Comparison of the virulence plasmid genomes of two strains of Shigella which lost the ability to bind Congo red

As an enteric pathogen and Gram negative bacte-rium, Shigella possesses high infectivity and leads to serious illness. Since its discovery in 1898 by Shiga, Shigella species have been studied widely. These studies have elucidated the Shigella pathogenicit…     

Comparison of the virulence plasmid genomes of two strains of Shigella which lost the ability to bind Congo red

We determined and analyzed the Shigella flexneri serotype 5 (pSF5) and S. dysenteriae serotype 1 (pSD1) virulence plasmid genomes. The total length of pSF5 is 136513 bp, including 165 open reading frames (ORFs). Of these ORFs, 133 were identified and 32 of those had no significant homology to proteins with known functions. The length of pSD1 is 182545 bp, including 224 ORFs, of which we identified 181. The remaining 43 ORFs were not significantly homologous to proteins with known functions. The insertion sequence (IS) elements are 53787 bp in pSF5, and 49616 bp in pSD1, which represents 39.4% and 27.1% of the genome, respectively. There are 22 IS element types in pSF5 and pSD1, among which we report ISEc8 and ISSbo6 for the first time in the Shigella virulence plasmid. Compared to pCP301, there are a large number of deleted genes and gene inversions in both pSF5 and pSD1. The ipa-mxi-spa locus in pSF5 is completely absent, and the genes related to the O-antigen biosynthesis are partially missing. In contrast, the above genes in pSD1 are integral, with the exception of virF. The whole genome analysis of the two plasmids shows that the loss of genes related to gene invasion or regulation also obliterates the ability of pPF5 and pSD1 to bind Congo red (Crb). Whether these genes determine the Crb function requires continued investigation.     

Comparison of the virulence plasmid genomes of two strains of Shigella which lost the ability to bind Congo red

We determined and analyzed the Shigella flexneri serotype 5 (pSF5) and S. dysenteriae serotype 1 (pSD1) virulence plasmid genomes. The total length of pSF5 is 136513 bp, including 165 open reading frames (ORFs). Of these ORFs, 133 were identified and 32 of those had no significant homology to proteins with known functions. The length of pSD1 is 182545 bp, including 224 ORFs, of which we identified 181. The remaining 43 ORFs were not significantly homologous to proteins with known functions. The insertion sequence (IS) elements are 53787 bp in pSF5, and 49616 bp in pSD1, which represents 39.4% and 27.1% of the genome, respectively. There are 22 IS element types in pSF5 and pSD1, among which we report ISEc8 and ISSbo6 for the first time in the Shigella virulence plasmid. Compared to pCP301, there are a large number of deleted genes and gene inversions in both pSF5 and pSD1. The ipa-mxi-spa locus in pSF5 is completely absent, and the genes related to the O-antigen biosynthesis are partially missing. In contrast, the above genes in pSD1 are integral, with the exception of virF. The whole genome analysis of the two plasmids shows that the loss of genes related to gene invasion or regulation also obliterates the ability of pPF5 and pSD1 to bind Congo red (Crb). Whether these genes determine the Crb function requires continued investigation. These authors contributed equally to this work.     

Identification of spores in the polycentric anaerobic gut fungi which enhance their ability to survive

Two new isolates of the gut fungi were obtained from the rumen digesta and faeces of a cow. These isolates, designated Anaeromyces following rDNA typing, displayed a polycentric growth habit but differed from all other gut fungi in that they were able to survive in the laboratory for considerable periods without the need for sub-culture. Light microscopy of preparations from old liquid-grown cultures revealed the presence of DNA-containing spores with two or four chambers. A comparative evaluation of the growth produced when fresh media were inoculated with a sample originating from young or old cultures revealed that active growth was delayed with the inoculum from the older culture. We propose that the chambered spores observed in these cultures provide an alternative path in the life cycle of these fungi and may function as a resting stage within the anaerobic environment of the herbivore gut.     

Transformed cells have lost control of ribosome number through their growth cycle.

Previous studies on the synthesis and function of the protein synthetic machinery through the growth cycle of normal cultured hamster embryo fibroblasts (HA) were extended here to a series of four different clonal lines of polyoma virus-transformed HA cells. Under our culture conditions, these transformed cells could enter a stationary phase characterized by no mitotic cells, very low rates of DNA synthesis, and arrest in a post-mitotic pre-DNA synthetic state. Cellular viability was initially high in stationary phase but, unlike normal cells, transformed cells slowly lost viability. The rate of protein synthesis in the stationary phase of the transformed cells fell to 25-30% of the exponential rate. Though this reduction was similar to that seen in normal cells, it was accomplished by different means. The specific reduction in the ribosome complement per cell to values below that of any cycling cell seen in normal cells, was not seen in any of the transformed lines. This observation, which implies a loss of normal control of ribisome synthesis through the growth cycle after transformation, was confirmed in normal Chinese hamster embryo fibroblasts and transformed CHO cell lines. Normal control of ribosome synthesis was restored in L-73 and LR-73, growth control revertants of one of the transformed CHO lines. The transformed lines reduced their protein synthetic rates in stationary phase either by a greater reduction in the proportion of functioning ribosomes than that seen in normal cells or by a decrease in the elongation rate of functioning ribosomes; the latter effect was not seen in the normal cells. A model for growth control of normal cells and its derangement in transformed cells is presented.     

Features of Fibrobacter intestinalis DR7 mutant which is impaired with its ability to adhere to cellulose

A spontaneous adhesion-defective mutant (DR7-M) of Fibrobacter intestinalis DR7 was isolated which was capable of growing on glucose and cellobiose, but impaired in its capacity to degrade cellulose. Levels of enzyme activities were determined in solubilized fractions of DR7 and DR7-M. Total endoglucanases and xylanase activity values of parent DR7 fractions were 2.84 and 1.85 folds higher than those of the mutant, and were distributed mainly in the bacterial envelope fractions, with some activity also found in the extracellular fluid. In a separate assay, measurement of the enzymatic activity bound to cellulose showed that a portion of the endoglucanase activity bound to cellulose while most xylanase activity did not bind. Notwithstanding, the wild type DR7 cells had 26-fold higher total activities of cellulose-degrading enzymes than the mutant, and 96% of its activity was exclusively located in outer membrane and periplasm fractions. In the mutant, the lower cellulose degrading enzymes activity was located only in the extracellular fluid. Most of the cellulose degrading enzymes activity of DR7 had the capability to bind to cellulose. SDS-page electrophoresis of outer membrane and periplasm cell fractions showed that DR7 and DR7-M possess similar molecular weight (MW) profiles but different quantities of 16 cellulose-binding-proteins (CBPs) in the MW range of 36 up to 225 kDa. Zymogram analysis with soluble substrates, either carboxymethylcellulose or soluble xylan, following SDS-page of DR7 and DR7-M fractions, suggested that CBPs of approximate MW 120, 110, 100, 90, 70 and 40 kDa have endoglucanase activity, and that CBPs of all fractions lack any xylanase activity.     

Colonization and persistence ability explain the extent to which plant species fill their potential range

Aim How species traits and environmental conditions affect biogeographical dynamics is poorly understood. Here we test whether estimates of a species’ evolutionary age, colonization and persistence ability can explain its current ‘range filling’ (the ratio between realized and potential range size). Location Fynbos biome (Cape Floristic Region, South Africa). Methods For 37 species of woody plants (Proteaceae), we estimate range filling using atlas data and distribution models, evolutionary age using molecular phylogenies, and persistence ability using estimates of individual longevity (which determines the probability of extinction of local populations). Colonization ability is estimated from validated process‐based seed dispersal models, the arrangement of potential habitat, and data on local abundance. To relate interspecific variation in range filling to evolutionary age, colonization and persistence ability, we use two complementary model types: phenomenological linear models and the process‐based metapopulation model of Levins. Results Linear model analyses show that range filling increases with a species’ colonization and persistence ability but is not affected by species age. Moreover, colonization ability is a better predictor of range filling than its component variables (local abundance and dispersal ability). The phylogenetically independent interaction between colonization and persistence ability is significant (P < 0.05) for 97% of 180 alternative phylogenies. While the selected linear model explains 42% of the variance in arcsine transformed range filling, the Levins model performs more poorly. It overestimates range filling for realistic parameter values and produces unrealistic parameter estimates when fitted statistically. Main conclusions Colonization and local extinction seem to shape Proteaceae range dynamics on ecological rather than macroevolutionary time‐scales. Our results suggest that the positive abundance–range size relationship in this group is due primarily to the effect of abundance on colonization. In summary, this study contributes to a process‐based understanding of range dynamics and highlights the importance of colonization for the future survival of Fynbos Proteaceae.     

Human cancer cells have specifically lost the ability to induce the synergistic state caused by tumor necrosis factor plus interferon-β

Tumor necrosis factor (TNF) and the members of the interferon (IFN) family are major inducible cytokines that function to counteract viral infections or cellular transformation. Recently, our lab has characterized a novel antiviral state which is induced in primary human fibroblasts by co-treatment with TNF plus IFNβ. Here, we demonstrate that this synergistic state is both antiviral and cytostatic for primary human cells. Significantly, we observed that a wide spectrum of transformed human cancer cells have universally lost the ability to induce the TNF/IFNβ synergistic state, as defined by three separate criteria. We hypothesize that the ability to induce the TNF/IFNβ synergistic state is a unique feature of primary cells and is incompatible with cellular immortalization and/or transformation.     

The properties of forms of Ruminococcus flavefaciens which differ in their ability to degrade cotton cellulose

Two mutant strains of Ruminococcus flavefaciens strain 007 that differ in their ability to hydrolyse cotton fibres have been shown also to differ in their cell-surface topology, in that the cotton degrading form possessed larger and more protuberant cell surface structures. The strains had similar CMCase, cellobiosidase and beta-glucosidase activities. The results indicate the importance of cell-surface properties in cotton degradation by R. flavefaciens.     

Four mutants of Micrococcus radiodurans defective in the ability to repair DNA damaged by mitomycin-C, two of which have wild-type resistance to ultraviolet radiation

Summary Four genes concerned with the resistance of wild-type Micrococcus radiodurans to the lethal action of mitomycin-C (MTC), mtcA, mtcB, uvsA and uvsB, have been identified by isolating mutants sensitive to MTC.Two strains of M. radiodurans, 302 and 262 carrying mutations in mtcA and mtcB respectively, are between forty and sixty times as sensitive as the wild-type to MTC, only slightly more sensitive than the wild-type to ionizing () radiation and have the same resistance as the wild-type to ultraviolet (u.v.) radiation. Strain 302 can be transformed at a high frequency to wild-type resistance to MTC with DNA from strain 262, and vice versa, indicating that mtcA and mtcB have different genetic locations.Two further strains of M. radiodurans, 303 and 263 having mutations in uvsA and uvsB respectively are only from four to eight times as sensitive as the wild-type to MTC, seven to thirteen times as sensitive to -radiation but between twenty to thirty-three times as sensitive to u.v. radiation. Strain 303 can be transformed with DNA from strain 263, or vice versa, to wild-type resistance to u.v. radiation, implying that uvsA and uvsB also have different genetic locations. M. radiodurans strain 301 which is mutant in both mtcA and uvsA, and strain 261 which is mutant in mtcB and uvsB are twenty to forty times as sensitive as the wild-type to both MTC and u.v. radiation and seven to ten times as sensitive to radiation. Neither mtcA and uvsA nor mtcB and uvsB are closely linked.None of the mutant strains is deficient in recombination, as measured by transformation. The repair of MTC-induced DNA damage in M. radiodurans must be different from that described for Escherichia coli.     

Environmental factors which may have led to the appearance of colour vision

It is hypothesized that colour vision and opponent processing of colour signals in the visual system evolved as a means of overcoming the extremely unfavourable lighting conditions in the natural environment of early vertebrates. The significant flicker of illumination inherent in the shallow-water environment complicated the visual process in the achromatic case, in particular preventing early detection of enemies. The presence of two spectral classes of photoreceptors and opponent interaction of their signals at a subsequent retinal level allowed elimination of the flicker from the retinal image. This new visual function provided certain advantages concerning reaction times and favoured survival. This assumption explains why the building blocks for colour vision arose so early, i.e. just after the active predatory lifestyle was mastered. The principal functions of colour vision inherent in extant animals required a more complex neural machinery for colour processing and evolved later as the result of a change in visual function favouring colour vision.     

Lysophospholipids and their receptors in the central nervous system

Lysophosphatidic acid (LPA) and sphingosine 1-phosphate (S1P), two of the best-studied lysophospholipids, are known to influence diverse biological events, including organismal development as well as function and pathogenesis within multiple organ systems. These functional roles are due to a family of at least 11 G protein-coupled receptors (GPCRs), named LPA_1–6 and S1P_1–5, which are widely distributed throughout the body and that activate multiple effector pathways initiated by a range of heterotrimeric G proteins including G_i/o, G_12/13, G_q and G_s, with actual activation dependent on receptor subtypes. In the central nervous system (CNS), a major locus for these signaling pathways, LPA and S1P have been shown to influence myriad responses in neurons and glial cell types through their cognate receptors. These receptor-mediated activities can contribute to disease pathogenesis and have therapeutic relevance to human CNS disorders as demonstrated for multiple sclerosis (MS) and possibly others that include congenital hydrocephalus, ischemic stroke, neurotrauma, neuropsychiatric disorders, developmental disorders, seizures, hearing loss, and Sandhoff disease, based upon the experimental literature. In particular, FTY720 (fingolimod, Gilenya, Novartis Pharma, AG) that becomes an analog of S1P upon phosphorylation, was approved by the FDA in 2010 as a first oral treatment for MS, validating this class of receptors as medicinal targets. This review will provide an overview and update on the biological functions of LPA and S1P signaling in the CNS, with a focus on results from studies using genetic null mutants for LPA and S1P receptors. This article is part of a Special Issue entitled Advances in Lysophospholipid Research.