What affects the magnitude of change in first arrival dates of migrant birds?

We analysed which among four factors (mean first arrival date, migration distance, changes in population size, detectability of species) influenced the magnitude of change (regression coefficient) in the first arrival dates of 30 migrant bird species in western Poland during 1983–2003. An examination suggested that several of these factors could be important: the regression coefficient was positively related to mean first arrival date (early species advancing their arrival date more) and negatively with change in population size (species in decline changing less). Moreover, significant differences in regression coefficient were detected between short and long distance migrants and between low detectable and highly detectable species. Undertaking a principal components analysis on the four factors produced an axis explaining 59% of the variance and whose positive values were associated with late arriving, long distance and low detectable species which were more likely to be in decline. However, the multi-collinearity of these factors is a problem that cannot be resolved here and we recommend that further work from different areas is needed to tease apart these effects.     

Nucleotide-induced conformational changes of PMP70, an ATP binding cassette transporter on rat liver peroxisomal membranes

Nucleotide-induced conformational changes of the 70-kDa peroxisomal membrane protein (PMP70) were investigated by means of limited-trypsin digestion. Rat liver peroxisomes preincubated with various nucleotides were subsequently digested by trypsin. The digestion products were subjected to immunoblot analysis with an anti-PMP70 antibody that recognizes the carboxyl-terminal 15 amino acids of the protein. PMP70 was initially cleaved in the boundary region between the transmembrane and nucleotide-binding domains and a carboxyl-terminal 30-kDa fragment resulted. The fragment in turn was progressively digested at the helical domain between the Walker A and B motifs. The fragment, however, could be stabilized with MgATP or MgADP. In contrast to MgATP, MgATP-gammaS protected whole PMP70 as well as the fragment. The 30-kDa fragment processed by trypsin was recovered in the post-peroxisomal fraction as a complex with a molecular mass of about 60 kDa irrespective of the presence of MgATP. These results suggest that PMP70 exists as a dimer on the peroxisomal membranes and the binding and hydrolysis of ATP induce conformational changes in PMP70 close to the boundary between the transmembrane and nucleotide binding domains and the helical domain between the Walker A and B motifs.     

Molecular motions and conformational changes of HPPK

6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) belongs to a class of catalytic enzymes involved in phosphoryl transfer and is a new target for the development of novel antimicrobial agents. In the present study, the fundamental consideration is to view the overall structure of HPPK as a network of interacting residues and to extract the most cooperative collective motions that define its global dynamics. A coarse-grained model, harmonically constrained according to HPPK's crystal structure is used. Four crystal structures of HPPK (one apo and three holo forms with different nucleotide and pterin analogs) are studied with the goal of providing insights about the function-dynamic correlation and ligand induced conformational changes. The dynamic differences are examined between HPPK's apo- and holo-forms, because they are involved in the catalytic reaction steps. Our results indicate that the palm-like structure of HPPK is nearly rigid, whereas the two flexible loops: L2 (residues 43-53) and L3 (residues 82-92) exhibit the most concerted motions for ligand recognition and presumably, catalysis. These two flexible loops are involved in the recognition of HPPKs nucleotide and pterin ligands, whereas the rigid palm region is associated with binding of these cognate ligands. Six domains of collective motions are identified, comprised of structurally close but not necessarily sequential residues. Two of these domains correspond to the flexible loops (L2 and L3), whereas the remaining domains correspond to the rigid part of the molecule.     

Electrooptical studies on proton-binding and -release of bacteriorhodopsin

Electric field induced pH changes of purple membrane suspensions were investigated in the pH range from 4.1 to 7.6 by measuring the absorbance change of pH indicators. In connection with the photocycle and proton pump ability, three different states of bacteriorhodopsin were used: (1) the native purple bacteriorhodopsin (magnesium and calcium ions are bound, the M intermediate exists in the photocycle and protons are pumped), (2) the cation-depleted blue bacteriorhodopsin (no M intermediate), and (3) the regenerated purple bacteriorhodopsin which is produced either by raising the pH or by adding magnesium ions (the M intermediate exists). In the native purple bacteriorhodopsin there are, at least, two types of proton binding sites: one releases protons and the other takes up protons in the presence of the electric field. On the other hand, blue bacteriorhodopsin and the regenerated purple bacteriorhodopsin (pH increase) show neither proton release nor proton uptake. When magnesium ions are added to the suspensions; the field-induced pH change is observed again. Thus, the stability of proton binding depends strongly on the state of bacteriorhodopsin and differences in proton binding are likely to be related to differences in proton pump activity. Furthermore, it is suggested that the appearance of the M intermediate and proton pumping are not necessarily related.     

Circumnutation in Phaseolus vulgaris. I. Growth, osmotic potential and cell ultrastructure in the free-moving part of the shoot

Circumnutation of Phaseolus vulgaris L. cv. Blanc de Juillet twining shoots was examined at the cellular level. Cell growth was monitored inside the free-moving part of the shoot as a function of time and position with respect to the terminal bud. Complete elongation of epidermal cells required >7 days. A 60% increase in length of the cells in the bending zone was observed. Scanning and transmission electron microscopy studies showed the elasticity of cell walls, the extent of plasmodesmata and endoplasmic reticulum of epidermal cells. The osmotic potential in epidermal cells of the bending zone displayed significant differences only between the concave and convex sides. The pattern of cell growth in twining shoots is discussed. Circumnutation could be seen as a consequence of periodic turgor changes inducing periodic growth.     

RNA editing of 10 Didymium iridis mitochondrial genes and comparison with the homologous genes in Physarum polycephalum

Regions of the Didymium iridis mitochondrial genome were identified with similarity to typical mitochondrial genes; however, these regions contained numerous stop codons. We used RT-PCR and DNA sequencing to determine whether, through RNA editing, these regions were transcribed into mRNAs that could encode functional proteins. Ten putative gene regions were examined: atp1, atp6, atp8, atp9, cox1, cox2, cytb, nad4L, nad6, and nad7. The cDNA sequences of each gene could encode a functional mitochondrial protein that was highly conserved compared with homologous genes. The type of editing events and editing sequence features were very similar to those observed in the homologous genes of Physarum polycephalum, though the actual editing locations showed a variable degree of conservation. Edited sites were compared with encoded sites in D. iridis and P. polycephalum for all 10 genes. Edited sequence for a portion of the cox1 gene was available for six myxomycetes, which, when compared, showed a high degree of conservation at the protein level. Different types of editing events showed varying degrees of site conservation with C-to-U base changes being the least conserved. Several aspects of single C insertion editing events led to the preferential creation of hydrophobic amino acid codons that may help to minimize adverse effects on the resulting protein structure.     

Longitudinal patterns of dissolved organic carbon concentration and suspended bacterial density along a blackwater river

Dissolved organic carbon (DOC) is the dominant form of carbon in transport in blackwater rivers, and bacteria are the major biological agents of its utilization. This study describes longitudinal patterns in DOC concentration and relates them to suspended bacterial populations in the channel. Concentrations of total DOC, three molecular weight fractions, and bacterial numbers were determined at 12 sites along the Ogeechee River in 1985–1986 and 1989 during periods of low and high discharge. Suspended bacterial populations were compared with DOC concentrations to determine if differences in bacterial abundance were related to longitudinal patterns of DOC concentration. Three distinct longitudinal patterns were observed: (1) The longitudinal pattern followed by both total and intermediate molecular weight DOC concentrations was a linear function of the geographic distance along the river. (2) During low flow conditions, there was a high degree of correspondence between patterns of bacterial numbers and low MW DOC (< 1000 apparent MW). (3) During periods of high discharge, the proportion of high (> 10,000) and intermediate (1000–10,000) MW fractions increased, and there was no longer a clear relationship between bacterial cells and low MW DOC.     

Stir-up effect of wind on a more-or-less stratified shallow lake phytoplankton community,Lake Balaton,Hungary

Microstratification of phytoplankton in the large shallow Lake Balaton (Hungary) was studied during a 24 h period. Dissolved O₂ showed biological stratification; flagellates exhibited a definite circadian rhythm. In the middle of the investigation a heavy storm broke out which was followed by the disappearance of differences between different layers of water. Storm-induced destratification is described by cluster-analysis. Abundances of dominant species changed differently in connection with the storm. Numbers of Nitzschia sp. increased due to stirring up from the sediment surface. Numbers of single-celled or colony-forming species (Cyclotella comta, Crucigenia quadrata, Coelosphaerium kuetzingianum) practically did not change. Numbers of all the three dominant filamentous species (Aphanizomenon fos-aquae f. klebahnii, Lyngbya limnetica, Planctonema lauterbornii) significantly decreased, which might be attributed to an unknown loss process and was followed by a competitive displacement by algae of small cell size.     

Structural and Functional Changes in the Leaves of Plants from Steppe Communities as Affected by Aridization of the Eurasian Climate

Morphological and physiological characteristics of leaves from plant species collected in steppe communities in the various climatic zones in Eurasia were compared. The changes in leaf structure correlated with the major climatic factors. The mean thickness of leaves increased with increasing mean temperature of July and decreasing mean precipitation, which corresponded to aridity increase. The increased leaf thickness correlated with an increase in the specific leaf weight. The content of chlorophylls (a + b) in leaves greatly varied with plant habitats, whereas the chlorophyll a/b ratio remained unchanged. The chlorophyll content in leaf tissues had a general tendency to decrease with increasing leaf thickness. The leaf chlorophyll content positively correlated (R ² = 0.77) with the proportion of chlorenchyma in leaf tissues. It is concluded that steppe plants adapt to climate aridization at the structural level by increasing the proportion of protective heterotrophic components of the leaf without changing the functional activity of photosynthetic tissues.