The shape of the spatial kernel and its implications for biological invasions in patchy environments

Ecological and epidemiological invasions occur in a spatial context. We investigated how these processes correlate to the distance dependence of spread or dispersal between spatial entities such as habitat patches or epidemiological units. Distance dependence is described by a spatial kernel, characterized by its shape (kurtosis) and width (variance). We also developed a novel method to analyse and generate point-pattern landscapes based on spectral representation. This involves two measures: continuity, which is related to autocorrelation and contrast, which refers to variation in patch density. We also analysed some empirical data where our results are expected to have implications, namely distributions of trees (Quercus and Ulmus) and farms in Sweden. Through a simulation study, we found that kernel shape was not important for predicting the invasion speed in randomly distributed patches. However, the shape may be essential when the distribution of patches deviates from randomness, particularly when the contrast is high. We conclude that the speed of invasions depends on the spatial context and the effect of the spatial kernel is intertwined with the spatial structure. This implies substantial demands on the empirical data, because it requires knowledge of shape and width of the spatial kernel, and spatial structure.     

Asymmetric synthesis of d-glyceric acid by an alditol oxidase and directed evolution for enhanced oxidative activity towards glycerol

Glycerol as a by-product of biodiesel production is an attractive precursor for producing d-glyceric acid. Here, we demonstrate the successful production of d-glyceric acid based on glycerol via glyceraldehyde in a two-step enzyme reaction with the FAD-dependent alditol oxidase from Streptomyces coelicolor A3(2). The hydrogen peroxide generated in the reaction can be used in detergent, food, and paper industry. In order to apply the alditol oxidase in industry, the enzyme was subjected to protein engineering. Different strategies were used to enhance the substrate specificity towards glycerol. Initial attempts based on rational protein design in the active site region were found unsuccessful to increase activity. However, through directed evolution, an alditol oxidase double mutant (V125M/A244T) with 1.5-fold improved activity for glycerol was found by screening 8,000 clones. Further improvement of activity was achieved by combinatorial experiments, which led to a quadruple mutant (V125M/A244T/V133M/G399R) with 2.4-fold higher specific activity towards glycerol compared to the wild-type enzyme. Through studying the effects of mutations created, we were able to understand the importance of certain amino acids in the structure of alditol oxidase, not only for conferring enzymatic structural stability but also with respect to their influence on oxidative activity.     

Helicobacter pylori AddAB helicase-nuclease and RecA promote recombination-related DNA repair and survival during stomach colonization

Helicobacter pylori colonization of the human stomach is characterized by profound disease-causing inflammation. Bacterial proteins that detoxify reactive oxygen species or recognize damaged DNA adducts promote infection, suggesting that H. pylori requires DNA damage repair for successful in vivo colonization. The molecular mechanisms of repair remain unknown. We identified homologues of the AddAB class of helicase-nuclease enzymes, related to the Escherichia coli RecBCD enzyme, which, with RecA, is required for repair of DNA breaks and homologous recombination. H. pylori mutants lacking addA or addB genes lack detectable ATP-dependent nuclease activity, and the cloned H. pylori addAB genes restore both nuclease and helicase activities to an E. coli recBCD deletion mutant. H. pylori addAB and recA mutants have a reduced capacity for stomach colonization. These mutants are sensitive to DNA damaging agents and have reduced frequencies of apparent gene conversion between homologous genes encoding outer membrane proteins. Our results reveal requirements for double-strand break repair and recombination during both acute and chronic phases of H. pylori stomach infection.     

Tumor necrosis factor-alpha-converting enzyme (TACE/ADAM-17) mediates the ectodomain cleavage of intercellular adhesion molecule-1 (ICAM-1)

Ectodomain shedding has emerged as an important regulatory step in the function of transmembrane proteins. Intercellular adhesion molecule-1 (ICAM-1), an adhesion receptor that mediates inflammatory and immune responses, undergoes shedding in the presence of inflammatory mediators and phorbol 12-myristate 13-acetate (PMA). The shedding of ICAM-1 in ICAM-1-transfected 293 cells upon PMA stimulation and in endothelial cells upon tumor necrosis factor-alpha stimulation was blocked by metalloproteinase inhibitors, whereas serine protease inhibitors were ineffective. p-Aminophenylmercuric acetate, a mercuric compound that is known to activate matrix metalloproteinases, up-regulated ICAM-1 shedding. TIMP-3 (but not TIMP-1 or -2) effectively blocked cleavage. This profile suggests the involvement of the ADAM family of proteases in the cleavage of ICAM-1. The introduction of enzymatically active tumor necrosis factor-alpha-converting enzyme (TACE) into ICAM-1-expressing cells up-regulated cleavage. Small interfering RNA directed against TACE blocked ICAM-1 cleavage. ICAM-1 transfected into TACE-/- fibroblasts did not show increased shedding over constitutive levels in the presence of PMA, whereas cleavage did occur in ICAM-1-transfected TACE+/+ cells. These results indicate that ICAM-1 shedding is mediated by TACE. Blocking the shedding of ICAM-1 altered the cell adhesive function, as ICAM-1-mediated cell adhesion was up-regulated in the presence of TACE small interfering RNA and TIMP-3, but not TIMP-1. However, cleavage was found to occur at multiple sites within the stalk domain of ICAM-1, and numerous point mutations within the region did not affect cleavage, indicating that TACE-mediated cleavage of ICAM-1 may not be sequence-specific.     

Relationship between mercury concentration in blood, cognitive performance, and blood pressure, in an elderly urban population

Concentration of mercury (Hg) in whole blood in an elderly urban population with a mean age of 87 years was studied in relation to cognitive function, arterial blood pressure (arterial BP), age, gender, body mass index (BMI) and smoking habits. This population-based study consisted of 106 subjects both males and females. Clinical assessment of the subjects included medical and social history, physical and neurologic examination and assessment of cognitive functions with Mini-Mental State Examination (MMSE). Information on use of all potentially anti-hypertensive drugs was collected. Whole blood from 106 subjects were collected and analysed for mercury by Cold Vapour Atomic Absorption Spectrometry (Milton Ray ASS-CV) with Seronorm Trace Element as matrix matched quality control. Males and females did not differ in blood-mercury (B-Hg) concentrations or in any of the other studied variables. B-Hg concentrations did not differ between smokers and non-smokers. Females were treated more often than males with antihypertensive drugs. There was no relation found between B-Hg concentration and cognitive function, arterial BP, age, gender or BMI. In conclusion, no relations were found between B-Hg concentrations and the studied variables.     

Residual Viral Replication during Antiretroviral Therapy Boosts Human Immunodeficiency Virus Type 1-Specific CD8+ T-Cell Responses in Subjects Treated Early after Infection

Human immunodeficiency virus type 1 (HIV-1)-infected subjects treated early after infection have preserved HIV-1-specific CD4+ T-cell function. We studied the effect of highly active antiretroviral therapy (HAART) on the frequency of HIV-1-specific CD8+ T cells in patients treated during early (n = 31) or chronic (n = 23) infection. The degree of viral suppression and time of initiation of treatment influenced the magnitude of the CD8+ T-cell response. HIV-1-specific CD8+ T cells can increase in number after HAART in subjects treated early after infection who have episodes of transient viremia.     

Autonomic control of the heart in the Asian swamp eel (Monopterus albus)

The Asian swamp eel (Monopterus albus) is an air-breathing teleost with very reduced gills that uses the buccal cavity for air-breathing. Here we characterise the cardiovascular changes associated with the intermittent breathing pattern in M. albus and we study the autonomic control of the heart during water- and air-breathing. The shift from water- to air-breathing was associated with a rise in heart rate from 27.7 ± 1.6 to 41.4 ± 2.6 min(-1) and an increase in cardiac output from 23.1 ± 3.0 to 58.7 ± 6.5 mLmin(-1)kg(-1), while mean systemic blood pressure did not change (39.0 ± 3.5 and 46.4 ± 1.3 cmH(2)O). The autonomic control of the heart during water- and air-breathing was revealed by infusion of the β-adrenergic antagonist propranolol and muscarinic antagonist atropine (3 mgkg(-1)) in eels instrumented with an arterial catheter. Inhibition of the sympathetic and parasympathetic innervations of the heart revealed a strong vagal tone on the heart of water-breathing eels and that the tachycardia during air-breathing is primarily mediated by withdrawal of cholinergic tone.     

Regulation of Helicobacter pylori adherence by gene conversion

Genetic diversification of Helicobacter pylori adhesin genes may allow adaptation of adherence properties to facilitate persistence despite host defences. The sabA gene encodes an adhesin that binds sialyl‐Lewis antigens on inflamed gastric tissue. We found variability in the copy number and locus of the sabA gene and the closely related sabB and omp27 genes due to gene conversion among 51 North American paediatric H. pylori strains. We determined that sabB to sabA gene conversion is predominantly the result of intra‐genomic recombination and RecA, RecG and AddA influence the rate at which it occurs. Although all clinical strains had at least one sabA gene copy, sabA and sabB were lost due to gene conversion at similar rates in vitro, suggesting host selection to maintain the sabA gene. sabA gene duplication resulted in increased SabA protein production and increased adherence to sialyl‐Lewis antigens and mouse gastric tissue. In conclusion, gene conversion is a mechanism for H. pylori to regulate sabA expression level and adherence.     

Validity and reliability of the Slovene version of the Morningness-Eveningness Questionnaire

ABSTRACT

Morningness-eveningness (ME) can be defined as individual differences in sleep-wake patterns, and the time of day people feel and perform best. Various self-report instruments that measure ME have been developed. The Horne and Östberg Morningness-Eveningness Questionnaire (MEQ) has most frequently been used for classifying ME types. The aim of this study was to investigate the validity and reliability of the Slovene version of the MEQ (Slovene MEQ). Two hundred and sixty-five participants (65.3% women, 34,7% men, mean age 38,1 years, range 19–67) took the Slovene MEQ twice, 2 weeks apart (MEQ test and retest). Internal consistency of the Slovene MEQ items was high, with Cronbach’s Alpha coefficients of 0.86. The test–retest reliability was also high, with intraclass correlation coefficient (ICC) of 0.96. The classification of chronotypes on middle-aged population offered a more balanced representation of the five chronotypes than those proposed by the authors Horne and Östberg . Age changes in chronotype could be confirmed in this study in the supposed direction with older adults being more morning-oriented. The criterion validity of the Slovene MEQ through the relationship of morningness and basic personality traits showed that conscientiousness and agreeableness demonstrated positive and significant correlations with morningness. A low negative correlation was observed between openness and morningness, with higher eveningness among more open participants.