Nitrogen-fixing activity in peat soils from a raised bog

The nitrogenase (acetylene reductase) activity in monolithic and minced peat samples was found to be low, no more than 0.014-0.022 mg N/(kg h). Incorporation of the 15N2 isotope into organic compounds of peat soil was from 2.71-8.13 mg N/kg over 15 days. The nitrogen-fixing activity was the highest in a 10-20 cm layer of soil and much lower in the upper (under green moss) and deeper (20-30 cm) layers. The addition of glucose to soil samples stimulated nitrogen fixation considerably after 18-26 h. The maximum nitrogenase activity (3.5-3.8 mg N/(kg h)) observed after 60-70 h coincided with the peak of respiratory activity. A repeated addition of glucose after its exhaustion increased nitrogenase activity without a lag period to 8.5 mg N/(kg h). Investigation of the effect of environmental factors (temperature, pH, aeration, and light intensity) on potential nitrogen-fixing activity in peat samples revealed that nitrogen fixation could proceed in a wide range of pH values (from 3.0 to 7.5) and temperatures (from 5 to 35 degrees C). The nitrogen-fixing bacteria belonging to different trophic groups were enumerated by using nitrogen-free media with pH values and mineralization levels close to those in situ. In samples of peat soil, diazotrophic methanol-utilizing bacteria prevailed (2.0-2.5 x 10(6) cells/g); the second largest group was facultatively anaerobic bacteria of the family Enterobacteriaceae.     

The crystal structure of mouse Exo70 reveals unique features of the mammalian exocyst

The exocyst is a eukaryotic tethering complex necessary for the fusion of exocytic vesicles with the plasma membrane. Its function in vivo is tightly regulated by interactions with multiple small GTPases. Exo70, one of the eight subunits of the exocyst, is important for the localization of the exocyst to the plasma membrane. It interacts with TC10 and Rho3 GTPases in mammals and yeast, respectively, and has been shown recently to bind to the actin-polymerization complex Arp2/3. Here, we present the crystal structure of Mus musculus Exo70 at 2.25 A resolution. Exo70 is composed of alpha-helices in a series of right-handed helix-turn-helix motifs organized into a long rod of length 170 A and width 35 A. Although the alpha-helical organization of this molecule is similar to that in Saccharomyces cerevisiae Exo70, major structural differences are observed on the surface of the molecule, at the domain boundaries, and in various loop structures. In particular, the C-terminal domain of M. musculus Exo70 adopts a new orientation relative to the N-terminal half not seen in S. cerevisiae Exo70 structures. Given the low level of sequence conservation within Exo70, this structure provides new insights into our understanding of many species-specific functions of the exocyst.     

Comparative analysis of the 15.5kD box C/D snoRNP core protein in the primitive eukaryote Giardia lamblia reveals unique structural and functional features

Box C/D ribonucleoproteins (RNP) guide the 2'-O-methylation of targeted nucleotides in archaeal and eukaryotic rRNAs. The archaeal L7Ae and eukaryotic 15.5kD box C/D RNP core protein homologues initiate RNP assembly by recognizing kink-turn (K-turn) motifs. The crystal structure of the 15.5kD core protein from the primitive eukaryote Giardia lamblia is described here to a resolution of 1.8 ?. The Giardia 15.5kD protein exhibits the typical α-β-α sandwich fold exhibited by both archaeal L7Ae and eukaryotic 15.5kD proteins. Characteristic of eukaryotic homologues, the Giardia 15.5kD protein binds the K-turn motif but not the variant K-loop motif. The highly conserved residues of loop 9, critical for RNA binding, also exhibit conformations similar to those of the human 15.5kD protein when bound to the K-turn motif. However, comparative sequence analysis indicated a distinct evolutionary position between Archaea and Eukarya. Indeed, assessment of the Giardia 15.5kD protein in denaturing experiments demonstrated an intermediate stability in protein structure when compared with that of the eukaryotic mouse 15.5kD and archaeal Methanocaldococcus jannaschii L7Ae proteins. Most notable was the ability of the Giardia 15.5kD protein to assemble in vitro a catalytically active chimeric box C/D RNP utilizing the archaeal M. jannaschii Nop56/58 and fibrillarin core proteins. In contrast, a catalytically competent chimeric RNP could not be assembled using the mouse 15.5kD protein. Collectively, these analyses suggest that the G. lamblia 15.5kD protein occupies a unique position in the evolution of this box C/D RNP core protein retaining structural and functional features characteristic of both archaeal L7Ae and higher eukaryotic 15.5kD homologues.     

Radiocarbon dating of peat macrofossils in the Cairngorm Mountains,Scotland

Summary

Radiocarbon dates for tree stumps at another three sites in the Cairngorm Mountains are presented. These are considered along with a previous set (Pears, 1969) and the evidence they provide for determining altitudinal limits of forest growth in the Flandrian Period is discussed. They support earlier tentative conclusions that the topographical factor and local site hydrology are the key factors in interpreting the macrofossil pattern.     

Comparative analysis of human and bovine protein kinases reveals unique relationship and functional diversity

Reversible protein phosphorylation by protein kinases and phosphatases is a common event in various cellular processes. The eukaryotic protein kinase superfamily, which is one of the largest superfamilies of eukaryotic proteins, plays several roles in cell signaling and diseases. We identified 482 eukaryotic protein kinases and 39 atypical protein kinases in the bovine genome, by searching publicly accessible genetic-sequence databases. Bovines have 512 putative protein kinases, each orthologous to a human kinase. Whereas orthologous kinase pairs are, on an average, 90.6% identical, orthologous kinase catalytic domain pairs are, on an average, 95.9% identical at the amino acid level. This bioinformatic study of bovine protein kinases provides a suitable framework for further characterization of their functional and structural properties.     

Structure of the DNA-binding domain of NgTRF1 reveals unique features of plant telomere-binding proteins

Telomeres are protein–DNA elements that are located at the ends of linear eukaryotic chromosomes. In concert with various telomere-binding proteins, they play an essential role in genome stability. We determined the structure of the DNA-binding domain of NgTRF1, a double-stranded telomere-binding protein of tobacco, using multidimensional NMR spectroscopy and X-ray crystallography. The DNA-binding domain of NgTRF1 contained the Myb-like domain and C-terminal Myb-extension that is characteristic of plant double-stranded telomere-binding proteins. It encompassed amino acids 561–681 (NgTRF1^561–681), and was composed of 4 α-helices. We also determined the structure of NgTRF1^561–681 bound to plant telomeric DNA. We identified several amino acid residues that interacted directly with DNA, and confirmed their role in the binding of NgTRF1 to telomere using site-directed mutagenesis. Based on a structural comparison of the DNA-binding domains of NgTRF1 and human TRF1 (hTRF1), NgTRF1 has both common and unique DNA-binding properties. Interaction of Myb-like domain with telomeric sequences is almost identical in NgTRF1^561–681 with the DNA-binding domain of hTRF1. The interaction of Arg-638 with the telomeric DNA, which is unique in NgTRF1^561–681, may provide the structural explanation for the specificity of NgTRF1 to the plant telomere sequences, (TTTAGGG)_n.     

Sequencing of porcine enterovirus groups II and III reveals unique features of both virus groups

The molecular classification of the porcine enterovirus (PEV) groups II and III was investigated. The sequence of the almost complete PEV-8 (group II) genome reveals that this virus has unique L and 2A gene regions. A reclassification of this group into a new picornavirus genus is suggested. PEV group III viruses are typical enteroviruses. They differ from other enteroviruses by a prolonged stem-loop D of the 5'-cloverleaf structure.     

Denitrification in the top and sub soil of grassland on peat soils

Denitrification is an important process in the nitrogen (N) balance of intensively managed grassland, especially on poorly drained peat soils. Aim of this study was to quantify the N loss through denitrification in the top and sub soil of grassland on peat soils. Sampling took place at 2 sites with both control (0 N) and N fertilised (+ N) treatments. Main difference between the sites was the ground water level. Denitrification was measured on a weekly basis for 2 years with a soil core incubation technique using acetylene (C₂H₂) inhibition. Soil cores were taken from the top soil (0–20 cm depth) and the sub soil (20–40 cm depth) and incubated in containers for 24 hours. The denitrification rate was calculated from the nitrous oxide production between 4 and 24 hours of incubation. Denitrification capacities of the soils and the soil layers were also determined.The top soil was the major layer for denitrification with losses ranging from 9 to 26 kg N ha^–1 yr^–1 from the O N treatment. Losses from the top soil of the + N treatment ranged from 13 to 49 kg N ha^–1 yr^–1. The sub soil contributed, on average, 20% of the total denitrification losses from the 0–40 layer. Losses from the 0–40 cm layer were 2 times higher on the + N treatment than on the O N treatment and totalled up to 70 kg N ha^–1 yr^–1. Significant correlation coefficients were found between denitrification activity on the one hand, and ground water level, water filled pore space and nitrate content on the other, in the top soil but not in the sub soil. The denitrification capacity experiment showed that the availability of easily decomposable organic carbon was an important limiting factor for the denitrification activity in the sub soil of these peat soils.     

Comparative analysis of basidiomycetous laccase genes in forest soils reveals differences at the cDNA and DNA levels

Aims

This study was undertaken to investigate laccase-containing basidiomycete communities at the cDNA and DNA levels and to assess the influences of vegetation and soil types on the basidiomycete communities in forest soils.

Materials and methods

Soil samples were collected from the upper soil layers of two typical subtropical forests (a broad-leaved forest developed in Karst limestone soil and an artificial coniferous forest with Pinus massoniana in red soil) in China. The basidiomycete communities were characterized by cloning and sequencing of the laccase genes at both the cDNA and DNA levels. Compositions of lignin monomers were determined by gas chromatography–mass spectrometry.

Results

Most of the laccase genes obtained in this study were new, highlighting the research gap of this functional group. The trends of the basidiomycetous laccase gene diversity among the upper soil layers of the two forests were consistent between the cDNA and DNA levels. The Agaricales had high activity because they dominated all the tested soils. However, the total basidiomycete communities reflected at the cDNA and DNA levels were significantly different due to the presence of some quiescent basidiomycetous groups. Almost all of the lignin components were decomposed from the O to the A layers in the two forests, and laccases produced by Agaricales were likely responsible for the decomposition of guaiacyl monomers. Both vegetation and soil types had great influences on the active laccase-containing basidiomycete communities, primarily via the pH, C/N, and the contents of lignin monomers.

Conclusions

The cDNA- and DNA-level approaches presented good consistency of diversities but different compositions of laccase-containing basidiomycete communities, thus emphasizing the importance of focusing on laccase genes at the cDNA level in future studies. It is the quality but not the quantity of SOM to determine the diversity and composition of the active laccase-containing basidiomycete communities.     

Comparative study of the thermal properties of mud and peat solutions applied in clinical practice.

Different peloids as e.g. mud and peat have been traditionally used for therapeutic purposes successfully, especially of there thermal actions. It was the aim of the experimental study to compare the thermal properties of two peloids, mud and peat, with a view to assessing their thermal effects when they are applied in clinical practice. The studies were carried out using peat of the marsh type of peats (Hochmoor), and curative Pomorie (Bulgaria) mud. As important parameters were determined the specific thermal capacity at constant pressure (Cp), the density of solutions (rho), the cooling rate (m), the coefficient of temperature transfer (a) of solutions and the coefficient of thermal conductivity (lambda) of solutions of peat and curative mud, compared to water bath. The comparative studies of the thermal properties of water and water solutions of peat and curative mud show that the thermal effect of the water bath is substantially smaller than that of the peat and mud applications. This difference is due to a greater extent to the high values of the dynamic viscosity, not allowing cooling by convection and protecting the surface of the skin upon applications of peloid solutions with a higher temperature.     

Long time-lapse imaging reveals unique features of PARK2/Parkin-mediated mitophagy in mature cortical neurons

Proper degradation of aged and damaged mitochondria through mitophagy is essential to ensure mitochondrial integrity and function. Translocation of PARK2/Parkin onto damaged mitochondria induces mitophagy in many non-neuronal cell types. However, direct evidence showing PARK2-mediated mitophagy in mature neurons is controversial, leaving unanswered questions as to how, where, and by what time course PARK2-mediated mitophagy occurs in neurons following mitochondrial depolarization. We applied long time-lapse imaging in live mature cortical neurons to monitor the slow but dynamic and spatial PARK2 translocation onto damaged mitochondria and subsequent degradation through the autophagy-lysosomal pathway. In comparison with non-neuronal cells, our study reveals unique features of PARK2-mediated mitophagy in mature neurons, which will advance our understanding of pathogenesis of several major neurodegenerative diseases characterized by damaged mitochondria or a dysfunctional autophagy-lysosomal system.     

Long time-lapse imaging reveals unique features of PARK2/Parkin-mediated mitophagy in mature cortical neurons

Proper degradation of aged and damaged mitochondria through mitophagy is essential to ensure mitochondrial integrity and function. Translocation of PARK2/Parkin onto damaged mitochondria induces mitophagy in many non-neuronal cell types. However, direct evidence showing PARK2-mediated mitophagy in mature neurons is controversial, leaving unanswered questions as to how, where, and by what time course PARK2-mediated mitophagy occurs in neurons following mitochondrial depolarization. We applied long time-lapse imaging in live mature cortical neurons to monitor the slow but dynamic and spatial PARK2 translocation onto damaged mitochondria and subsequent degradation through the autophagy-lysosomal pathway. In comparison with non-neuronal cells, our study reveals unique features of PARK2-mediated mitophagy in mature neurons, which will advance our understanding of pathogenesis of several major neurodegenerative diseases characterized by damaged mitochondria or a dysfunctional autophagy-lysosomal system.