Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow

Background  

In the post-genome era, most research scientists working in the field of proteomics are confronted with difficulties in management of large volumes of data, which they are required to keep in formats suitable for subsequent data mining. Therefore, a well-developed open source laboratory information management system (LIMS) should be available for their proteomics research studies.     

Vinyl polymers based on L-histidine residues. Part 2. Swelling and electric behavior of smart poly(ampholyte) hydrogels for biomedical applications

Hydrogels based on the uncharged N-isopropylacrylamide and the ionic ampholyte N-acryloyl-L-histidine showed a reversible multiple-responsive volume change and volume phase transition behavior in aqueous solution. The phase transition phenomenon was induced by the temperature, the pH, the salt-type concentration, and the electric potential. The kind of cation (Na+, K+, Cs+, Mg2+, Ca2+, Sr2+) and anion (Cl-, ClO4-, NO3-, SO4(2-)) strongly influenced the critical concentration that improved the phase separation of the gels. The volume of the collapsed gel can be hundred times smaller than that of the swollen one. The oscillatory swelling of the gels in response to temperature and pH (4 and 9) changes was fast and reversible, while the contractile behavior in the electric field showed response only at pH 9, i.e., when the amount of negative charges on the L-histidine residues predominated. The electrically induced anisotropic gel deswelling was attributed to the syneresis of water from the gel. The nontoxicity against the RAW264 cell line and the low osmotic pressure exhibited by the swollen gels make these compounds useful scaffolds for human organs. The ability to load and release an ionizable drug molecular model (ferulic acid) from the hydrogels was shown also at different pH values.     

6-Carboxy-5,7-diarylcyclopenteno[1,2-b]pyridine derivatives: a novel class of endothelin receptor antagonists

Compounds (2-5) with a 6-carboxy-5,7-diarylcyclopentenopyridine skeleton were designed, synthesized, and identified as a new class of potent non-peptide endothelin receptor antagonists. The regio-isomer 2 was found to show potent inhibitory activity with an IC(50) value of 2.4 nM against (125)I-labeled ET-1 binding to human ET(A) receptors and a 170-fold selectivity for ET(A) over ET(B) receptors. Furthermore, 2 displayed more potent in vivo activity than did the indan-type compound 1 in a mouse ET-1 induced lethality model, suggesting the potential of 2 as a new lead structure. Derivatization on substituted phenyl groups at the 5- and 7-positions of 2 revealed that a 3,4-methylenedioxyphenyl group at the 5-position and a 4-methoxyphenyl group at the 7-position were optimal for binding affinity. Further derivatization of 2 by incorporating a substituent into the 2-position of the 4-methoxyphenyl group led to the identification of a more potent ET(A) selective antagonist 2p with an IC(50) value of 0.87 nM for ET(A) receptors and a 470-fold selectivity. In addition, 2p showed highly potent in vivo efficacy (AD(50): 0.04 mg/kg) in the lethality model.     

Preparation of glycosylated amino acid derivatives for glycoprotein synthesis by in vitro translation system

General preparation of glycosylated amino acylated nucleotide for in vitro peptide synthesis was described. Both O-glycosylated amino acyl nucleotides and C-glycosylated amino acyl nucleotide were synthesized by choosing the appropriate protecting group.     

The Sec protein-translocation pathway

The Sec machinery (or translocase) provides a major pathway of protein translocation from the cytosol across the cytoplasmic membrane in bacteria. The SecA ATPase interacts dynamically with the SecYEG integral membrane components to drive the transmembrane movement of newly synthesized preproteins. This pathway is also used for integration of some membrane proteins and the Sec translocase interacts with other cellular components to achieve its cellular roles. The detailed protein interactions involved in these processes are being actively studied and a structural understanding of the protein-conducting channel has started to emerge.     

Chromosome studies in 500 induced abortions.

A survey of the chromosome constitution in 500 induced abortions (5-12 menstrual weeks) was undertaken over a period of 1 1/2 years. There were 34 cases (6.8%) of gross chromosome anomalies: 2 cases of trisomy A; 5 of trisomy C (including XXX and XXY); 1 of mosaic trisomy C; 4 of trisomy D; 2 of trisomy E; 2 of trisomy G; 1 of double trisomy E and G; 1 of XYY; 4 of monosmy C (including XO); 2 of mosaic monosomy C; 1 of mosaicism of ring D chromosome; 1 of extra small metacentric chromosome; 3 of triploidy (including triploidy with double trisomy C and G); and 5 of tetraploidy and its mosaicism. An increased risk for the occurrence of trisomic anomalies was found with advancing age of the mothers. In contrast, the production of monosomies was not age-related. Trisomies were the most common type of anomalies and were found almost at random, regardless of the characteristics of chromosomes. Neither satellited nor small chromosomes were predominantly involved in the formation of chromosome anomalies.     

Solution structures of the double-stranded RNA-binding domains from RNA helicase A

RNA helicase A (RHA) is a highly conserved protein with multifaceted functions in the gene expression of cellular and viral mRNAs. RHA recognizes highly structured nucleotides and catalytically rearranges the various interactions between RNA, DNA, and protein molecules to provide a platform for the ribonucleoprotein complex. We present the first solution structures of the double-stranded RNA-binding domains (dsRBDs), dsRBD1 and dsRBD2, from mouse RHA. We discuss the binding mode of the dsRBDs of RHA, in comparison with the known dsRBD structures in their complexes. Our structural data provide important information for the elucidation of the molecular reassembly mediated by RHA.     

Demonstration of osmotically dependent promotion of aerenchyma formation at different levels in the primary roots of rice using a 'sandwich' method and X-ray computed tomography

Background and Aims

The effect of environmental factors on the regulation of aerenchyma formation in rice roots has been discussed for a long time, because aerenchyma is constitutively formed under aerated conditions. To elucidate this problem, a unique method has been developed that enables sensitive detection of differences in the development of aerenchyma under two different environmental conditions. The method is tested to determine whether aerenchyma development in rice roots is affected by osmotic stress.

Methods

To examine aerenchyma formation both with and without mannitol treatment in the same root, germinating rice (Oryza sativa) caryopses were sandwiched between two agar slabs, one of which contained 270 mm of mannitol. The roots were grown touching both slabs and were thereby exposed unilaterally to osmotic stress. As a non-invasive approach, refraction contrast X-ray computed tomography (CT) using a third-generation synchrotron facility, SPring-8 (Super photon ring 8 GeV, Japan Synchrotron Radiation Research Institute), was used to visualize the three-dimensional (3-D) intact structure of aerenchyma and its formation in situ in rice roots. The effects of unilateral mannitol treatment on the development of aerenchyma were quantitatively examined using conventional light microscopy.

Key Results

Structural continuity of aerenchyma was clearly visualized in 3-D in the primary root of rice and in situ using X-ray CT. Light microscopy and X-ray CT showed that the development of aerenchyma was promoted on the mannitol-treated side of the root. Detailed light microscopic analysis of cross-sections cut along the root axis from the tip to the basal region demonstrated that aerenchyma developed significantly closer to the root tip on the mannitol-treated side of the root.

Conclusions

Continuity of the aerenchyma along the rice root axis was morphologically demonstrated using X-ray CT. By using this ‘sandwich’ method it was shown that mannitol promoted aerenchyma formation in the primary roots of rice.