Effect of phospholipids on conformational structure of bovine pancreatic trypsin inhibitor (BPTI) and its thermolabile mutants

The effects of negatively charged phosphatidylserine-prepared membranes (PS) and neutral phosphatidylcholine-prepared membranes (PC) on the structure of wild-type and mutant bovine pancreatic trypsin inhibitor (BPTI) at neutral pH were investigated. The presence of PC did not have any effect on the protein structure while PS induced a non-native structure in three mutant BPTI proteins. However, the negatively charged membrane did not have any effect on wild-type BPTI. The findings revealed that (i) elimination of some disulphide bonds results in dramatic change in protein structure, and, (ii) that this biochemical interaction is surface-driven and electrostatic interactions may play a very strong role in influencing the fore-stated changes in protein structure. Of further interest were the results obtained from investigating the possible role of PS fluidity and concentration in altering mutant. When the value of Gibbs free-energy change of unfolding (DeltaG(U)) was positive, various non-native structures were formed in a concentration-dependent manner. However, when the value of DeltaG(U) was negative, only two types of non-native structures were formed: one with high beta structure content at low PS fluidity state, and the other with a high alpha-helical content at high PS fluidity state. Our study reveals how particular combinations of phospholipid:protein interactions can induce a protein conformation transition from a native to a non-native one at neutral pH, especially when the native structure is predestabilized by amino acid substitutions. This revelation may open up opportunities to explore alternative ways in which phospholipids may play a role in protein mis-folding and the related pathologies.     

Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110.

The complete nucleotide sequence of the genome of a symbiotic bacterium Bradyrhizobium japonicum USDA110 was determined. The genome of B. japonicum was a single circular chromosome 9,105,828 bp in length with an average GC content of 64.1%. No plasmid was detected. The chromosome comprises 8317 potential protein-coding genes, one set of rRNA genes and 50 tRNA genes. Fifty-two percent of the potential protein genes showed sequence similarity to genes of known function and 30% to hypothetical genes. The remaining 18% had no apparent similarity to reported genes. Thirty-four percent of the B. japonicum genes showed significant sequence similarity to those of both Mesorhizobium loti and Sinorhizobium meliloti, while 23% were unique to this species. A presumptive symbiosis island 681 kb in length, which includes a 410-kb symbiotic region previously reported by G?ttfert et al., was identified. Six hundred fifty-five putative protein-coding genes were assigned in this region, and the functions of 301 genes, including those related to symbiotic nitrogen fixation and DNA transmission, were deduced. A total of 167 genes for transposases/104 copies of insertion sequences were identified in the genome. It was remarkable that 100 out of 167 transposase genes are located in the presumptive symbiotic island. DNA segments of 4 to 97 kb inserted into tRNA genes were found at 14 locations in the genome, which generates partial duplication of the target tRNA genes. These observations suggest plasticity of the B. japonicum genome, which is probably due to complex genome rearrangements such as horizontal transfer and insertion of various DNA elements, and to homologous recombination.     

Occurrence and abundance of bregmacerotid larvae in Kagoshima Bay,southern Japan,with descriptions of ontogenetic larval characters

Regular collections of ichthyoplankton were made with a larva net at 9–14 stations from Oct. 1983 to Dec. 1988 in Kagoshima Bay, totalling 817 collections from 66 cruises. A total of 2172 bregmacerotid larvae obtained from 195 collections of 33 cruises were identified asB. atlanticus (2001),B. neonectabanus (169),B. macclellandii (1) andB. nectabanus (1, tentative identification). The peaks of mean densities of larvae collected occurred in autumn forB. atlanticus andB. neonectabanus. The larvae ofB. atlanticus occurred throughout the bay, and their densities and frequency of occurrence were lower in the northern part of the bay. In the southern part of the bay, stations in its southwest quadrant showed higher densities than the others. The larvae ofB. neonectabanus occurred only in the southern part of the bay in which stations in the northwest quadrant showed higher densities than the others.     

Changes in fatigue,autonomic functions,and blood biomarkers due to sitting isometric yoga in patients with chronic fatigue syndrome

Background

In a previous randomized controlled trial, we found that sitting isometric yoga improves fatigue in patients with chronic fatigue syndrome (CFS) who are resistant to conventional therapy. The aim of this study was to investigate possible mechanisms behind this finding, focusing on the short-term fatigue-relieving effect, by comparing autonomic nervous function and blood biomarkers before and after a session of isometric yoga.

Methods

Fifteen patients with CFS who remained symptomatic despite at least 6 months of conventional therapy practiced sitting isometric yoga (biweekly 20 min practice with a yoga instructor and daily home practice) for eight weeks. Acute effects of sitting isometric yoga on fatigue, autonomic function, and blood biomarkers were investigated after the final session with an instructor. The effect of a single session of sitting isometric yoga on fatigue was assessed by the Profile of Mood Status (POMS) questionnaire immediately before and after the session. Autonomic nervous function (heart rate (HR) variability) and blood biomarkers (cortisol, DHEA-S, TNF-α, IL-6, IFN-γ, IFN-α, prolactin, carnitine, TGF-β1, BDNF, MHPG, and HVA) were compared before and after the session.

Results

Sitting isometric yoga significantly reduced the POMS fatigue score (p?<?0.01) and increased the vigor score (p?<?0.01). It also reduced HR (p?<?0.05) and increased the high frequency power (p?<?0.05) of HR variability. Sitting isometric yoga increased serum levels of DHEA-S (p?<?0.05), reduced levels of cortisol (p?<?0.05) and TNF-α (p?<?0.05), and had a tendency to reduce serum levels of prolactin (p?<?0.1). Decreases in fatigue scores correlated with changes in plasma levels of TGF-β1 and BDNF. In contrast, increased vigor positively correlated with HVA.

Conclusions

A single session of sitting isometric yoga reduced fatigue and increased vigor in patients with CFS. Yoga also increased vagal nerve function and changed blood biomarkers in a pattern that suggested anti-stress and anti-inflammatory effects. These changes appear to be related to the short-term fatigue-relieving effect of sitting isometric yoga in patients with CFS. Furthermore, dopaminergic nervous system activation might account for sitting isometric yoga-induced increases in energy in this patient population.

Trial registration

University Hospital Medical Information Network (UMIN CTR) UMIN000009646. Registered Dec 27, 2012.

     

Circumnutation and distribution of phytohormones in <Emphasis Type="Italic">Vigna angularis</Emphasis> epicotyls

Circumnutation is a plant growth movement in which the tips of axial organs draw a circular orbit. Although it has been studied since the nineteenth century, its mechanism and significance are still unclear. Greened adzuki bean (Vigna angularis) epicotyls exhibited a clockwise circumnutation in the top view with a constant period of 60 min under continuous white light. The bending zone of circumnutation on the epicotyls was always located in the region 1–3 cm below the tip, and its basal end was almost identical to the apical end of the region where the epicotyl had completely elongated. Therefore, epidermal cells that construct the bending zone are constantly turning over with their elongation growth. Since exogenously applied auxin transport inhibitors and indole-3-acetic acid (IAA) impaired circumnutation without any effect on the elongation rate of epicotyls, we attempted to identify the distribution pattern of endogenous auxin. Taking advantage of its large size, we separated the bending zone of epicotyls into two halves along the longitudinal axis, either convex/concave pairs in the plane of curvature of circumnutation or pre-convex/pre-concave pairs perpendicular to the plane. By liquid chromatography–mass spectrometry, we found, for the first time, that IAA and gibberellin A₁ were asymmetrically distributed in the pre-convex part in the region 1–2 cm below the tip. This region of epicotyl sections exhibited the highest responsiveness to exogenously applied hormones, and the latent period between the hormone application and the detection of a significant enhancement in elongation was 15 min. Our results suggest that circumnutation in adzuki bean epicotyls with a 60 min period is maintained by differential growth in the bending zone, which reflects the hormonal status 15 min before and which is shifting sequentially in a circumferential direction. Cortical microtubules do not seem to be involved in this regulation.     

Structural analysis of a Lotus japonicus genome. II. Sequence features and mapping of sixty-five TAC clones which cover the 6.5-mb regions of the genome.

Sixty-five TAC (transformation-competent artificial chromosomes) clones were selected from a genomic library of Lotus japonicus accession MG-20 based on the sequence information of expressed sequences tags (ESTs), cDNA and gene information, and their nucleotide sequences were determined. The average insert size of the TAC clone was approximately 100 kb, and the total length of the sequenced regions in this study is 6,556,100 bp. Together with the nucleotide sequences of 56 TAC clones previously reported, the regions sequenced so far total 12,029,295 bp. By comparison with the sequences in protein and EST databases and by analysis with computer programs for gene modeling, a total of 711 potential protein-encoding genes with known or predicted functions, 239 gene segments and 90 pseudogenes were identified in the newly sequenced regions. The average gene density assigned so far was 1 gene/9140 bp. The average length of the assigned genes was 2.6 kb, which is considerably larger than that assigned in the Arabidopsis thaliana genome (1.9 kb for 6451 genes). Introns were identified in approximately 73% of the potential genes, and the average number and length of the introns per gene were 3.4 and 377 bp, respectively. Simple sequence repeat length polymorphism (SSLP) or derived cleaved amplified polymorphic sequence (dCAPS) markers were generated based on the nucleotide sequences of the genomic clones obtained, and each clone was mapped onto the linkage map using the F2 mapping population derived from a cross of two accessions of L. japonicus, Gifu B-129 and Miyakojima MG-20. The sequence data, gene information and mapping information are available through the World Wide Web at http://www.kazusa.or.jp/lotus/.