Conversion of the tetrameric restriction endonuclease Bse634I into a dimer: oligomeric structure-stability-function correlations

The Bse634I restriction endonuclease is a tetramer and belongs to the type IIF subtype of restriction enzymes. It requires two recognition sites for its optimal activity and cleaves plasmid DNA with two sites much faster than a single-site DNA. We show that disruption of the tetramerisation interface of Bse634I by site-directed mutagenesis converts the tetrameric enzyme into a dimer. Dimeric W228A mutant cleaves plasmid DNA containing one or two sites with the same efficiency as the tetramer cleaves the two-site plasmid. Hence, the catalytic activity of the Bse634I tetramer on a single-site DNA is down-regulated due to the cross-talking interactions between the individual dimers. The autoinhibition within the Bse634I tetramer is relieved by bridging two DNA copies into the synaptic complex that promotes fast and concerted cleavage at both sites. Cleavage analysis of the oligonucleotide attached to the solid support revealed that Bse634I is able to form catalytically competent synaptic complexes by bridging two molecules of the cognate DNA, cognate DNA-miscognate DNA and cognate DNA-product DNA. Taken together, our data demonstrate that a single W228A mutation converts a tetrameric type IIF restriction enzyme Bse634I into the orthodox dimeric type IIP restriction endonuclease. However, the stability of the dimer towards chemical denaturants, thermal inactivation and proteolytic degradation are compromised.     

Mutations in the Na+/K+ -ATPase alpha3 gene ATP1A3 are associated with rapid-onset dystonia parkinsonism

Rapid-onset dystonia-parkinsonism (RDP, DYT12) is a distinctive autosomal-dominant movement disorder with variable expressivity and reduced penetrance characterized by abrupt onset of dystonia, usually accompanied by signs of parkinsonism. The sudden onset of symptoms over hours to a few weeks, often associated with physical or emotional stress, suggests a trigger initiating a nervous system insult resulting in permanent neurologic disability. We report the finding of six missense mutations in the gene for the Na+/K+ -ATPase alpha3 subunit (ATP1A3) in seven unrelated families with RDP. Functional studies and structural analysis of the protein suggest that these mutations impair enzyme activity or stability. This finding implicates the Na+/K+ pump, a crucial protein responsible for the electrochemical gradient across the cell membrane, in dystonia and parkinsonism.     

Polymorphism of trinucleotide repeats in non-translated regions of SCA8 and SCA12 genes: allele distribution in a Polish control group

Spinocerebellar ataxias are a group of neurodegenerative disorders caused by dynamic mutations of microsatellite repeats. Two novel forms of SCAs have been described recently: SCA8, with expansions of CTA/CTG repeats in 3'UTR of the SCA8 gene, and SCA12, caused by expansion of the CAG tract in 5'UTR of the SCA12/PP2R2B gene. Analysis of CTA/CTG and CAG polymorphism in those two genes was performed in a Polish control group consisting of 100 individuals without any neurological signs. The distribution and ranges of the number of non-pathogenic repeats were similar to those observed in other populations described previously. Expansion of CTA/CTG repeats in the SCA8 locus was found in 2 of 100 controls and in 5 probands among 150 pedigrees affected with unidentified ataxias. As such expanded alleles were also observed in their healthy relatives, the pathogenic role of expansions in the SCA8 gene remains uncertain.     

Sight: automating genomic data-mining without programming skills

SUMMARY: We created and tested Sight, a Java-based package that provides a user-friendly interface to generate and connect agents for automatic genomic data-mining for individual requirements without requiring programming skills from the user. AVAILABILITY: http://physiologie.uni-ulm.de//Seiten/Arbeitsgruppe/Jurkat-Rott/Jurkat-Rott.htm. The system does not require additional components and runs on IBM PCs under Windows (NT 4.0, 2000 and XP) or Linux (Phat 4.0 and Mandrake 9.0).     

Rapid increase in training load affects markers of skeletal muscle damage and mechanical performance

ABSTRACT: Kamandulis, S, Snieckus, A, Venckunas, T, Aagaard, P, Masiulis, N, and Skurvydas, A. Rapid increase in training load affects markers of skeletal muscle damage and mechanical performance. J Strength Cond Res 26(11): 2953-2961, 2012-The aim of this study was to monitor the changes in indirect markers of muscle damage during 3 weeks (9 training sessions) of stretch-shortening (drop jump) exercise with constant load alternated with steep increases in load. Physically active men (n = 9, mean age 19.1 years) performed a program involving a rapid stepwise increase in the number of jumps, drop height, and squat depth, and the addition of weight. Concentric, isometric maximal voluntary contraction (MVC), and stimulated knee extension torque were measured before and 10 minutes after each session. Muscle soreness and plasma creatine kinase activity were assessed after each session. Steep increments in stretch-shortening exercise load in sessions 4 and 7 amplified the postexercise decrease in stimulated muscle torque and slightly increased muscle soreness but had a minimal effect on the recovery of MVC and stimulated torque. Maximal jump height increased by 7.8 ± 6.3% (p < 0.05), 11.4 ± 3.3% (p < 0.05), and 12.8 ± 3.6% (p < 0.05) at 3, 10, and 17 days after the final training session, respectively. Gains in isometric knee extension MVC (7.9 ± 8.2%) and 100-Hz-evoked torque (9.9 ± 9.6%) (both p < 0.05) were observed within 17 days after the end of the training. The magnitude of improvement was greater after this protocol than that induced by a continuous constant progression loading pattern with small gradual load increments in each training session. These findings suggest that plyometric training using infrequent but steep increases in loading intensity and volume may be beneficial to athletic performance.     

Occurrence and impact of the root-rot biocontrol agent Phlebiopsis gigantea on soil fungal communities in Picea abies forests of northern Europe

The aim of this study was to assess belowground occurrence, persistence and possible impact of the biocontrol agent Phlebiopsis gigantea (Fr.) Jülich on soil fungi. Sampling of soil and roots of Picea abies (L.) H. Karst. was carried out at 12 P. gigantea-treated and five nontreated control sites representing 1- to 60-month-old clear-cuts and thinned forest sites in Finland and Latvia. The 454-sequencing of ITS rRNA from fine roots, humus and mineral soil resulted in 8626 high-quality fungal sequences. Phlebiopsis gigantea represented 1.3% of all fungal sequences and was found in 14 treated and nontreated sites and in all three substrates. In different substrates, the relative abundance of P. gigantea at stump treatment sites either did not differ significantly or was significantly lower than in nontreated controls. No significant correlation was found between the time elapsed since the tree harvesting and/or application of the biocontrol and abundance of P. gigantea in different substrates. In conclusion, the results demonstrate that P. gigantea occasionally occurs belowground in forest ecosystems but that stump treatment with the biocontrol agent has little or no impact on occurrence and persistence of P. gigantea belowground, and consequently no significant impact on soil fungi.     

Synchronization of estrus and ovulation in sows not conceiving in a scheduled fixed-time insemination program

A field study was conducted to investigate the effectiveness of a treatment with altrenogest, eCG and hCG or the GnRH-analogue D-Phe(6)-LHRH to synchronize estrus and ovulation of sows diagnosed as non-pregnant in order to reintegrate them back into a scheduled fixed-time insemination program. Sows (n=531) diagnosed as non-pregnant by ultrasonography on days 21-35 after insemination were subjected to one of three treatments: (1) 16 mg altrenogest/day/animal orally for 15 days to block follicular growth, followed by injection of 1000 IU eCG intramuscularly (i.m.) 24h after withdrawal of altrenogest to stimulate follicular growth and 500 IU hCG i.m. 78-80 h after eCG to induce ovulation; (2) similar to (1) except that 20mg altrenogest and 800 IU eCG were used and (3) similar to (2) except that 50 microg D-Phe(6)-LHRH was used to induce ovulation. Females were artificially inseminated (AI) twice at 24 and 40 h, respectively, after hCG/D-Phe(6)-LHRH. Success of treatments was checked by ultrasonography of the ovaries. Rates of conception and farrowing (CR, FR), and number of total and live born piglets (TB, LB) were recorded and compared to those of synchronized first served sows. Females had differing ovarian structures prior to treatment. Altrenogest effectively blocked follicular growth in >80% of the females irrespective of dosage, but 16 mg increased the development of polycystic ovarian degeneration. Four to 18% of the females still had corpora lutea after altrenogest. Most females ovulated either between both inseminations or thereafter (P<0.05). Females treated with D-Phe(6)-LHRH tended to ovulate earlier than those injected with hCG. The CR and FR were up to 25% lower for sows diagnosed as non-pregnant than for sows after first service (P<0.05). Among sows diagnosed as non-pregnant the CR was higher in females treated with D-Phe(6)-LHRH (P<0.05). No differences were found in regard to numbers of TB and LB. In conclusion, a treatment with 20mg altrenogest per day per animal, followed by 800 IU eCG and 50 microg the GnRH-analogue D-Phe(6)-LHRH is appropriate to synchronize estrus and ovulation of sows diagnosed as non-pregnant. Whether there might be a need to feed altrenogest for a longer interval of 18 days has to be investigated.     

Mitochondrial COI and morphological evidence for host specificity of the black cherry aphids Myzus cerasi (Fabricius, 1775) collected from different cherry tree species in Europe (Hemiptera,Aphididae)

Partial sequences of the mitochondrial COI gene of forty eight European and two Turkish population samples of Myzus cerasi from different winter hosts (Prunus spp.) were subjected to phylogenetic analyses. The analysed M. cerasi samples emerged as paraphyletic relative to a Myzus borealis sample used as an out-group, and formed two major clades in neighbor joining, maximum parsimony, maximum likelihood and Bayesian inference trees, corresponding to subspecies living specifically on Prunus avium and P. cerasus. Multivariate discriminant analysis (method of canonical variates) was applied to find out if morphological variation of samples correlated with mitochondrial COI and host plant information. Mean scores on the first two canonical variables clustered samples fully in accordance with their COI haplotypes and host plants confirming the existence of two morphologically similar winter host - specific subspecies of M. cerasi in Europe. No single morphological character enabled satisfactory discrimination between apterous viviparous females of the two subspecies. A three-character linear discriminant function enabled 92.37% correct identification of apterous viviparous females of M. cerasi cerasi (n = 118) and 93.64% of M. cerasi pruniavium (n = 110). A key for the morphological identification of the two subspecies is presented and their taxonomic status is discussed.     

Influence of N- and/or C-terminal regions on activity, expression, characteristics and structure of lipase from Geobacillus sp. 95

GD-95 lipase from Geobacillus sp. strain 95 and its modified variants lacking N-terminal signal peptide and/or 10 or 20 C-terminal amino acids were successfully cloned, expressed and purified. To our knowledge, GD-95 lipase precursor (Pre-GD-95) is the first Geobacillus lipase possessing more than 80 % lipolytic activity at 5 °C. It has maximum activity at 55 °C and displays a broad pH activity range. GD-95 lipase was shown to hydrolyze p-NP dodecanoate, tricaprylin and canola oil better than other analyzed substrates. Structural and sequence alignments of bacterial lipases and GD-95 lipase revealed that the C-terminus forms an α helix, which is a conserved structure in lipases from Pseudomonas, Clostridium or Staphylococcus bacteria. This work demonstrates that 10 and 20 C-terminal amino acids of GD-95 lipase significantly affect stability and other physicochemical properties of this enzyme, which has never been reported before and can help create lipases with more specific properties for industrial application. GD-95 lipase and its modified variants GD-95-10 can be successfully applied to biofuel production, in leather and pulp industries, for the production of cosmetics or perfumes. These lipases are potential biocatalysts in processes, which require extreme conditions: low or high temperature, strongly acidic or alkaline environment and various organic solvents.