Systematic error is of minor importance to feedback structure estimates derived from time series of nonlinear population indices

Most modern population dynamics analyses of time series use simple population indices for ecological inference. These indices, collected for many years for various agricultural pests or game animals, are generally believed not to distort systematically feedback estimates because the assumption of linearity to population size roughly holds. To assess the relative importance of this assumption, we examined the effect of nonlinearity in a burrow index for voles on feedback estimates obtained through autoregressive modeling. We show that the issue of linearity is of less importance to ecological inference because the feedback estimates are routinely obtained on a logarithmic scale. Transforming data to logs has a strong linearization effect, removing most of the nonlinearity observed on the original scale. We conclude that the statistical tools for ecological inference, such as autoregressive log-linear models, are sufficiently robust to the systematic error imposed by index nonlinearity and that indices are valuable sources of ecological information even in situations when the assumed linear functional forms to population size were not exactly validated. We suggest that for time series modelers, the issue of a large sampling variation in small “noisy” populations is by far a more burning one than the systematic error due to index nonlinearity.     

Influence of antioxidant effect of stobadine derivative in condition of kidney ischemia-reperfusion in a pre-clinical experiment (effect in prophylaxis)

The goal of the study was to monitor the antioxidative effect of stobadine derivative in the conditions of ischemia-reperfusion of laboratory rat kidney tissue. The animals were divided by random selection into 5 groups (n = 10). The treated groups were given stobadine derivate in peroral doses of 5, 10 and 20 mg/kg in 0.5 % solution of Avicel once a day; the placebo group was given only the solution of Avicel. The last group was an intact group (without ischemia-reperfusion and without treatment). After conclusion of medication on the 15th day all animals were subjected to kidney tissue ischemia (60 min.) followed by reperfusion (10 min.). All animals were subsequently exsanquined and single identification of superoxiddismutase, glutathion peroxidase, total antioxidative capacity, and malondialdehyde level in the blood were determined. Kidneys were recovered for histopathological examination. A statistically significant decrease of the superoxiddismutase and statistically significant increase of the glutathione peroxidase catalytic activity in the treated groups compared to the groups of placebo and intact was discovered. There was also a statistically highly significant increase of total antioxidative capacity in the treated groups compared to the groups of placebo and intact. A statistically significant decrease of malondialdehyde level was identified in the treated groups compared to the groups of placebo and intact. The results of biochemical examination show a protective antioxidative effect of stobadine derivative. The results of histopathological examination support this assumption.     

Characterization of a eukaryotic type serine/threonine protein kinase and protein phosphatase of Streptococcus pneumoniae and identification of kinase substrates

Searching the genome sequence of Streptococcus pneumoniae revealed the presence of a single Ser/Thr protein kinase gene stkP linked to protein phosphatase phpP. Biochemical studies performed with recombinant StkP suggest that this protein is a functional eukaryotic-type Ser/Thr protein kinase. In vitro kinase assays and Western blots of S. pneumoniae subcellular fractions revealed that StkP is a membrane protein. PhpP is a soluble protein with manganese-dependent phosphatase activity in vitro against a synthetic substrate RRA(pT)VA. Mutations in the invariant aspartate residues implicated in the metal binding completely abolished PhpP activity. Autophosphorylated form of StkP was shown to be a substrate for PhpP. These results suggest that StkP and PhpP could operate as a functional pair in vivo. Analysis of phosphoproteome maps of both wild-type and stkP null mutant strains labeled in vivo and subsequent phosphoprotein identification by peptide mass fingerprinting revealed two possible substrates for StkP. The evidence is presented that StkP can phosphorylate in vitro phosphoglucosamine mutase GlmM which catalyzes the first step in the biosynthetic pathway leading to the formation of UDP-N-acetylglucosamine, an essential common precursor to cell envelope components.     

Molecular dynamics simulations of glycosyltransferase LgtC

Molecular dynamics simulations have been performed on fully solvated alpha-(1-->4)-galactosyltransferase LgtC from Neisseria meningitidis with and without the donor substrate UDP-Gal and in the presence of the manganese ion. The analysis of the trajectories revealed a limited movement in the loop X (residues 75-80) and a larger conformational change in the loop Y (residues 246-251) in the simulation, when UDP-Gal was not present. In this case, the loops X and Y open by almost 10A, exposing the active site to the solvent. The 'hinge region' responsible for the opening is composed of residues 246-247. We have also analyzed the behavior of the manganese ion in the simulations. The coordination number is 6 when UDP-Gal is present and it increases to 7 when it is absent. In the latter case, three water molecules become coordinated to the ion. In both cases, the coordination is very stable implying that the manganese ion is tightly bound in the active site of the enzyme even if UDP-Gal is not present. Further analysis of the structural water molecules location confirmed that the mobility of water molecules in the active site and the accessibility of this site for solvent are higher in the absence of the substrate.     

Toward the insulin-IGF-I intermediate structures: functional and structural properties of the [TyrB25NMePheB26] insulin mutant

The origins of differentiation of insulin from insulin-like growth factor I (IGF-I) are still unknown. To address the problem of a structural and biological switch from the mostly metabolic hormonal activity of insulin to the predominant growth factor activities of IGF-I, an insulin analogue with IGF-I-like structural features has been synthesized. Insulin residues Phe(B25) and Tyr(B26) have been swapped with the IGF-I-like Tyr(24) and Phe(25) sequence with a simultaneous methylation of the peptide nitrogen of residue Phe(B26). These modifications were expected to introduce a substantial kink in the main chain, as observed at residue Phe(25) in the IGF-I crystal structure. These alterations should provide insight into the structural origins of insulin-IGF-I structural and functional divergence. The [Tyr(B25)NMePhe(B26)] mutant has been characterized, and its crystal structure has been determined. Surprisingly, all of these changes are well accommodated within an insulin R6 hexamer. Only one molecule of each dimer in the hexamer responds to the structural alterations, the other remaining very similar to wild-type insulin. All alterations, modest in their scale, cumulate in the C-terminal part of the B-chain (residues B23-B30), which moves toward the core of the insulin molecule and is associated with a significant shift of the A1 helix toward the C-terminus of the B-chain. These changes do not produce the expected bend of the main chain, but the fold of the mutant does reflect some structural characteristics of IGF-1, and in addition establishes the CO(A19)-NH(B25) hydrogen bond, which is normally characteristic of T-state insulin.     

Mutations in TMEM76* cause mucopolysaccharidosis IIIC (Sanfilippo C syndrome)

Mucopolysaccharidosis IIIC (MPS IIIC, or Sanfilippo C syndrome) is a lysosomal storage disorder caused by the inherited deficiency of the lysosomal membrane enzyme acetyl-coenzyme A: alpha -glucosaminide N-acetyltransferase (N-acetyltransferase), which leads to impaired degradation of heparan sulfate. We report the narrowing of the candidate region to a 2.6-cM interval between D8S1051 and D8S1831 and the identification of the transmembrane protein 76 gene (TMEM76), which encodes a 73-kDa protein with predicted multiple transmembrane domains and glycosylation sites, as the gene that causes MPS IIIC when it is mutated. Four nonsense mutations, 3 frameshift mutations due to deletions or a duplication, 6 splice-site mutations, and 14 missense mutations were identified among 30 probands with MPS IIIC. Functional expression of human TMEM76 and the mouse ortholog demonstrates that it is the gene that encodes the lysosomal N-acetyltransferase and suggests that this enzyme belongs to a new structural class of proteins that transport the activated acetyl residues across the cell membrane.     

Fe-hydrogenase maturases in the hydrogenosomes of Trichomonas vaginalis

Assembly of active Fe-hydrogenase in the chloroplasts of the green alga Chlamydomonas reinhardtii requires auxiliary maturases, the S-adenosylmethionine-dependent enzymes HydG and HydE and the GTPase HydF. Genes encoding homologous maturases had been found in the genomes of all eubacteria that contain Fe-hydrogenase genes but not yet in any other eukaryote. By means of proteomic analysis, we identified a homologue of HydG in the hydrogenosomes, mitochondrion-related organelles that produce hydrogen under anaerobiosis by the activity of Fe-hydrogenase, in the pathogenic protist Trichomonas vaginalis. Genes encoding two other components of the Hyd system, HydE and HydF, were found in the T. vaginalis genome database. Overexpression of HydG, HydE, and HydF in trichomonads showed that all three proteins are specifically targeted to the hydrogenosomes, the site of Fe-hydrogenase maturation. The results of Neighbor-Net analyses of sequence similarities are consistent with a common eubacterial ancestor of HydG, HydE, and HydF in T. vaginalis and C. reinhardtii, supporting a monophyletic origin of Fe-hydrogenase maturases in the two eukaryotes. Although Fe-hydrogenases exist in only a few eukaryotes, related Narf proteins with different cellular functions are widely distributed. Thus, we propose that the acquisition of Fe-hydrogenases, together with Hyd maturases, occurred once in eukaryotic evolution, followed by the appearance of Narf through gene duplication of the Fe-hydrogenase gene and subsequent loss of the Hyd proteins in eukaryotes in which Fe-hydrogenase function was lost.     

Occurrence of adventitious sprouting in short-lived monocarpic herbs: a field study of 22 weedy species

Background and Aims

Adventitious sprouting from the hypocotyle and roots in monocarpic herbs has been confirmed in previous experimental studies as a means to avoid bud limitation after severe injury in annual and biennial plants. Data regarding the role of adventitious sprouting in natural populations, however, were lacking. The aim of the present study was to assess whether adventitious sprouting occurs in natural populations and how it is affected by plant size, plant injury, plant cover and environmental characteristics.

Methods

Data were sampled from 14 037 individual plants from 389 populations belonging to 22 annual and biennial species. Growth parameters were measured in individual plants, species composition and plant cover in communities were evaluated, and environmental characteristics were estimated using Ellenberg indicator values.

Key Results

It was confirmed that adventitious sprouting occurs in natural populations of all but five species examined. Adventitious sprouting was positively affected by plant size and plant injury. Environmental factors including availability of soil nitrogen were not shown to affect adventitious sprouting. Annual and biennial plants did not differ in sprouting, but upright annuals had a lower number of and longer adventitious shoots than prostrate annuals.

Conclusions

Adventitious bud formation is used to overcome meristem limitation when stem parts are lost due to injury, and thus resprouting in short-lived monocarps should not be overlooked.     

Protein reutilisation in corms of Colchicum autumnale

Colchicum autumnale L. is a monocotyledonous geophyte with hysteranthous leaves, i.e. flowering and leaf growth occur in different time periods. Because after the starch, the second prominent storage compound of corm is represented by proteins, we were interested in nitrogen remobilisation during the annual life cycle of C. autumnale. In this context the content of soluble and insoluble proteins were measured in parallel with determination of some exo-and endopeptidase activities. Our results indicate that the continual proteolysis occurs in both mother and new daughter corms during the whole life-cycle of the plant. L-Ala-aminopeptidase and trypsin-like endopeptidase were the most active peptidases in both mother and daughter corms. As the protein level of mother corm did not change significantly during the development of the future above-ground part under the soil surface (the first, autumnal developmental stage), the developmental profile of nitrate reductase activity was estimated followed by evaluation of total nitrogen and amino acid contents. Significant activity of root nitrate reductase was detected in the roots only in the second, vernal stage. Our results showed that the stored proteins constituted a relevant nitrogen source partly required by the growth processes of the late autumnal stage, but mainly by the intensive growth of leaves and reproductive structures during the second, photosynthetically active stage of the life-cycle.