In silico identification and Bayesian phylogenetic analysis of multiple new mammalian kallikrein gene families

Kallikrein gene families have been identified previously in genomes of the human, the mouse, and the rat, and individual kallikrein-like genes have been found in many more species. This study presents the in silico identification of kallikrein gene families in the recently sequenced genomes of four additional mammalian species, the chimpanzee, the dog, the pig, and the opossum. Phylogenies were constructed with gene sequences from all seven mammalian families, using Bayesian analysis, which clarified the evolutionary relationships between these genes. Individual gene sequences, as well as concatenated constructs of multiple sequences, were used. Fifteen kallikrein genes were located in the chimpanzee (Pan troglodytes) genome, while only 14 were identified in the canine (Canis familiaris) genome as no orthologue to human KLK3 was found. Thirteen genes were identified from the pig (Sus scrofa) genome, which lacked homologues to KLK2 and KLK3, and 11 genes, orthologous to human KLK5 through KLK15, were found in the opossum (Monodelphis domestica) genome. No kallikrein genes were identified from the available genome sequences of the chicken (Gallus gallus) or African clawed frog (Xenopus tropicalis). Within the family of kallikreins several subfamilies were suggested by phylogenetic analysis. One consisted of KLK4, KLK5, and KLK14; another of KLK9, KLK11, and KLK15; a third of KLK10 and KLK12; a fourth of KLK6 and KLK13; and finally one of KLK8 and the classical kallikreins (KLK1, KLK2, and KLK3).     

Effects of supercritical CO2 exposure and depressurization on immobilized lipase activity

Lipozyme IM20 from Novo Nordisk (Denmark) was examined after various treatments. Conditions were chosen to reflect those that would be considered in the design of an industrial process. A two-level factorial design was employed to assess the effects of pressurization/depressurization cycles, rate of depressurization and exposure length. A significant three-factor interaction was observed. Lowest residual activity was observed for runs in which the depressurization rate was 86–89 bar min^–1. Incubation for 12 h also yielded low residual activity but only when exposing the immobilized enzyme to one cycle. The highest residual activity was obtained for immobilized enzymes repeatedly exposed for periods of 12 h (5 times) with a depressurization rate of 4.3 to 4.45 bar min^–1. This effect may be due to the extraction of an inhibiting compound. Tuning process parameters can lead to a seven-fold change in residual activity.     

Prevalence and seasonal variations of six bee viruses in Apis mellifera L. and Varroa destructor mite populations in France

A survey of six bee viruses on a large geographic scale was undertaken by using seemingly healthy bee colonies and the PCR technique. Samples of adult bees and pupae were collected from 36 apiaries in the spring, summer, and autumn during 2002. Varroa destructor samples were collected at the end of summer following acaricide treatment. In adult bees, during the year deformed wing virus (DWV) was found at least once in 97% of the apiaries, sacbrood virus (SBV) was found in 86% of the apiaries, chronic bee paralysis virus (CBPV) was found in 28% of the apiaries, acute bee paralysis virus (ABPV) was found in 58% of the apiaries, black queen cell virus (BQCV) was found in 86% of the apiaries, and Kashmir bee virus (KBV) was found in 17% of the apiaries. For pupae, the following frequencies were obtained: DWV, 94% of the apiaries; SBV, 80% of the apiaries; CBPV, none of the apiaries; ABPV, 23% of the apiaries; BQCV, 23% of the apiaries; and KBV, 6% of the apiaries. In Varroa samples, the following four viruses were identified: DWV (100% of the apiaries), SBV (45% of the apiaries), ABPV (36% of the apiaries), and KBV (5% of the apiaries). The latter findings support the putative role of mites in transmitting these viruses. Taken together, these data indicate that bee virus infections occur persistently in bee populations despite the lack of clinical signs, suggesting that colony disease outbreaks might result from environmental factors that lead to activation of viral replication in bees.     

K2P18.1 translates T cell receptor signals into thymic regulatory T cell development

It remains largely unclear how thymocytes translate relative differences in T cell receptor (TCR) signal strength into distinct developmental programs that driv...     

Molecular characterization of the proteinase-encoding gene, prb1, related to mycoparasitism by Trichoderma harzianum

The soil fungus Trichoderma harzianum is a mycoparasitic fungus known for its use as a biocontrol agent of phytopathogenic fungi. Among other factors, Trichoderma produces a series of antibiotics and fungal cell wall-degrading enzymes. These enzymes are believed to play an important role in mycoparasitism. Among the hydrolytic enzymes, we have identified a basic proteinase (Prb1) which is induced by either autoclaved mycelia, fungal cell wall preparation or chitin; however, the induction does not occur in the presence of glucose. The proteinase was purified and biochemically characterized as a serine proteinase of 31 kDa and pl 9.2. Based on the sequence of three internal peptides, synthetic oligonudeotide probes were designed. These probes allowed subsequent isolation of a cDNA and its corresponding genomic clone. The deduced amino acid sequence indicates that the proteinase is synthesized as a pre-proenzyme and allows its classification as a serine proteinase. Northen analysis shows that the induction of this enzyme is due to an increase in the corresponding mRNA level.     

Evolutionary analysis of life span, competition, and adaptive radiation, motivated by the Pacific rockfishes (Sebastes)

The Pacific rockfishes (Sebastes spp) are remarkable for both their diversity (on the order of 100 species) and range of maximum life span ( approximately 10 years for Calico rockfish to approximately 200 years for Rougheye rockfish). We describe the natural history and patterns of diversity and life span in these species and then use independent contrasts to explore correlates of these. When phylogenetic history is taken into account, maximum life span is explained by age at maturity, size at maturity, and the interaction of these two. We introduce a life-history model that allows insight into the origin of these correlations. We then describe a variety of mechanisms that may increase lifepans and diversity. These include fluctuating environments (in which organisms basically have to "wait out" bad periods to reproduce successfully), diversity, and longevity inspired by interspecific competition and physiological complexity in growth and accumulation of cellular damage. All of the results point toward the importance of flat or "indifferent" fitness surfaces as a key element in the evolution of diversity. We conclude that further development of the theory of flat or indifferent fitness surfaces as applied to diversity and life span is clearly warranted.     

Comparison of Models Describing Light Dependence of N2 Fixation in Heterocystous Cyanobacteria

The abilities of four models to describe nitrogenase light-response curves were compared, using the heterocystous cyanobacterium Nodularia spumigena and a cyanobacterial bloom from the Baltic Sea as examples. All tested models gave a good fit of the data, and the rectangular hyperbola model is recommended for fitting nitrogenase-light response curves. This model describes an enzymatic process, while the others are empirical. It was possible to convert the process parameters between the four models and compare N₂ fixation with photosynthesis. The physiological meanings of the process parameters are discussed and compared to those of photosynthesis.     

Relationship of chronotype to sleep, light exposure, and work-related fatigue in student workers

Students who work during the school year face the potential of sleep deprivation and its effects, since they have to juggle between school and work responsibilities along with social life. This may leave them with less time left for sleep than their nonworking counterparts. Chronotype is a factor that may exert an influence on the sleep of student workers. Also, light and social zeitgebers may have an impact on the sleep-related problems of this population. This study aimed to document sleep, light exposure patterns, social rhythms, and work-related fatigue of student workers aged 19-21 yrs and explore possible associations with chronotype. A total of 88 student workers (mean ± SD: 20.18 ± .44 yrs of age; 36 males/52 females) wore an actigraph (Actiwatch-L; Mini-Mitter/Respironics,Bend, OR) and filled out the Social Rhythm Metric for two consecutive weeks during the school year. Also, they completed the Morningness-Eveningness Questionnaire (MEQ), Epworth Sleepiness Scale (ESS), Pittsburgh Sleep Quality Index (PSQI), and Occupational Fatigue Exhaustion/Recovery Scale (OFER). Repeated and one-way analyses of variance (ANOVAs), Pearson's chi-square tests, and correlation coefficients were used for statistical comparisons. Subjects slept an average of 06:28 h/night. Actigraphic sleep parameters, such as sleep duration, sleep efficiency, wake after sleep onset, and sleep latency, did not differ between chronotypes. Results also show that evening types (n = 17) presented lower subjective sleep quality than intermediate types (n = 58) and morning types (n = 13). Moreover, evening types reported higher levels of chronic work-related fatigue, exhibited less regular social rhythms, and were exposed to lower levels of light during their waking hours (between 2 and 11 h after wake time) as compared to intermediate types and morning types. In addition, exposure to light intensities between 100 and 500 lux was lower in evening types than in intermediate types and morning types. However, bright light exposure (≥ 1000 lux) did not differ between chronotypes. In conclusion, results suggest that student workers may constitute a high-risk population for sleep deprivation. Evening types seemed to cope less well with sleep deprivation, reporting poorer sleep quality and higher levels of work-related fatigue than intermediate types and morning types. The higher chronic work-related fatigue of evening types may be linked to their attenuated level of light exposure and weaker social zeitgebers. These results add credence to the hypothesis that eveningness entails a higher risk of health-impairing behaviors.     

The Arabidopsis METACASPASE9 Degradome

Metacaspases are distant relatives of the metazoan caspases, found in plants, fungi, and protists. However, in contrast with caspases, information about the physiological substrates of metacaspases is still scarce. By means of N-terminal combined fractional diagonal chromatography, the physiological substrates of METACASPASE9 (MC9; AT5G04200) were identified in young seedlings of Arabidopsis thaliana on the proteome-wide level, providing additional insight into MC9 cleavage specificity and revealing a previously unknown preference for acidic residues at the substrate prime site position P1′. The functionalities of the identified MC9 substrates hinted at metacaspase functions other than those related to cell death. These results allowed us to resolve the substrate specificity of MC9 in more detail and indicated that the activity of phosphoenolpyruvate carboxykinase 1 (AT4G37870), a key enzyme in gluconeogenesis, is enhanced upon MC9-dependent proteolysis.