Autogenic succession, land-use change, and climatic influences on the Holocene development of a kettle-hole mire in Northern Poland

We reconstructed the Holocene developmental history of a kettle-hole peatland in the Tuchola Forest of Northern Poland, using pollen, testat amoebae and plant macrofossil indicators. Our aims were to determine the timing and pattern of autogenic succession and natural and anthropogenic influences on the peatland. Northern Poland is under mixed oceanic and continental climatic influences but has so far been less studied in a palaeoecological context than more oceanic regions of Europe. In the first terrestrial developmental phase of the mire, the testate amoebae-inferred depth to water table revealed two major dry shifts at ca. 9400 (end of lake phase) and ca. 7100 cal BP (a period of global cooling and dry shift in Western Europe). Conditions became wetter again in two steps at ca. 6700 and ca. 5800 BP after a dry event at ca. 6100 BP. The timing of the wet shift at 5800 BP corresponds to wet periods in Western Europe. Peat accumulation rates were low (0.1 mm yr^− 1) between ca. 5600 and ca. 3000 BP when sedges dominated the peatland. In the last 2500 yrs surface moisture fluctuated with wet events at ca. 2750–2400, and 2000 BP, and dry events at ca. 2250–2100 and 1450 BP. After 1450 BP a trend towards wetter conditions culminated at ca. 500 cal BP, possibly caused by local deforestation. Over the mire history, pH (inferred from testate amoebae) was mostly low (around 5) with two short-lived shifts to alkaline conditions (7.5) at ca. 6100 and 1450 BP indicating a minerotrophic influence from surface run-off into the mire. Up to about 1000 BP the ecological shifts inferred from the three proxies agree with palaeoclimatic records from Poland and Western Europe. After this date, however correlation is less clear suggesting an increasing local anthropogenic impact on the mire. This study confirms that kettle-hole peatlands can yield useful palaeoenvironmental data as well as recording land-use change and calls for more comparable studies in regions are the interface between major climate influences.     

The immunosuppressive activity and solution structures of ubiquitin fragments

Recently, ubiquitin was suggested as a promising anti‐inflammatory protein therapeutic. We found that a peptide fragment corresponding to the ubiquitin^50–59 sequence (LEDGRTLSDY) possessed the immunosuppressive activity comparable with that of ubiquitin. CD and NMR spectroscopies were used to determine the conformational preferences of LEDGRTLSDY in solution. The peptide mixture, obtained by pepsin digestion of ubiquitin, was even more potent than the intact protein. Although the peptide exhibited a well‐defined conformation in methanol, its structure was distinct from the corresponding 50–59 fragment in the native ubiquitin molecule. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 423–431, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Development and reproductive capacity of the predatory mite <Emphasis Type="Italic">Parasitus consanguineus</Emphasis> (Acari: Parasitidae) reared on the larval stages of <Emphasis Type="Italic">Megaselia halterata</Emphasis> and <Emphasis Type="Italic">Lycoriella ingenua</Emphasis>

Development and reproduction of the predatory mite Parasitus consanguineus Oudemans et Voigts (Acari: Parasitidae) reared on a diet of first and second instars of Megaselia halterata (Diptera: Phoridae) or Lycoriella ingenua (Diptera: Sciaridae) were studied. Mites were allowed to feed on these diets until death. The developmental time of immature stages of P. consanguineus was significantly longer when reared on L. ingenua than on M. halterata larvae (8.3 vs. 7.9 days, respectively). Survival to adulthood of P. consanguineus reared on L. ingenua or M. halterata larvae was 63 and 49%, and mite fecundity was 17.8 and 12.3 eggs/female, respectively. Adult females reared on L. ingenua lived on average 6.9 days, whereas those reared on M. halterata lived for 5.7 days. Mite survival, female longevity and fecundity were significantly different among the two diet types.     

SLP‐2 is required for stress‐induced mitochondrial hyperfusion

Mitochondria are dynamic organelles, the morphology of which results from an equilibrium between two opposing processes, fusion and fission. Mitochondrial fusion relies on dynamin‐related GTPases, the mitofusins (MFN1 and 2) in the outer mitochondrial membrane and OPA1 (optic atrophy 1) in the inner mitochondrial membrane. Apart from a role in the maintenance of mitochondrial DNA, little is known about the physiological role of mitochondrial fusion. Here we report that mitochondria hyperfuse and form a highly interconnected network in cells exposed to selective stresses. This process precedes mitochondrial fission when it is triggered by apoptotic stimuli such as UV irradiation or actinomycin D. Stress‐induced mitochondrial hyperfusion (SIMH) is independent of MFN2, BAX/BAK, and prohibitins, but requires L‐OPA1, MFN1, and the mitochondrial inner membrane protein SLP‐2. In the absence of SLP‐2, L‐OPA1 is lost and SIMH is prevented. SIMH is accompanied by increased mitochondrial ATP production and represents a novel adaptive pro‐survival response against stress.     

Mitochondrial fusion and division: Regulation and role in cell viability

Discovery of various molecular components regulating dynamics and organization of the mitochondria in cells, together with novel insights into the role of mitochondrial fusion and division in the maintenance of cellular homeostasis, have provided some of the most exciting breakthroughs in the last decade of mitochondrial research. The focus of this review is on the regulation of mitochondrial fusion and division machineries. The newly identified factors associated with mitofusin/OPA1-dependent mitochondrial fusion, and Drp1-dependent mitochondrial division are discussed. Furthermore, the most recent findings on the role of mitochondrial fusion and division in the maintenance of cell function are also reviewed here in some detail.     

Interactions between the endoplasmic reticulum, mitochondria, plasma membrane and other subcellular organelles

Several recent works show structurally and functionally dynamic contacts between mitochondria, the plasma membrane, the endoplasmic reticulum, and other subcellular organelles. Many cellular processes require proper cooperation between the plasma membrane, the nucleus and subcellular vesicular/tubular networks such as mitochondria and the endoplasmic reticulum. It has been suggested that such contacts are crucial for the synthesis and intracellular transport of phospholipids as well as for intracellular Ca²⁺ homeostasis, controlling fundamental processes like motility and contraction, secretion, cell growth, proliferation and apoptosis. Close contacts between smooth sub-domains of the endoplasmic reticulum and mitochondria have been shown to be required also for maintaining mitochondrial structure. The overall distance between the associating organelle membranes as quantified by electron microscopy is small enough to allow contact formation by proteins present on their surfaces, allowing and regulating their interactions. In this review we give a historical overview of studies on organelle interactions, and summarize the present knowledge and hypotheses concerning their regulation and (patho)physiological consequences.     

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

Background  

Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization.     

Crystal structure of plant asparaginase

In plants, specialized enzymes are required to catalyze the release of ammonia from asparagine, which is the main nitrogen-relocation molecule in these organisms. In addition, K+-independent plant asparaginases are also active in splitting the aberrant isoaspartyl peptide bonds, which makes these proteins important for seed viability and germination. Here, we present the crystal structure of potassium-independent L-asparaginase from yellow lupine (LlA) and confirm the classification of this group of enzymes in the family of Ntn-hydrolases. The alpha- and beta-subunits that form the mature (alphabeta)2 enzyme arise from autoproteolytic cleavage of two copies of a precursor protein. In common with other Ntn-hydrolases, the (alphabeta) heterodimer has a sandwich-like fold with two beta-sheets flanked by two layers of alpha-helices (alphabetabetaalpha). The nucleophilic Thr193 residue, which is liberated in the autocatalytic event at the N terminus of subunit beta, is part of an active site that is similar to that observed in a homologous bacterial enzyme. An unusual sodium-binding loop of the bacterial protein, necessary for proper positioning of all components of the active site, shows strictly conserved conformation and metal coordination in the plant enzyme. A chloride anion complexed in the LlA structure marks the position of the alpha-carboxylate group of the L-aspartyl substrate/product moiety. Detailed analysis of the active site suggests why the plant enzyme hydrolyzes asparagine and its beta-peptides but is inactive towards substrates accepted by similar Ntn-hydrolases, such as taspase1, an enzyme implicated in some human leukemias. Structural comparisons of LlA and taspase1 provide interesting insights into the role of small inorganic ions in the latter enzyme.