Geographical variation in circadian eclosion rhythm and photoperiodic adult diapause inDrosophila littoralis

Summary The time measuring system ofDrosophila littoralis strains originating between 40–70° N was found to be highly variable and latitude dependent. The critical daylength for photoperiodic adult diapause varied from 12 h or no diapause response in the south to 20 h in north. The median timing of pupal eclosion rhythm varied correspondingly from 21 h to 12 h from lights off in LD 321, and the period of free-running rhythm of eclosion from 24 h to 19 h. The phase of the free-running rhythm was also variable, and correlated with the phase of the entrained rhythm. Latitudinal variation in the entrained rhythm of eclosion and in diapause is adaptive, leading to eclosion early in the morning and to overwintering at the adult stage. In some strains with a late phase of eclosion, strong transient cycles were seen following the transition from LL to DD. A total damping of the free-running eclosion rhythm within 2–7 days was common to all strains. This damping was more pronounced in the northern strains. The phase and period of eclosion rhythms were statistically independent. Diapause was not correlated with any parameters of the eclosion rhythm in the analysis. Diapause may still be influenced by the period of the eclosion rhythm, even though its minor contribution may be masked by a more variable, eclosion rhythm independent system in the determination of diapause.Abbreviations, symbols and terms LD Light/dark; as in LD 321 meaning a cycle of 3 h light21 h darkness - LL Continuous light - DD Continuous darkness - T Period of a Zeitgeber cycle - Natural period of eclosion rhythm in constant conditions - _EL Phase of the free-running rhythm of eclosion - A Amplitude of the free-running rhythm of eclosion; possible range is from 4.17% (no rhythmicity) to 20% (the daily eclosion peaks 2–6 within 5 h each) - P Persistence of the free-running rhythm of eclosion; the number of daily eclosion peaks where the mean for five highest hourly percentages still exceed 6% - A phase shift, expressed in h; a re-setting of a rhythm; either as an advance shift (i.e. earlier= +), or as a delay shift (i.e. later = –) - PRC Phase-response curve - _LD Phase of entrained rhythm of eclosion; e.g. _{LD 321} is the median hour of eclosion peak from lights off at LD 321 - SD _ecl Amplitude of the entrained rhythm of eclosion; the smaller SD_ecl the higher the amplitude - PPRC Photoperiodic response curve; proportion of females in diapause displayed as a function of daylength - CDL Critical photoperiod; the photoperiod in the 24 h LD cycle at which 50% of the population studied diapauses - SD _diap Accuracy of diapause response of a strain; the smaller the SD_diap the more accurate the response - Cdl The main locus controlling CDL inD. littoralis     

Penicillium subrubescens, a new species efficiently producing inulinase

Inulin is a reserve carbohydrate in about 15 % of the flowering plants and is accumulated in underground tubers of e.g. chicory, dahlia and Jerusalem artichoke. This carbohydrate consists of linear chains of β-(2,1)-linked fructose attached to a sucrose molecule. Inulinases hydrolyse inulin into fructose and glucose. To find efficient inulin degrading fungi, 126 fungal strains from the Fungal Biotechnology Culture Collection (FBCC) at University of Helsinki and 74 freshly isolated strains from soil around Jerusalem artichoke tubers were screened in liquid cultures with inulin as a sole source of carbon or ground Jerusalem artichoke tubers, which contains up to 19 % (fresh weight) inulin. Inulinase and invertase activities were assayed by the dinitrosalicylic acid (DNS) method and a freshly isolated Penicillium strain originating from agricultural soil (FBCC 1632) was the most efficient inulinase producer. When it was cultivated at pH 6 and 28 °C in 2 litre bioreactors using inulin and Jerusalem artichoke as a carbon source, inulinase and invertase activities were on day 4 7.7 and 3.1 U mL^?1, respectively. The released sugars analysed by TLC and HPLC showed that considerable amounts of fructose were released while the levels of oligofructans were low, indicating an exoinulinase type of activity. Taxonomic study of the inulinase producing strain showed that this isolate represents a new species belonging in Penicillium section Lanata-divaricata. This new species produces a unique combination of extrolites and is phenotypically and phylogenetically closely related to Penicillium pulvillorum. We propose the name Penicillium subrubescens sp. nov. (CBS 132785^T = FBCC 1632^T) for this new species.     

STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes

Background  

The integration of many aspects of protein/DNA structure analysis is an important requirement for software products in general area of structural bioinformatics. In fact, there are too few software packages on the internet which can be described as successful in this respect. We might say that what is still missing is publicly available, web based software for interactive analysis of the sequence/structure/function of proteins and their complexes with DNA and ligands. Some of existing software packages do have certain level of integration and do offer analysis of several structure related parameters, however not to the extent generally demanded by a user.     

CMPF Does Not Associate with Impaired Glucose Metabolism in Individuals with Features of Metabolic Syndrome

Objective

3-carboxy-4-methyl-5-propyl-2-furanpropanoic acid (CMPF) is a metabolite produced endogenously from dietary sources of furan fatty acids. The richest source of furan fatty acids in human diet is fish. CMPF was recently shown to be elevated in fasting plasma in individuals with gestational diabetes and type 2 diabetes, and mechanistically high level of CMPF was linked to β cell dysfunction. Here we aimed to study the association between plasma CMPF level and glucose metabolism in persons with impaired glucose metabolism.

Methods

Plasma CMPF concentration was measured from plasma samples of the study participants in an earlier controlled dietary intervention. All of them had impaired glucose metabolism and two other characteristics of the metabolic syndrome. Altogether 106 men and women were randomized into three groups for 12 weeks with different fish consumption (either three fatty fish meals per week, habitual fish consumption or maximum of one fish meal per week). Associations between concentration of CMPF and various glucose metabolism parameters at an oral glucose tolerance test at baseline and at the end of the study were studied.

Results

Fasting plasma CMPF concentration was significantly increased after a 12-week consumption of fatty fish three times per week, but the concentration remained much lower compared to concentrations reported in diabetic patients. Increases of plasma CMPF concentrations mostly due to increased fish consumption were not associated with impaired glucose metabolism in this study. Instead, elevated plasma CMPF concentration was associated with decreased 2-hour insulin concentration in OGTT.

Conclusions

Moderately elevated concentration of CMPF in plasma resulting from increased intake of fish is not harmful to glucose metabolism. Further studies are needed to fully explore the role of CMPF in the pathogenesis of impaired glucose metabolism.

Trial Registration

ClinicalTrials.gov NCT00573781     

Genome-scale metabolic reconstruction and <Emphasis Type="Italic">in silico</Emphasis> analysis of methylotrophic yeast <Emphasis Type="Italic">Pichia pastoris</Emphasis> for strain improvement

Background  

Pichia pastoris has been recognized as an effective host for recombinant protein production. A number of studies have been reported for improving this expression system. However, its physiology and cellular metabolism still remained largely uncharacterized. Thus, it is highly desirable to establish a systems biotechnological framework, in which a comprehensive in silico model of P. pastoris can be employed together with high throughput experimental data analysis, for better understanding of the methylotrophic yeast's metabolism.     

Delayed stigma receptivity in Collinsia heterophylla (Plantaginaceae): genetic variation and adaptive significance in relation to pollen competition, delayed self-pollination, and mating-system evolution

To increase our knowledge about mating-system evolution, we need to understand the relationship between specific floral traits and mating system. Species of Collinsia (Plantaginaceae) vary extensively in mating system; this variation is associated with variation in floral morphology and development and with the timing of self-pollination. Counterintuitively, large-flowered, more outcrossing species tend to have delayed stigma receptivity, reducing the amount of time that the stigma is receptive to cross-pollination before autonomous self-pollination. To understand how the timing of stigma receptivity is related to mating-system evolution, we studied in detail the timing of both stigma receptivity and self-pollination (anther-stigma contact) in two greenhouse-grown populations of large-flowered Collinsia heterophylla. Crosses on emasculated flowers at different stages of floral development always produced seeds, suggesting that cross-fertilization can be effected by pollen arriving prior to physiological receptivity. Phenotypic and genetic variation within populations in the timing of stigma receptivity and anther-stigma contact was substantial, although slightly less for the contact. Despite strong interspecific and interpopulation correlations, we did not find an among-genet phenotypic correlation between the traits. This indicates that each trait may respond independently to selection, and the trait association may be the result of correlational selection.     

Spatial distribution and hatching of overwintered eggs of a fish ectoparasite, Argulus coregoni (Crustacea: Branchiura).

The habitat distribution of overwintered eggs, which were found to be the only source of spring recruitment of Argulus coregoni Thorell, was studied at a commercial fish farm in Central Finland. The frequency of occurrence of egg clutches in the deep parts of the canals and ponds was 50 to 80% and the percentage cover of the surface of stones with egg clutches was 1.7 to 6.4%, while in the shallow parts these values were 8 to 27% and 0.1 to 0.3%, respectively. A greater proportion of empty egg-shells was observed in shallow water in the mid-May, suggesting an earlier hatching there stimulated by the increased temperature and higher illumination. Under laboratory conditions, only elevated UV illumination, but not diurnally fluctuating temperature, significantly accelerated hatching. Normally overwintered eggs produced a pronounced peak of hatched larvae at the end of May and hatching continued at a much slower rate throughout the summer. Eggs that overwintered twice, first normally and then for a second time buried under sediments, were exposed to the same laboratory conditions simultaneously with normally overwintered eggs, but their hatching was delayed until August. The hatching rate was low, but markedly increased in December.     

Characterization of collagenous peptides bound to lysyl hydroxylase isoforms

Lysyl hydroxylase (LH, EC 1.14.11.4) is the enzyme catalyzing the formation of hydroxylysyl residues in collagens and other proteins with collagenous domains. Although lower species, such as Caenorhabditis elegans, have only one LH orthologue, LH activity in higher species, such as human, rat, and mouse, is present in three molecules, LH1, LH2, and LH3, encoded by three different genes. In addition, LH2 is present in two alternatively spliced forms (LH2a, LH2b). To understand the functions of the four molecular forms of LH in vertebrates, we analyzed differences in the binding and hydroxylation of various collagenous peptides by the LH isoforms. Nine-amino acid-long synthetic peptides on Pepspot were used for the binding analysis and an activity assay to measure hydroxylation. Our data with 727 collagenous peptides indicated that a positive charge on the peptide and specific amino acid residues in close proximity to the lysyl residues in the collagenous sequences are the key factors promoting peptide binding to the LH isoforms. The data suggest that the LH binding site is not a deep hydrophobic pocket but is open and hydrophilic where acidic amino acids play an important role in the binding. The data do not indicate strict sequence specificity for the LH isoforms, but the data indicated that there was a clear preference for some sequences to be bound and hydroxylated by a certain isoform.     

Characterization of recombinant amino-terminal NC4 domain of human collagen IX: interaction with glycosaminoglycans and cartilage oligomeric matrix protein

The N-terminal NC4 domain of collagen IX is a globular structure projecting away from the surface of the cartilage collagen fibril. Several interactions have been suggested for this domain, reflecting its location and its characteristic high isoelectric point. In an attempt to characterize the NC4 domain in more detail, we set up a prokaryotic expression system to produce the domain. The purified 27.5-kDa product was analyzed for its glycosaminoglycan-binding potential by surface plasmon resonance and solid-state assays. The results show that the NC4 domain of collagen IX specifically binds heparin with a K(d) of 0.6 microm, and the full-length recombinant collagen IX has an even stronger interaction with heparin, with an apparent K(d) of 3.6 nm. The heparin-binding site of the NC4 domain was located in the extreme N terminus, containing a heparin-binding consensus sequence, whereas electron microscopy suggested the presence of at least three additional heparin-binding sites on full-length collagen IX. The NC4 domain was also shown to bind cartilage oligomeric matrix protein. This interaction and the association of cartilage oligomeric matrix protein with other regions of collagen IX were found to be heparin-competitive. Circular dichroism analyses of the NC4 domain indicated the presence of stabilizing disulfide bonds and a thermal denaturation point of about 80 degrees C. The pattern of disulfide bond formation within the NC4 domain was identified by tryptic peptide mass mapping of the NC4 in native and reduced states. A similar pattern was demonstrated for the NC4 domain of full-length recombinant collagen IX.