Molecular phylogenetic study and expression analysis of ATP-binding cassette transporter gene family in Oryza sativa in response to salt stress

ATP-binding cassette (ABC) transporter is a large gene superfamily that utilizes the energy released from ATP hydrolysis for transporting myriad of substrates across the biological membranes. Although many investigations have been done on the structural and functional analysis of the ABC transporters in Oryza sativa, much less is known about molecular phylogenetic and global expression pattern of the complete ABC family in rice. In this study, we have carried out a comprehensive phylogenetic analysis constructing neighbor-joining and maximum-likelihood trees based on various statistical methods of different ABC protein subfamily of five plant lineages including Chlamydomonas reinhardtii (green algae), Physcomitrella patens (moss), Selaginella moellendorffii (lycophyte), Arabidopsis thaliana (dicot) and O. sativa (monocot) to explore the origin and evolutionary patterns of these ABC genes. We have identified several conserved motifs in nucleotide binding domain (NBD) of ABC proteins among all plant lineages during evolution. Amongst the different ABC protein subfamilies, ‘ABCE’ has not yet been identified in lower plant genomes (algae, moss and lycophytes). The result indicated that gene duplication and diversification process acted upon these genes as a major operative force creating new groups and subgroups and functional divergence during evolution. We have demonstrated that rice ABCI subfamily consists of only half size transporters that represented highly dynamic members showing maximum sequence variations among the other rice ABC subfamilies. The evolutionary and the expression analysis contribute to a deep insight into the evolution and diversity of rice ABC proteins and their roles in response to salt stress that facilitate our further understanding on rice ABC transporters.     

Comprehensive comparison of two protein family of P-ATPases (13A1 and 13A3) in insects

The P-type ATPases (P-ATPases) are present in all living cells where they mediate ion transport across membranes on the expense of ATP hydrolysis. Different ions which are transported by these pumps are protons like calcium, sodium, potassium, and heavy metals such as manganese, iron, copper, and zinc. Maintenance of the proper gradients for essential ions across cellular membranes makes P-ATPases crucial for cell survival. In this study, characterization of two families of P-ATPases including P-ATPase 13A1 and P-ATPase 13A3 protein was compared in two different insect species from different orders. According to the conserved motifs found with MEME, nine motifs were shared by insects of 13A1 family but eight in 13A3 family. Seven different insect species from 13A1 and five samples from 13A3 family were selected as the representative samples for functional and structural analyses. The structural and functional analyses were performed with ProtParam, SOPMA, SignalP 4.1, TMHMM 2.0, ProtScale and ProDom tools in the ExPASy database. The tertiary structure of Bombus terrestris as a sample of each family of insects were predicted by the Phyre2 and TM-score servers and their similarities were verified by SuperPose server. The tertiary structures were predicted via the “c3b9bA” model (PDB Accession Code: 3B9B) in P-ATPase 13A1 family and “c2zxeA” model (PDB Accession Code: 2ZXE) in P-ATPase 13A3 family. A phylogenetic tree was constructed with MEGA 6.06 software using the Neighbor-joining method. According to the results, there was a high identity of P-ATPase families so that they should be derived from a common ancestor however they belonged to separate groups. In protein–protein interaction analysis by STRING 10.0, six common enriched pathways of KEGG were identified in B. terrestris in both families. The obtained data provide a background for bioinformatic studies of the function and evolution of other insects and organisms.     

Cellulose synthesis in maize: isolation and expression analysis of the cellulose synthase (CesA) gene family

Stalk lodging in maize results in significant yield losses. We have determined that cellulose per unit length of the stalk is the primary determinant of internodal strength. An increase in cellulose concentration in the wall might allow simultaneous improvements in stalk strength and harvest index. Cellulose formation in plants can be perturbed by mutations in the genes involved in cellulose synthesis, post-synthetic cellulose alteration or deposition, N-glycosylation, and some other genes with as yet unknown functions. We have isolated 12 members of the cellulose synthase (CesA) gene family from maize. The genes involved in primary wall formation appear to have duplicated relatively independently in dicots and monocots. The deduced amino acid sequences of three of the maize genes, ZmCesA10–12, cluster with the Arabidopsis CesA sequences that have been shown to be involved in secondary wall formation. Based on their expression patterns across multiple tissues, these three genes appear to be coordinately expressed. The remaining genes show overlapping expression to varying degrees with ZmCesA1, 7, and 8 forming one group, ZmCesA3 and 5 a second group, and ZmCesA2 and 6 exhibiting independent expression of any other gene. This suggests that the varying levels of coexpression may just be incidental except in the case of ZmCesA10–12, which may interact with each other to form a functional enzyme complex. Isolation of the expressed CesA genes from maize and their association with primary or secondary wall formation has made it possible to test their respective roles in cellulose synthesis through mutational genetics or transgenic approaches. This information would be useful in improving stalk strength.     

Return to the RNAi world: rethinking gene expression and evolution (Nobel Lecture)

It's wonderful to be here today, I would like to start with the most important part, by saying thank you. First of all, I want to thank Andy Fire for being such a tremendous colleague, friend, and collaborator going back over the years. Without Andy I definitely wouldn't be here today. I need to thank the University of Massachusetts for providing for my laboratory, for believing in me, and for giving me not only a place and money, but great colleagues with whom to pursue my research. Without UMass and the great environment provided for me there, I probably would not be here today. And, of course my family; I'm not going to spend time now thanking them individually, but they know how important they are.     

Comparative analysis of amino acid composition in the active site of nirk gene encoding copper-containing nitrite reductase (CuNiR) in bacterial spp.

The nirk gene encoding the copper-containing nitrite reductase (CuNiR), a key catalytic enzyme in the environmental denitrification process that helps to produce nitric oxide from nitrite. The molecular mechanism of denitrification process is definitely complex and in this case a theoretical investigation has been conducted to know the sequence information and amino acid composition of the active site of CuNiR enzyme using various Bioinformatics tools. 10 Fasta formatted sequences were retrieved from the NCBI database and the domain and disordered regions identification and phylogenetic analyses were done on these sequences. The comparative modeling of protein was performed through Modeller 9v14 program and visualized by PyMOL tools. Validated protein models were deposited in the Protein Model Database (PMDB) (PMDB id: PM0080150 to PM0080159). Active sites of nirk encoding CuNiR enzyme were identified by Castp server. The PROCHECK showed significant scores for four protein models in the most favored regions of the Ramachandran plot. Active sites and cavities prediction exhibited that the amino acid, namely Glycine, Alanine, Histidine, Aspartic acid, Glutamic acid, Threonine, and Glutamine were common in four predicted protein models. The present in silico study anticipates that active site analyses result will pave the way for further research on the complex denitrification mechanism of the selected species in the experimental laboratory.     

In silico structural and functional characterization and phylogenetic study of alkaline phosphatase in bacterium,Rhizobium leguminosarum (Frank 1879)

Phosphorus is one of the primary macronutrient of plants, which is present in soil. It is essential for normal growth and development of plants. Plants use inorganic form of phosphate but organic form can also be assimilated with the help of soil inhabiting bacteria. Alkaline phosphatase is an enzyme present in Rizobium bacteria. This enzyme is responsible for solubilization and mineralization of organic phosphate and makes it readily available for plants. In the present study, nine different strains of Rhizobium leguminosarum were selected for a detailed computational structural and functional characterization and phylogenetic studies of alkaline phosphatase. Amino acid sequences were retrieved from UniProt and saved in FASTA format for use in analysis. Phylogenetic analysis of these strains was done by using MEGA7. 3D structure prediction was performed by using online server I-Tasser. Galaxy Web and 3D Refine were used for structure refinement. The refined structures were evaluated using two validation servers, QMEAN and SAVES. Protein-protein interaction analysis was done by using STRING. For detailed functional characterization, Cofactor, Coach, RaptorX, PSORT and MEME were used. Overall quality of predicted protein models was above 80%. Refined and validated models were submitted into PMDB. Seven out of nine strains were closely related and other two were distantly related. Protein-Protein interaction showed no significant co-expression among the interaction partners.     

X-ray analysis of the structure of a copoly(ester-imide)

The structure of a thermotropic liquid crystalline copoly(ester-imide) prepared from p-hydroxybenzoic acid (48 mol %), 4,4′-dihydroxybenzophenone (26 mol %), and N,N′-bis(trimellitimide)hexane (26 mol %) has been investigated by X-ray diffraction. X-ray fiber diagrams of as-spun and annealed fibers contain a series of aperiodic layer lines reminiscent of those seen for fibers of other copolymers that have extended chain conformations and completely random monomer sequences. The positions of these layer lines were reproduced approximately in simulation of the X-ray scattering by a fully extended chain of completely random sequence, and the match was improved to within experimental error when we considered a stereochemically acceptable sinuous chain. This agreement was lost when the sequence statistics deviated were completely random. © 1998 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 36: 3137–3145, 1998     

Synthesis,crystal structure,and spectral analysis of a 1-D Mn(II) coordination polymer

A manganese(II) coordination polymer [Mn(TMB)₂?·?H₂O] _n (1) (HTMB?=?3,4,5-trimethoxybenzoic acid) has been synthesized under hydrothermal conditions and characterized by single-crystal X-ray diffraction, elemental analysis, powder X-ray diffraction analysis, spectroscopic (IR, solid state UV-Vis), and thermal methods. The crystal belongs to orthorhombic system, space group P2₁2₁2₁, with cell parameters a?=?7.3001(8), b?=?11.4146(13), c?=?27.053(3)?Å, α?=?β?=?γ?=?90°, V?=?2254.3(4)?ų, Z?=?4. In 1, TMB in two different coordination modes bridges six-coordinate manganese(II) centers forming a 1-D infinite chain coordination framework. The spectral and thermal properties of the complexes have also been studied.     

Synthesis,structure, network and thermal analysis of four 5-(pyrazinyl)tetrazolato copper(II) and cobalt(II) complexes

Three new copper complexes and one cobalt complex with 5-(pyrazinyl)tetrazolate anion, (pyztz)⁻, as chelating bidentate ligand, were obtained by the reaction of pyrazinecarbonitrile with sodium azide in the presence of copper(II) nitrate or cobalt(II)chloride. Complexes of composition [Cu(pyztz)₂(H₂O)] (1) deep blue crystals, [Cu(pyztz)₂(H₂O)₂] (2a) green crystals, [Co(pyztz)₂(H₂O)₂] (2b) orange crystals, [Cu(pyztz)₂(H₂O)₂] · (H₂O) (3) blue crystals were obtained. The single crystal X-ray diffraction revealed that complex 1 has square pyramidal structure with one water molecule at apical and two pyrazine-tetrazolato ligands at basal sites, while structures of 2a, 2b and 3 consist of octahedrally coordinated metal ions, where two pyztz anions act as bidentate ligands via one of the pyrazine-N atoms and one of the tetrazole-N atoms in trans-positions and two trans water molecules. Complex 3 contains one extra lattice water molecule. Hydrogen bonds of the types O–H?O and O–H?N connect the mononuclear units to a three-dimensional network structure in 2 (a and b are isostructural) and 3. Although the H-bond patterns look complex it is shown that they can be related to the well-known three- and six-connected rutile net (rtl) in 2 and the four- and six-connected fsh-net in 3.     

Nonisotopic single-strand conformation polymorphism analysis of sequence variability in ribosomal DNA expansion segments within the genus Trichinella (Nematoda: Adenophorea)

A nonisotopic single-strand conformation polymorphism (SSCP) approach was employed to 'fingerprint' sequence variability in the expansion segment 5 (ES5) of domain IV and the D3 domain of nuclear ribosomal DNA within and/or among isolates and individual muscle (first-stage) larvae representing all currently recognized species/genotypes of Trichinella. In addition, phylogenetic analyses of the D3 sequence data set, employing three different tree-building algorithms, examined the relationships among all of them. These analyses showed strong support that the encapsulated species T. spiralis and T. nelsoni formed a group to the exclusion of the other encapsulated species T. britovi and its related genotypes Trichinella T8 and T9 and T. murrelli, and T. nativa and Trichinella T6, and strong support that T. nativa and Trichinella T6 grouped together. Also, these eight encapsulated members grouped to the exclusion of the nonencapsulated species T. papuae and T. zimbabwensis and the three representatives of T. pseudospiralis investigated. The findings showed that nonencapsulated species constitute a complex group which is distinct from the encapsulated species and supported the current hypothesis that encapsulated Trichinella group external to the nonencapsulated forms, in accordance with independent biological and biochemical data sets.     

Synthesis, properties, and the crystal structure of the complex Cp2Yb(DAD)

The diazadiene complex of trivalent ytterbium, Cp₂Yb(DAD) (1) (DAD=Bu^t−N=CH−CH=N−Bu^t) was prepared according to three different procedures, namely, by oxidation of Cp₂Yb(THF)₂ with diazadiene in THF, by the reaction of Cp₂YbCl with DAD²⁻Na⁺ ₂ taken in a ratio of 2∶1, and by the reaction of Cp₂YbCl(THF) with DAD²⁻Na⁺ ₂ taken in a ratio of 1∶1. Complex1 was characterized by microanalysis, IR spectroscopy, magnetochemistry, and X-ray diffraction analysis. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 384–386, February, 1999.     

Chemical analysis of the Chinese herbal medicine Gan-Cao (licorice)

Gan-Cao, or licorice, is a popular Chinese herbal medicine derived from the dried roots and rhizomes of Glycyrrhiza uralensis, G. glabra, and G. inflata. The main bioactive constituents of licorice are triterpene saponins and various types of flavonoids. The contents of these compounds may vary in different licorice batches and thus affect the therapeutic effects. In order to ensure its efficacy and safety, sensitive and accurate methods for the qualitative and quantitative analyses of saponins and flavonoids are of significance for the comprehensive quality control of licorice. This review describes the progress in chemical analysis of licorice and its preparations since 2000. Newly established methods are summarized, including spectroscopy, thin-layer chromatography, gas chromatography, high-performance liquid chromatography (HPLC), liquid chromatography/mass spectrometry (LC/MS), capillary electrophoresis, high-speed counter-current chromatography (HSCCC), electrochemistry, and immunoassay. The sensitivity, selectivity and powerful separation capability of HPLC and CE allows the simultaneous detection of multiple compounds in licorice. LC/MS provides characteristic fragmentations for the rapid structural identification of licorice saponins and flavonoids. The combination of HPLC and LC/MS is currently the most powerful technique for the quality control of licorice.     

Chemical-physical aspects of formation and evolution of phase structure in multi-polymers: Intensity fluctuation, phase structure and its fractal characteristics in blends of isotactic polypropylene with poly(cis-1,4-butadiene) rubber

This paper studies the formation and evolution of phase structure of isotactic polypropylene/poly(cis-1,4-butadiene) (iPP/PcBR) blends during molten and mixing in a visual mixer by on-line analysis of the small angle light back scattering. The density fluctuation of iPP/PcBR blends during molten and mixing is discussed using the integral-intensity Js, of the scattering intensity of the blends. The "invariant" Q, which shows fluctuation of the system, is calculated by data of the small angle light back scattering, and the variation of Q with the blending time, temperature and shear rate during molten and mixing in iPP/PcBR blends is discussed. The structure parameters which characterize dimensions of phase in the blends, as the correlation distance ac, and the average chord lengths of two-phase, as li PP and lP cBR, are calculated by data of scattering intensity. The average diameters dp of dispersed phases are calculated from SEM images. The variation of ac, dp, li PP and lP cBR with the blending time and compositions in the blends during molten and mixing is discussed. The scale law is analyzed to find multi-scale characteristics in this system. The generalized fractal dimension Dp is calculated and the relation of Dp with generalized entropy function is discussed to determine that Dp is state function and the physical significance of Dp is the same as that of the generalized entropy function.