Lineage-specific evolution and gene flow in Listeria monocytogenes are independent of bacteriophages

Listeria monocytogenes is a foodborne pathogen causing systemic infection with high mortality. To allow efficient tracking of outbreaks a clear definition of the genomic signature of a cluster of related isolates is required, but lineage-specific characteristics call for a more detailed understanding of evolution. In our work, we used core genome MLST (cgMLST) to identify new outbreaks combined to core genome SNP analysis to characterize the population structure and gene flow between lineages. Whilst analysing differences between the four lineages of L. monocytogenes we have detected differences in the recombination rate, and interestingly also divergence in the SNP differences between sub-lineages. In addition, the exchange of core genome variation between the lineages exhibited a distinct pattern, with lineage III being the best donor for horizontal gene transfer. Whilst attempting to link bacteriophage-mediated transduction to observed gene transfer, we found an inverse correlation between phage presence in a lineage and the extent of recombination. Irrespective of the profound differences in recombination rates observed between sub-lineages and lineages, we found that the previously proposed cut-off of 10 allelic differences in cgMLST can be still considered valid for the definition of a foodborne outbreak cluster of L. monocytogenes.     

Programmed death of peripheral pioneer neurons in the grasshopper embryo

The Ti1 pioneer neurons arise at the distal tip of the metathoracic leg in the grasshopper embryo, and are the first neurons in the limb bud to extend axons to the central nervous system (C. M. Bate (1976) Nature (London) 260, 54-56; H. Keshishian (1980) Dev. Biol. 80, 388-397). By providing a neural pathway along which growth cones of later arising neurons migrate, these pioneer axons establish the route of one of the major nerve trunks in the leg (Keshishian, 1980; R. K. Ho and C. S. Goodman (1982) Nature (London) 297, 404-406; D. Bentley and H. Keshishian (1982) Science 218, 1082-1088). Here, we demonstrate that at the 55-59% stage of development, the two Ti1 pioneer neurons undergo programmed death. The role which these pioneers serve in establishing a nerve route appears to be their only function, and may be important for the normal development of the peripheral nervous system. The Ti1 pioneers provide an example of a previously hypothesized class (J. W. Truman (1984) Annu. Rev. Neurosci. 7, 171-188) of programmed neuron death: obsolete neurons whose function was developmental rather than behavioral.     

Experimental study of tissue response to ruptured gel-filled mammary prostheses.

Miniature "soft gel" filled breast prostheses were implanted into rats, and half of these were purposefully ruptured upon insertion. At sacrifice of the animals later, the position of the exuded gel, the variability of the capsule thickness, and the extent of the capsule formation were evaluated. The capsule thickness was significantly increased around the ruptured prostheses, in response to the exuded gel. Also, the gel migrated through the fibrous capsule and into the surrounding tissue, eliciting an inflammatory response there to produce capsule thickening.     

Crystallization of the first three domains of the human insulin-like growth factor-1 receptor.

The insulin-like growth factor-1 receptor (IGF-1R) is a tyrosine kinase receptor of central importance in cell proliferation. A fragment (residues 1-462) comprising the L1-cysteine rich-L2 domains of the human IGF-1R ectodomain has been overexpressed in glycosylation-deficient Lec8 cells and has been affinity-purified via a c-myc tag followed by gel filtration. The fragment was recognized by two anti-IGF-1R monoclonal antibodies, 24-31 and 24-60, but showed no detectable binding of IGF-1 or IGF-2. Isocratic elution of IGF-1R/462 on anion-exchange chromatography reduced sample heterogeneity, permitting the production of crystals that diffracted to 2.6 A resolution with cell dimensions a = 77.0 A, b = 99.5 A, c = 120.1 A, and space group P2(1)2(1)2(1).     

Improved Fixation of Cellulose-Acetate Reverse-Osmosis Membrane for Scanning Electron Microscopy

Fixation of cellulose-acetate membranes with either glutaraldehyde-osmium tetroxide or glutaraldehyde-ruthenium tetroxide resulted in extensive electron beam damage. Beam damage was eliminated and the bacterial surface structure was preserved, however, when cellulose-acetate membranes were fixed with glutaraldehyderuthenium tetroxide and treated successively with thiocarbohydrazide and osmium tetroxide.     

HIV-1 Tat Activates Neuronal Ryanodine Receptors with Rapid Induction of the Unfolded Protein Response and Mitochondrial Hyperpolarization

Neurologic disease caused by human immunodeficiency virus type 1 (HIV-1) is ultimately refractory to highly active antiretroviral therapy (HAART) because of failure of complete virus eradication in the central nervous system (CNS), and disruption of normal neural signaling events by virally induced chronic neuroinflammation. We have previously reported that HIV-1 Tat can induce mitochondrial hyperpolarization in cortical neurons, thus compromising the ability of the neuron to buffer calcium and sustain energy production for normal synaptic communication. In this report, we demonstrate that Tat induces rapid loss of ER calcium mediated by the ryanodine receptor (RyR), followed by the unfolded protein response (UPR) and pathologic dilatation of the ER in cortical neurons in vitro. RyR antagonism attenuated both Tat-mediated mitochondrial hyperpolarization and UPR induction. Delivery of Tat to murine CNS in vivo also leads to long-lasting pathologic ER dilatation and mitochondrial morphologic abnormalities. Finally, we performed ultrastructural studies that demonstrated mitochondria with abnormal morphology and dilated endoplasmic reticulum (ER) in brain tissue of patients with HIV-1 inflammation and neurodegeneration. Collectively, these data suggest that abnormal RyR signaling mediates the neuronal UPR with failure of mitochondrial energy metabolism, and is a critical locus for the neuropathogenesis of HIV-1 in the CNS.     

Marenzelleria cf. wireni (Polychaeta: Spionidae) from the Tay estuary. Metabolic response to severe hypoxia and hydrogen sulphide

The appearance of the spionid polychaete Marenzelleria spp. in the Tay estuary (Scotland) was first reported in 1984. Since estuaries are known as environments where abiotic conditions fluctuate widely, a laboratory study was conducted aimed to elucidate how this introduced species deals with low oxygen concentrations and exposure to hydrogen sulphide. Experimental evidence reveals that during severe hypoxia Marenzelleria cf. wireni switched to anaerobic pathways known from other marine invertebrates. Under the influence of sulphide (1 mmol l^-1) accumulation of anaerobic end products is more pronounced. It is assumed that in the presence of sulphide, due to its inhibition of aerobic respiration, the worms have to switch to anaerobic energy production directly after the onset of hypoxia. Seasonal differences in the metabolic reaction were found. It was shown that in specimens that were filled with gametes (winter), accumulation of end products of anaerobic metabolism was more pronounced than in immature worms (summer). The amount of succinate, an indicator for anaerobic energy production for instance, was nearly twice as high in the winter specimens. Since the amount of thiosulphate (a typical sulphide detoxification product) in the tissues is relatively low, it is suggested that Marenzelleria cf. wireni also accumulates other detoxification products. Sulphite, however, also known as a detoxification product, was found only in traces. Field measurements provide evidence that the potential of Marenzelleria cf. wireni to survive low oxygen and high sulphide concentrations is clearly higher than that normally needed in the Tay estuary.     

Bioinformatic identification of novel regulatory DNA sequence motifs in <Emphasis Type="Italic">Streptomyces coelicolor</Emphasis>

Background  

Streptomyces coelicolor is a bacterium with a vast repertoire of metabolic functions and complex systems of cellular development. Its genome sequence is rich in genes that encode regulatory proteins to control these processes in response to its changing environment. We wished to apply a recently published bioinformatic method for identifying novel regulatory sequence signals to gain new insights into regulation in S. coelicolor.     

Association between DNA Damage Response and Repair Genes and Risk of Invasive Serous Ovarian Cancer

Background

We analyzed the association between 53 genes related to DNA repair and p53-mediated damage response and serous ovarian cancer risk using case-control data from the North Carolina Ovarian Cancer Study (NCOCS), a population-based, case-control study.

Methods/Principal Findings

The analysis was restricted to 364 invasive serous ovarian cancer cases and 761 controls of white, non-Hispanic race. Statistical analysis was two staged: a screen using marginal Bayes factors (BFs) for 484 SNPs and a modeling stage in which we calculated multivariate adjusted posterior probabilities of association for 77 SNPs that passed the screen. These probabilities were conditional on subject age at diagnosis/interview, batch, a DNA quality metric and genotypes of other SNPs and allowed for uncertainty in the genetic parameterizations of the SNPs and number of associated SNPs. Six SNPs had Bayes factors greater than 10 in favor of an association with invasive serous ovarian cancer. These included rs5762746 (median OR(odds ratio)_{per allele} = 0.66; 95% credible interval (CI) = 0.44–1.00) and rs6005835 (median OR_{per allele}  = 0.69; 95% CI  = 0.53–0.91) in CHEK2, rs2078486 (median OR_{per allele}  = 1.65; 95% CI = 1.21–2.25) and rs12951053 (median OR_{per allele}  = 1.65; 95% CI = 1.20–2.26) in TP53, rs411697 (median OR _{rare homozygote}  = 0.53; 95% CI  = 0.35 – 0.79) in BACH1 and rs10131 (median OR _{rare homozygote}  =  not estimable) in LIG4. The six most highly associated SNPs are either predicted to be functionally significant or are in LD with such a variant. The variants in TP53 were confirmed to be associated in a large follow-up study.

Conclusions/Significance

Based on our findings, further follow-up of the DNA repair and response pathways in a larger dataset is warranted to confirm these results.