In silico evolutionary analysis of Helicobacter pylori outer membrane phospholipase A (OMPLA)

ABSTRACT: BACKGROUND: In the past decade, researchers have proposed that the pldA gene for outer membrane phospholipase A (OMPLA) is important for bacterial colonization of the human gastric ventricle. Several conserved Helicobacter pylori genes have distinct genotypes in different parts of the world, biogeographic patterns that can be analyzed through phylogenetic trees. The current study will shed light on the importance of the pldA gene in H. pylori. In silico sequence analysis will be used to investigate whether the bacteria are in the process of preserving, optimizing, or rejecting the pldA gene. The pldA gene will be phylogenetically compared to other housekeeping (HK) gene, and a possible origin via horizontal gene transfer (HGT) will be evaluated through both at intra- and inter-species evolutionary analyses. RESULTS: In this study, pldA gene sequences were phylogenetically analyzed and compared with a large reference set of concatenated HK gene sequences. A total of 246 pldA nucleotide sequences were used; 207 were from Norwegian isolates, 20 were from Korean isolates, and 19 were from the NCBI database. Best-fit evolutionary models were determined with MEGA5 ModelTest for the pldA (K80 + I + G) and HK (GTR + I + G) sequences, and maximum likelihood trees were constructed. Both HK and pldA genes showed biogeographic clustering. Horizontal gene transfer was inferred based on significantly different GC contents, the codon adaptation index, and a phylogenetic conflict between a tree of OMPLA protein sequences representing 171 species and a tree of the AtpA HK protein for 169 species. Although a vast majority of the residues in OMPLA were predicted to be under purifying selection, sites undergoing positive selection were also found. CONCLUSIONS: Our findings indicate that the pldA gene could have been more recently acquired than seven of the HK genes found in H. pylori. However, the common biogeographic patterns of both the HK and pldA sequences indicated that the transfer occurred long ago. Our results indicate that the bacterium is preserving the function of OMPLA, although some sites are still being evolutionarily optimized.     

Dephosphorylation of cardiac proteins in vitro - a matter of phosphatase specificity

Protein phosphorylation is reversibly regulated by the interplay between kinases and phosphatases. Recent developments within the field of proteomics have revealed the extent of this modification in nature. To date there is still a lack of information about phosphatase specificity for different proteomes and their conditions to achieve maximum enzyme activity. This information is important per se, and in addition often requested in functional and biochemical in vitro studies, where a dephosphorylated sample is needed as a negative control to define baseline conditions. In this study, we have addressed the effectiveness of two phosphatases endogenously present in the heart (protein phosphatases 1 and 2A) and two generic phosphatases (alkaline phosphatase and lambda protein phosphatase) on three cardiac subproteomes known to be regulated by phosphorylation. We optimized the dephoshorylating conditions on a cardiac tissue fraction comprising cytosolic and myofilament proteins using 2DE and MS. The two most efficient conditions were further investigated on a mitochondrial-enriched fraction. Dephosphorylation of specific proteins depends on the phosphatase, its concentration, as well as sample preparation including buffer composition. Finally, we analyzed the efficiency of alkaline phosphatase, the phosphatase with the broadest substrate specificity, using TiO(2) peptide enrichment and 2DLC-MS/MS. Under these conditions, 95% of the detected cardiac cytoplasmic-enriched phospho-proteome was dephosphorylated. In summary, targeting dephosphorylation of the cardiac muscle subproteomes or a specific protein will drive the selection of the specific phosphatase, and each requires different conditions for optimal performance.     

Early Environmental Influences on Growth of Arcto-Norwegian Cod, Gadus Morhua, From The 0-group To Adults

A high growth rate for Arcto-Norwegian cod, Gadus morhua, in the Barents Sea and adjacent areas from the larva period to the 0-group enhances survival and ultimately recruitment to the fishery. However, it appeared that high growth rates for a cohort through the 0-group were not continued as the cohort ages. Based on survey data, there was a significant negative correlation between the average length at the 0-group and its average length at ages 2 through 8. We provided evidence suggesting that this phenomenon was caused by the inter-annual variability in inflow of warm, prey-rich Atlantic water into the Barents Sea from the Norwegian Sea. Enhanced inflow provided favorable conditions for cod growth during the larva and juvenile pelagic intervals. However, this same strong inflow carried a proportion of the cohort farther to the east in the Barents Sea, where the bottom water is colder than in the west. The colder conditions experienced by such cohorts, as compared to cohorts that have a more westerly settlement, led to slower growth prior to age 2. Slow growth during this interval appeared to be the reason for these cohorts' relatively smaller mean length at older ages.     

Mice carrying a conditional Serca2 allele for the generation of Ca handling-deficient mouse models

Sarco(endo)plasmic reticulum calcium ATPases (SERCA) are cellular pumps that transport Ca²⁺ into the sarcoplasmic reticulum (SR). Serca2 is the most widely expressed gene family member. The very early embryonic lethality of Serca2^null mouse embryos has precluded further evaluation of loss of Serca2 function in the context of organ physiology. We have generated mice carrying a conditional Serca2^flox allele which allows disruption of the Serca2 gene in an organ-specific and/or inducible manner. The model was tested by mating Serca2^flox mice with MLC-2v^wt/Cre mice and with αMHC-Cre transgenic mice. In heterozygous Serca2^wt/floxMLC-2v^wt/Cre mice, the expression of SERCA2a and SERCA2b proteins were reduced in the heart and slow skeletal muscle, in accordance with the expression pattern of the MLC-2v gene. In Serca2^flox/flox Tg(αMHC-Cre) embryos with early homozygous cardiac Serca2 disruption, normal embryonic development and yolk sac circulation was maintained up to at least embryonic stage E10.5. The Serca2^flox mouse is the first murine conditional gene disruption model for the SERCA family of Ca²⁺ ATPases, and should be a powerful tool for investigating specific physiological roles of SERCA2 function in a range of tissues and organs in vivo both in adult and embryonic stages.     

Incubation Behaviour in Northern Lapwings: Nocturnal Nest Attentiveness and Possible Importance of Individual Breeding Quality

Previous studies of sex roles in the polygynous Northern Lapwing Vanellus vanellus have shown that males incubate less than females, perhaps suggesting that sexual selection is important in shaping the parental behaviour of this species. The purpose of this study was to (1) examine for the first time the possibility that males compensate for low diurnal nest attentiveness by increasing their nocturnal assistance and (2) evaluate the hypotheses that sexual selection and individual breeding quality determines incubation behaviour in lapwings. Males were never found incubating at night in 19 nests, although median diurnal male attentiveness was 15.3% in 16 of the same pairs. Nor were there any differences among monogamous and polygynous males in the time spent in four categories of behaviour (incubation, guarding, maintenance and mating activities). The time males spent in mating and incubation behaviours was weakly negatively correlated, and the time spent incubating varied considerably among males (0–74%). Further, female body condition was positively related with male nest attentiveness and there was a negative relationship between nest attentiveness and date of arrival to the study area in monogamous, but not in polygynous, males. We argue that sexual selection could not alone explain all sides of Northern Lapwing incubation, and suggest that individual differences in breeding quality may also be important.     

Early onset of reproductive senescence in domestic sheep Ovis aries

A central theme in life history theory is to determine how reproduction varies with age in iteroparous organisms. Evidence of ageing and senescence, defined as the progressive loss of function accompanied by decreased performance with age, remains poorly documented for large herbivores, in particular as it relates to reproduction. Analyses of body weight of 87 532 domestic sheep lambs demonstrates that onset of reproductive senescence in ewes occurs already at 5 and 6 years of age when measured, respectively, as lamb weight and litter size produced. This provides convincing evidence of early onset of reproductive senescence in this highly domesticated sheep breed. As this is earlier than indicated for other Ovis species as well as for the Soay sheep, an ancient and lightly domesticated sheep, we hypothesize that there may be a cost of selection for large litter size in mammalian herbivores.     

Body mass regulation during incubation in female common eiders Somateria mollissima

We investigated changes in incubation behaviour induced by body fuel depletion in incubating female common eiders, which, in contrast to pelagic seabirds, fast despite being close to marine food sources. In the Svalbard Archipelago, electronic scales were placed under eider nests and the incubation of six birds was prolonged by using wax-filled eggs. Based on changes in the rate of body mass loss in normally incubating females and in ten captive birds that did not incubate, body reserves neared depletion on average four days after hatching. During prolonged incubation, females took more frequent and longer recesses. Nest attentiveness consequently decreased, but was still high. In contrast to recesses during normal incubation, during which body mass of the birds decreased, mass remained constant during the recesses of prolonged incubation. The body stores of female eiders seemed to enable them to complete incubation with a limited safety margin. A further drop in body mass is avoided when a critical body mass is reached, because birds then start feeding enough to maintain mass while continuing incubation. Presumably, a similar mechanism will enable eiders to continue incubation when body reserves are prematurely depleted before hatching.     

Verrucophora farcimen gen. et sp. nov. (Dictyochophyceae,Heterokonta)—a bloom‐forming ichthyotoxic flagellate from the Skagerrak,Norway1

Since 1998, a heterokont flagellate initially named Chattonella aff. verruculosa has formed recurrent extensive blooms in the North Sea and the Skagerrak, causing fish mortalities. Cells were isolated from the 2001 bloom off the south coast of Norway, and monoalgal cultures were established and compared with the Chattonella verruculosa Y. Hara et Chihara reference strain NIES 670 from Japan. The cells in Norwegian cultured isolates were very variable in size and form, being large oblong (up to 34 μm long) to small rounded (5–9 μm in diameter) with two unequal flagella, numerous chloroplasts, and mucocysts. The SSU and partial LSU rDNA sequences of strains from Norway and Japan were compared and differed by 0.4% (SSU) and 1.3% (LSU), respectively. Five strains from Norway were identical in the LSU rDNA region. Phylogenetic analyses based on heterokont SSU and concatenated SSU + LSU rDNA sequences placed C. aff. verruculosa and the Japanese C. verruculosa within the clade of Dictyochophyceae, with the picoflagellate Florenciella parvula Eikrem as the closest relative. Ultrastructure, morphology, and pigment composition supported this affinity. We propose the name Verrucophora farcimen sp. et gen. nov. for this flagellate and systematically place it within the class Dictyochophyceae. Our studies also show that C. verruculosa from Japan is genetically and morphologically different but closely related to V. farcimen. The species is transferred from the class Raphidophyceae to the class Dictyochophyceae and renamed Verrucophora verruculosa. We propose a new order, Florenciellales, to accommodate V. farcimen, V. verruculosa, and F. parvula.