to amplify, clone, and sequence a segment of the nifH gene from a natural assemblage of Trichodesmium thiebautii. Examination of the DNA and presumed amino acid sequence shows that the gene is most closely related to that of Anabaena spp. and therefore is most likely a cyanobacterial nifH gene. The use of degenerate oligonucleotides, in concert with the polymerase chain reaction, can be a powerful tool for the cloning and sequencing of a variety of genes from microorganisms in the environment.     

Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium thiebautii.

Trichodesmium spp. are marine filamentous, nonheterocystous, nitrogen-fixing cyanobacteria which are an important component of marine ecosystems. This organism has never been maintained in axenic culture, and there has remained some doubt as to the identity of the organism responsible for nitrogen fixation in Trichodesmium aggregates. By using degenerate oligonucleotide primers, it has been possible to amplify, clone, and sequence a segment of the nifH gene from a natural assemblage of Trichodesmium thiebautii. Examination of the DNA and presumed amino acid sequence shows that the gene is most closely related to that of Anabaena spp. and therefore is most likely a cyanobacterial nifH gene. The use of degenerate oligonucleotides, in concert with the polymerase chain reaction, can be a powerful tool for the cloning and sequencing of a variety of genes from microorganisms in the environment.