Klebsiella michiganensis sp. nov., A New Bacterium Isolated from a Tooth Brush Holder

Isolate W14^T recovered from a household tooth brush holder was found to be gram-negative, a facultative anaerobic, non-motile, capsulated, and a non-endospore-forming straight rod. Based on phylogenetic analysis with 16S rRNA gene sequence, isolate W14^T was affiliated to the genus Klebsiella. The closest phylogenetic relative was K. oxytoca with 99 % similarity in the 16S rRNA gene sequence. The major whole-cell fatty acids were C_16:0 (31.23 %), C_18:1ω6c/C_18:1ω7c (21.10 %), and C_16:1ω7c/C_16:1ω6c (19.05 %). The sequence similarities of isolate W14^T based on rpoB, gyrA, and gyrB were 97, 98, and 98 % with K. oxytoca, and 97, 93, and 90 % with K. mobilis (=Enterobacter aerogenes), respectively. The ribotyping pattern showed a 0.46 similarity with K. oxytoca ATCC 13182^T and 0.24 with K. mobilis ATCC 13048^T. The DNA G+C content of isolate W14^T was 54.6 mol%. The DNA–DNA relatedness was 55.7 % with K. oxytoca ATCC 13182^T. Using the identification technology of MALDI-TOF mass spectrometry, the top matches for this isolate were K. oxytoca ATCC 13182^T (Match Factor Score 1.998) and K. mobilis (Score 1.797). On the basis of phenotypic, biochemical, chemotaxonomic, and molecular studies, isolate W14^T could be differentiated from other members of the genus Klebsiella including K. mobilis. Therefore, it is proposed that isolate W14^T (=ATCC BAA-2403^T=DSM 25444^T) should be classified as the type strain of a novel species of the genus Klebsiella, K. michiganensis sp. nov.     

comK prophage junction fragments as markers for Listeria monocytogenes genotypes unique to individual meat and poultry processing plants and a model for rapid niche-specific adaptation, biofilm formation, and persistence

Different strains of Listeria monocytogenes are well known to persist in individual food processing plants and to contaminate foods for many years; however, the specific genotypic and phenotypic mechanisms responsible for persistence of these unique strains remain largely unknown. Based on sequences in comK prophage junction fragments, different strains of epidemic clones (ECs), which included ECII, ECIII, and ECV, were identified and shown to be specific to individual meat and poultry processing plants. The comK prophage-containing strains showed significantly higher cell densities after incubation at 30°C for 48 h on meat and poultry food-conditioning films than did strains lacking the comK prophage (P < 0.05). Overall, the type of strain, the type of conditioning film, and the interaction between the two were all highly significant (P < 0.001). Recombination analysis indicated that the comK prophage junction fragments in these strains had evolved due to extensive recombination. Based on the results of the present study, we propose a novel model in which the concept of defective comK prophage was replaced with the rapid adaptation island (RAI). Genes within the RAI were recharacterized as "adaptons," as these genes may allow L. monocytogenes to rapidly adapt to different food processing facilities and foods. If confirmed, the model presented would help explain Listeria's rapid niche adaptation, biofilm formation, persistence, and subsequent transmission to foods. Also, comK prophage junction fragment sequences may permit accurate tracking of persistent strains back to and within individual food processing operations and thus allow the design of more effective intervention strategies to reduce contamination and enhance food safety.     

Adaptive evolution after duplication of penaeidin antimicrobial peptides

Penaeidin antimicrobial peptides in penaeid shrimps are an important component of their innate immune system that provides immunity against infection caused by several gram-positive bacteria and filamentous fungal species. Despite the knowledge on the identification and characterization of these peptides in penaeid shrimps, little is known about the evolutionary pattern of these peptides and the underlying genetic mechanisms that maintain high sequence diversities in the penaeidin gene family. Based on the phylogenetic analyses and maximum likelihood-based codon substitution analyses, here we present the convincing evidence that multiple copies of penaeidins have evolved by gene duplication, and positive Darwinian selection (adaptive evolution) is the likely cause of accelerated rate of amino acid substitutions among these duplicated genes. While the average ratio of non-synonymous to synonymous substitutions (omega) for the entire coding region of both active domains is 0.9805, few codon sites showed significantly higher omega (3.73). The likelihood ratio tests that compare models incorporating positive selection (omega>1) at certain codon sites with models not incorporating positive selection (omega<1), failed to reject (p=0) the evidence of positive Darwinian selection. The rapid adaptive evolution of this gene family might be directed by the pathogens and the faster rate of amino acid substitutions in the N-terminal proline-rich and C-terminal cysteine-rich domains could be due to their direct involvement in the protection against pathogens. When the host expose to different habitats/environment an accelerated rate of amino acid substitutions in both the active domains may also be expected.     

Ecology of aphidophagous predators in pomegranate ecosystem in India

The aphid, Aphis punicae Passerini (Homoptera : Aphididae) is a serious pest attacking pomegranate (Punica granatum L.), an important semi arid fruit crop grown widely in most parts of the country. The major predators found preying on A. punicae in pomegranate ecosystem were Cheilomenes sexmaculata (Fabricius), Scymnus sp., Pseudaspidemerus circumflexo (Motsch.), Paragus serratus (Fabricius), Ischiodon scutellaris (Fabricius) and Chrysopa sp. The population dynamics and spatial distribution of these predators in an unsprayed pomegranate ecosystem were studied at Indian Institute of Horticultural Research, Bangalore (12 degrees 58' N; 77 degrees 35'E), India during 2000-2002. The predators were found to be distributed uniformly among different tree quadrants and followed the same distributional pattern of A. punicae during their peak in January and February. The predator density was relatively higher in lower canopies than upper canopies. The spatial distribution of predators showed aggregate distribution pattern at higher mean densities and exhibited regular or under-dispersed distribution at lower mean densities. The temporal distribution of aphidophagous predators on A. punicae showed two peaks one during January - February and second during August - September The population of predators started building up along with aphid population and reached maximum at high aphid densities and declined as the prey availability declined. This indicated that predators followed the same trend of their prey, A. punicae, showing a clear numerical response.     

Positive Darwinian selection on crustacean hyperglycemic hormone (CHH) of the green shore crab, Carcinus maenas

The tissue-specific expression and differential function of the crustacean hyperglycemic hormone (CHH) in Carcinus maenas indicate an interesting evolutionary history. Previous studies have shown that CHH from the sinus gland X-organ (XO-type) has hyperglycemic activity, whereas the CHH from the pericardial organ (PO-type) neither shows hyperglycemic activity nor it inhibits Y-organ ecdysteroid synthesis. Here we examined the types of selective pressures operating on the variants of CHH in Carcinus maenas. Maximum likelihood-based codon substitution analyses revealed that the variants of this neuropeptide in C. maenas have been subjected to positive Darwinian selection indicating adaptive evolution and functional divergence among the CHH variants leading to two unique groups (PO and XO-type). Although the average ratio of nonsynonymous to synonymous substitution (omega) for the entire coding region is 0.5096, few codon sites showed significantly higher omega (10.95). Comparison of models that incorporate positive selection (omega > 1) with models not incorporating positive selection (omega <1) at certain codon sites failed to reject (p=0) evidence of positive Darwinian selection.     

Model-based characterization of ventilatory stability using spontaneous breathing

Cyclic ventilatory instabilities are widely attributed to an increase in the sensitivity or loop gain of the chemoreflex feedback loop controlling ventilation. A major limitation in the conventional characterization of this feedback loop is the need for labor-intensive methodologies. To overcome this limitation, we developed a method based on trivariate autoregressive modeling using ventilation, end-tidal Pco(2) and Po(2); this method provides for estimation of the overall "loop gain" of the respiratory control system and its components, chemoreflex gain and plant gain. Our method was applied to recordings of spontaneous breathing in 15 anesthetized, tracheostomized, newborn lambs before and after administration of domperidone (a dopamine D(2)-receptor antagonist that increases carotid body sensitivity). We quantified the known increase in hypoxic ventilatory sensitivity in response to domperidone; controller gain for O(2) increased from 0.06 (0.03, 0.09) l·min(-1)·mmHg(-1) to 0.09 (0.08, 0.13) l·min(-1)·mmHg(-1); median (interquartile-range). We also report that domperidone increased the loop gain of the control system more than twofold [0.14 (0.12, 0.22) to 0.40 (0.15, 0.57)]. We observed no significant changes in CO(2) controller gain, or plant gains for O(2) and CO(2). Furthermore, our estimate of the cycle duration of periodic breathing compared favorably with that observed experimentally [measured: 7.5 (7.2, 9.1) vs. predicted: 7.9 (7.0, 9.2) breaths]. Our results demonstrate that model-based analysis of spontaneous breathing can 1) characterize the dynamics of the respiratory control system, and 2) provide a simple tool for elucidating an individual's propensity for ventilatory instability, in turn allowing potential therapies to be directed at the underlying mechanisms.     

In vitro investigation of renal epithelial injury suggests that primary cilium length is regulated by hypoxia-inducible mechanisms

Primary cilia are non-motile sensory organelles that project from cells in many tissues. The role of renal primary cilium-based signalling in regulating epithelial cell proliferation and differentiation is highlighted by studies showing that defects of the cilium lead to epithelial de-differentiation, over proliferation and polycystic kidney disease. Recent studies show that renal primary cilia may also play a role in controlling epithelial differentiation during renal repair. After injury, renal cilium length increases dramatically and then undergoes a normalization that coincides with structural and functional repair in both human patients and mouse models of renal injury. These changes in cilium length are likely to modulate cilium-based signalling, but the injury-related factors that influence renal primary cilium length have yet to be determined. Here, we investigated the effect of three factors commonly associated with renal injury on renal cilium length in an in vitro setting. MDCK (Madin Darby canine kidney) cell cultures bearing primary cilia were treated with BSA to simulate albuminuria, cobalt chloride to simulate hypoxia and the inflammation-related cytokine tumour necrosis factor α. Primary cilium length was only increased in cultures treated with cobalt chloride. Our results suggest a role for hypoxia and the induction of HIF-1α (hypoxia-inducible factor 1α) in increasing renal primary cilium length following renal injury.     

First steps in the direction of synthetic,allosteric, direct inhibitors of thrombin and factor Xa

Designing non-saccharide functional mimics of heparin is a major challenge. In this work, a library of small, aromatic molecules based on the sulfated DHP scaffold was synthesized and screened against thrombin and factor Xa. The results reveal that (i) selected monomeric benzofuran derivatives inhibit the two enzymes, albeit weakly; (ii) the two enzymes recognize different structural features in the benzofurans studied suggesting significant selectivity of recognition; and (iii) the mechanism of inhibition is allosteric. The molecules represent the first allosteric small molecule inhibitors of the two enzymes.