Dwijendra Gupta
University of Allahabad, Biochemistry and Bioinformatics, Faculty Member
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Diallel cross hybrids obtained by crossing six opaque-2 (o 2) converted inbred lines were compared with a similar series of crosses made between the analogous normal inbred lines together with the parents, for a number of protein quality... more
Diallel cross hybrids obtained by crossing six opaque-2 (o 2) converted inbred lines were compared with a similar series of crosses made between the analogous normal inbred lines together with the parents, for a number of protein quality and oil traits. The results obtained show that there is only a minor decrease in percent protein or yield of protein per hectare caused by the presence of the o 2 gene in recessive homozygous condition, compared with its normal counterpart. On the other hand, percent lysine in the whole kernel, lysine yield per hectare and percent lysine in protein are increased by 53, 45 and 55 percent, respectively, in the o 2 inbred lines and hybrids compared with their normal analogues. Percent oil and oil yield remain almost unaltered by the presence or absence of the o 2 gene. As well as lysine, the content of other amino acids, such as aspartic acid, arginine, glycine, threonine, valine and histidine are also, in general, increased by the presence of the o 2 ...
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Cystinosin and sialin proteins are the major constituent of lysosomal membrane and play an important role in the transport of the metabolite across the lysosomal membrane. Any mutation in these genes causes autosomal recessive lysosomal... more
Cystinosin and sialin proteins are the major constituent of lysosomal membrane and play an important role in the transport of the metabolite across the lysosomal membrane. Any mutation in these genes causes autosomal recessive lysosomal storage disorders named as cystinosis and salla disease. To understand cause of these metabolic disorders and their evolutionary relation, genomics based study of these proteins were facilitated by bioinformatics tools like BLAST, ClustalW, MEGA4, BioEdit (version 7.0.5.3) etc. This work established the molecular phylogenetic relationship among the different taxa of cystinosin and sialin. Structural properties were concluded by their amino acid frequency, hydrophobicity profile, entropy and conserved domains present. Both the protein showed that mean hydrophobicity for most of the positions in all the species was around zero and was basically hydrophobic in nature. These informations facilitate to explore the molecular basis of the lysosomal storage ...
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Mentha species are the main source of a number of natural aroma chemicals. In this paper, an attempt has been made to study some important Mentha species, viz., M. piperita, M. canadensis and M. arvensis. In-silico approaches were used... more
Mentha species are the main source of a number of natural aroma chemicals. In this paper, an attempt has been made to study some important Mentha species, viz., M. piperita, M. canadensis and M. arvensis. In-silico approaches were used for EST assembly, comparative genomics, homology modeling, molecular threading, domain and fold recognition, secondary structure analysis, physicochemical and functional characterization. Totally, 164 different proteins were reported from contigs which were subjected to ...
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Mulberry silkworm, Bombyx mori and non-mulberry silkworm, Philosamia ricini both are an economically important lepidopteron, being a producer of silk. Mulberry (Bombyx mori) accounts for 92% and eri (Philosamia ricini) accounts for 5.5%... more
Mulberry silkworm, Bombyx mori and non-mulberry silkworm, Philosamia ricini both are an economically important lepidopteron, being a producer of silk. Mulberry (Bombyx mori) accounts for 92% and eri (Philosamia ricini) accounts for 5.5% of the total raw silk production of the country. The silk produce by P. ricini is not as fine or delicate as that of B. mori, but it is more durable. The present study was focused on the life cycle of both types of mulberry and non-mulberry silkworms. In the light of the study, it was observed that, however, both are of the same family Saturniidae there is variation between the days of one stage to another stages and even diseases which occurs during the life cycle are also different.
Alzheimer's disease (AD) is a progressive neurodegenerative disease of central nervous system among elderly people. Human acetylcholinesterase (hAChE), an important enzyme in neuronal signaling, is responsible for... more
Alzheimer's disease (AD) is a progressive neurodegenerative disease of central nervous system among elderly people. Human acetylcholinesterase (hAChE), an important enzyme in neuronal signaling, is responsible for the degradation of acetylcholine which in turn prevents the post synaptic signal transmissions. hAChE has been an attractive target of drug discovery for the search of therapeutics against AD. In the recent past hAChE has become hot target for the investigation of new potential therapeutics. We performed virtual screening of entire database against hAChE. Further, the extra precision molecular docking was carried out to refine the docking results and the best complex was passed for molecular dynamics simulations in order of understanding the hAChE dynamics and its behavior in complex with the ligand which corroborate the outcomes of virtual screening. This also provides binding free energy data that establishes the ligands efficiency for inhibiting hAChE. The computational findings discussed in this paper provide initial information of inhibitory effects of ligand, (drugbank entry DB00983), over hAChE.
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The presence of several hormones in milk occurring either by passive diffusion or by active concentrating mechanism from blood can be of great concern to the neonate. According to Fulkerson [1979] when the clearance rates of the hormones... more
The presence of several hormones in milk occurring either by passive diffusion or by active concentrating mechanism from blood can be of great concern to the neonate. According to Fulkerson [1979] when the clearance rates of the hormones out of blood is considered, this worry is unwarranted. Concerning the steroids, when their levels have been monitored in milk after lactogenesis, the worry for the baby seems to be unfounded. But with the new finding of high level of LH-RH in milk whose concentration far exceeds that of blood, care should be taken to examine in the neonates whether the levels of LH and FSH become disproportionately high and induce the secretion of gonadal steroids at a higher level.
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ABSTRACT Lysosomes,the endocytic subcellular compartments play a very important role in the disintegration and recycling of cellular substances. The lysosomal associated membrane proteins LAMP-1 and LAMP-2 are major constituents of the... more
ABSTRACT Lysosomes,the endocytic subcellular compartments play a very important role in the disintegration and recycling of cellular substances. The lysosomal associated membrane proteins LAMP-1 and LAMP-2 are major constituents of the lysosomal membrane. Using ...
Abstract This study reports differentially expressed proteins in the middle silkglands of normal and cold stress treated 5th instar Philosamia ricini larvae by using high resolution two-dimensional polyacrylamide gel electrophoresis.... more
Abstract This study reports differentially expressed proteins in the middle silkglands of normal and cold stress treated 5th instar Philosamia ricini larvae by using high resolution two-dimensional polyacrylamide gel electrophoresis. About 300 protein spots were resolved in both type of the larvae. Most of the proteins were shown to be distributed in the area from 20 to 70 kDa ranging between pH 4 and 8. Six proteins showed considerably decreased expression in cold stress treated samples. Three proteins displayed increased level of expression after cold stress treatment, while two other proteins were expressed exclusively in cold stress treated silkgland tissues.
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Casein kinase-1 (CK1) isoforms actively participate in the down-regulation of canonical Wnt signaling pathway; however recent studies have shown their active roles in oncogenesis of various tissues through this pathway. Functional loss of... more
Casein kinase-1 (CK1) isoforms actively participate in the down-regulation of canonical Wnt signaling pathway; however recent studies have shown their active roles in oncogenesis of various tissues through this pathway. Functional loss of two isoforms (CK1-α/ε) has been shown to activate the carcinogenic pathway which involves the stabilization of of cytoplasmic β-catenin. Development of anticancer therapeutics is very laborious task and depends upon the structural and conformational details of the target. This study focuses on, how the structural dynamics and conformational changes of two CK1 isoforms are synchronized in carcinogenic pathway. The conformational dynamics in kinases is the responsible for their action as has been supported by the molecular docking experiments.
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Silk is a biological fiber produced by the caterpillars of Philosamia ricini moths at the end of their larval phase. Silk glands of silkworm secrete two major classes of proteins, the fibroin fiber, protein and sericin glue protein. The... more
Silk is a biological fiber produced by the caterpillars of Philosamia ricini moths at the end of their larval phase. Silk glands of silkworm secrete two major classes of proteins, the fibroin fiber, protein and sericin glue protein. The cocoon of silkworm is mainly composed of these two proteins. The present study focused on the development of new inhibitory protein under the condition of low temperature. The gene, produce these proteins, express in fifth instar stage at 29 ± 2 0 C and humidity 90 % i. e. in normal rearing conditions. It is noteworthy that sericin show distinct bands on polyacrylamide gel electrophoresis, whereas fibroin did not. This suggests that components of sericin, but not fibroin, have definite molecular weights. Electrophoretic analysis of cold stressed silk gland protein in 12.5 % SDS – PAGE showed the development of new high molecular weight proteins in the cold stressed Philosamia ricini larvae when compared to control. Our results fulfills the aim of our study, which describes that when the fifth instar larvae of castor moth were acclimated to 4 0 C for a few days, expression of two major proteins of silk gland was hindered which were expressed in normal rearing conditions. In this case, emergence of new protein takes place comprising the molecular mass of more than 66 KDa.
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Secreted epithelial mucins are large macromolecules which exhibit extreme polydispersity, the molecular basis of which is not fully understood. We have obtained partial sequences of two genes (BSM1 and BSM2) coding for two distinct... more
Secreted epithelial mucins are large macromolecules which exhibit extreme polydispersity, the molecular basis of which is not fully understood. We have obtained partial sequences of two genes (BSM1 and BSM2) coding for two distinct molecules. This is the first time that such closely-related genes have been identified for any mucin from an animal. We propose that a combination of multiple homologous genes, alternative splicing, differential glycosylation, and additional post-translational processing all contribute to the extreme polydispersity of mucins. The multiple domain structure and non-identical tandem repeats are also very important for the generation of the saccharide diversities of mucins.
Research Interests: Biology, Medicine, Animals, Alternative splicing, Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis, and 10 moreCattle, Molecular cloning, Amino Acids, Alternative Splicing, Short Tandem Repeat, Mucins, Biochemistry and cell biology, Domain Structure, Oligosaccharides, and Restriction Mapping
Carbonic anhydrases (CAs I-VII) are products of a gene family that encodes seven isoenzymes and several CA-related proteins. We report the cloning and sequencing of the cDNA clones encoding one of these isoenzymes, CA VI, from bovine... more
Carbonic anhydrases (CAs I-VII) are products of a gene family that encodes seven isoenzymes and several CA-related proteins. We report the cloning and sequencing of the cDNA clones encoding one of these isoenzymes, CA VI, from bovine submaxillary gland. The translated polypeptide consists of 319 amino acids, including a signal peptide (14 amino acids) typical of secreted proteins. The predicted mature protein contains 305 amino acids including a 13-amino-acid C-terminal sequence that is also present in the sheep but absent in human CA VI. The deduced mature bovine protein is 87% and 68% identical to that of sheep and human CA VI, respectively. Active-site residues of the enzyme, as well as the three zinc-binding histidines and the two cysteines involved in an intra-chain disulphide bond, are all conserved in the three species. Two potential Asn-glycosylation sites are also conserved, both of which appear to be glycosylated in sheep and bovine CA VI. Two potential peptide recognition...
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Precursors of cathepsin D and beta-hexosaminidase synthesized in the U937 monocyte line are processed to mature forms with similar kinetics as in fibroblasts. In U937 cells the processing of the precursor of the beta-chain of... more
Precursors of cathepsin D and beta-hexosaminidase synthesized in the U937 monocyte line are processed to mature forms with similar kinetics as in fibroblasts. In U937 cells the processing of the precursor of the beta-chain of beta-hexosaminidase, however, results in a larger fragment that resembles a processing intermediate in fibroblasts. This difference is explained by differences in the equipment of the cells with proteinases, since cross-feeding of the precursors to the cells results in a processing characteristic for the recipient cell type. In sucrose gradients the precursors are found partly in a low- and partly in a high-density region. Mature polypeptides and activity of lysosomal enzymes fractionate mainly in the higher density region. In U937 cells the transport and maturation of endogenous lysosomal enzymes are less sensitive to bases (NH4Cl, chloroquine, tilorone) and to antibody against the mannose 6-phosphate specific receptors than in fibroblasts. A small portion of ...
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The biotransformation of testosterone to its metabolites by the anterior pituitary gland and the relation between the products formed and the circulating levels of LH and FSH were examined in male rats at various stages of sexual... more
The biotransformation of testosterone to its metabolites by the anterior pituitary gland and the relation between the products formed and the circulating levels of LH and FSH were examined in male rats at various stages of sexual maturation. The animals were either intact controls or castrated 4 and 7 days prior to the investigation. Castration greatly increased testosterone biotransformation to its 5alpha-reduced products, but did not affect the formation of androstendione. It was concluded that castration and the eventual rise of LH-RH stimulated the 5alpha-reductase activity but not the 17beta-ol-dehydrogenase system. This is reflected in the significant relationship between the circulating gonadotropins and 5alpha-metabolites of testosterone but not androstendione.
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Changes in pituitary and serum concentrations of LH and FSH, determined by radioimmunoassay, were studied after administration of LH-RH to intact male rats of various ages. Although injection of LH-RH resulted in a depletion of pituitary... more
Changes in pituitary and serum concentrations of LH and FSH, determined by radioimmunoassay, were studied after administration of LH-RH to intact male rats of various ages. Although injection of LH-RH resulted in a depletion of pituitary LH and FSH in almost all age groups, thereby increasing the serum levels of these hormones, the magnitude and time course of the effects varied. Serum LH in the prepubertal and pubertal rats was maximal at 10 min after LH-RH injection, whereas the mature animals showed maximal increase only after 30 min. Peak serum concentrations of FSH found at 10 min in the prepubertal animals, but between 30 and 60 min in the pubertal and adult animals. At 35 days of age, significant pituitary depletion of LH and FSH occurred.
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Cancer recognized as one of the leading irrepressible health issues is contributing to increasing mortality-rate day-by-day. The tumor microenvironment is an important field of cancer to understand the detection, treatment and prevention... more
Cancer recognized as one of the leading irrepressible health issues is contributing to increasing mortality-rate day-by-day. The tumor microenvironment is an important field of cancer to understand the detection, treatment and prevention of cancer. Recently, cancer stem cell (CSC) research has shown promising results aiming towards cancer diagnostics and treatment. Here, we found that prostate and breast cancer stem cells secreted vesicles of endosomal origin, called exosomes showed strong connection between autophagy and exosomes released from CSCs. Exosomes may serve as vesicles to communicate with neoplastic cells (autocrine and paracrine manner) and normal cells (paracrine and endocrine manner) and thereby suppress immune systems and regulate neoplastic growth, and metastasis. They can also be used as biomarkers for various cancers. We detected tetraspanin proteins (CD9, CD63, CD81), Alix and tumor susceptibility gene-101 (TSG101) of exosomal markers from rotenone treated CSCs. ...
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Introduction Antibiotic resistance is a type of drug resistance in which a genetic change results in a microorganism becoming able to survive expo-sure to an antibiotic. This possibly is due to a spontaneous or in-duced genetic mutation,... more
Introduction Antibiotic resistance is a type of drug resistance in which a genetic change results in a microorganism becoming able to survive expo-sure to an antibiotic. This possibly is due to a spontaneous or in-duced genetic mutation, or by horizontal transfer of acquiring antibi-otic resistance genes from other bacterial species through. conjuga-tion, transduction, or transformation [1]. Aminoglycosides are among the most commonly used broad-spectrum antibiotics and act usually by binding to the bacterial 30S ribosomal subunit through some work by binding to the 50S subunit and thus inhibiting the step of peptidyl-tRNA translocation from the A-site to the P-site and consequently causing misreading of mRNA. This renders bacterium unable to synthesize essential growth pro-teins. Aminoglycoside antibiotics vary amongst themselves with regard to their binding specificities to different sites on the rRNA based on their mutual structural complementarit. The structural modifications of...
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Influenza A virus H1N1, a novel strain with high morbidity is the causative agent behind the recent outbreak of swine influenza. Fifty one sequences of H1N1 influenza A viruses for the proteins-hemagglutinin and neuraminidase were taken... more
Influenza A virus H1N1, a novel strain with high morbidity is the causative agent behind the recent outbreak of swine influenza. Fifty one sequences of H1N1 influenza A viruses for the proteins-hemagglutinin and neuraminidase were taken from GenBank. The sequences were aligned using ClustalW and BioEdit 7.0.2, both and the results were interpreted. The phylogenetic analysis was performed using MEGA 4. From the study conducted, the results suggested that the new influenza A virus strain H1N1 has a close phylogenetic relationship with the H1N1 viruses previously isolated from North America, Europe and Asia.
GPI anchors consist of three parts; protein, glycan and the phospholipids. The GPI anchored proteins work as cell surface hydrolases, protozoal antigens, adhesion molecules, mammalian antigens and involved in other significant cellular... more
GPI anchors consist of three parts; protein, glycan and the phospholipids. The GPI anchored proteins work as cell surface hydrolases, protozoal antigens, adhesion molecules, mammalian antigens and involved in other significant cellular functions like dense packing of proteins on cell surface, increased protein mobility on cell surface , specific release from cell surface, control of exit from endoplasmic reticulum and toxin binding. Mutations in these proteins lead to Paroxysomal Nocturnal Haemogolbinuria and other disorders. This study was executed by combining comparative proteomics and phylogenetic approaches in order to address a cross family evolution of GPI anchor proteins from 23 different species. The results of revealed some unexplored specifics about the conserved domains GPI anchored proteins across different taxa of organisms. The results also demonstrated hierarchical assemblage based inconsistency in variation in the GPI anchored proteins
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Wnt signaling pathway regulates several developmental processes in human; however recently this pathway has been associated with development of different types of cancers. Casein kinase-1 (CK1) constitutes a family of serine-threonine... more
Wnt signaling pathway regulates several developmental processes in human; however recently this pathway has been associated with development of different types of cancers. Casein kinase-1 (CK1) constitutes a family of serine-threonine protein kinase; various members of this family participate in Wnt signal transduction pathway and serve as molecular switch to this pathway. Among the known six isoforms of CK1, in human, at least three isoforms (viz. alpha, delta and epsilon) have been reported as oncogenic. The development of common therapeutics against these kinases is an arduous task; unless we have the detailed information of their tertiary structures and conformational properties. In the present work, the dynamical and conformational properties for each of three isoforms of CK1 are explored through molecular dynamics (MD) simulations. The conformational space distribution of backbone atoms is evaluated using principal component analysis of MD data, which are further validated on ...
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Neisseria meningitidis is a gram negative, diplococcic pathogen responsible for the meningococcal disease and fulminant septicemia. Penicillin-binding proteins-2 (PBPs) is crucial for the cell wall biosynthesis during cell proliferation... more
Neisseria meningitidis is a gram negative, diplococcic pathogen responsible for the meningococcal disease and fulminant septicemia. Penicillin-binding proteins-2 (PBPs) is crucial for the cell wall biosynthesis during cell proliferation of N. meningitidis and these are the target for β-lactam antibiotics. For many years penicillin has been recognized as the antibiotic for meningococcal disease but the meningococcus has seemed to be antibiotic resistance. In the present work we have verified the molecular interaction of Penicillin binding protein-2 N. meningitidis to different generation of β-lactam antibiotics and concluded that the third generation of β-lactam antibiotics shows efficient binding with Penicillin binding protein-2 of N. meningitidis. On the basis of binding efficiency and inhibition constant, ceftazidime emerged as the most efficient antibiotic amongst the other advanced β-lactam antibiotics against Penicillin-binding protein-2 of N. meningitidis.
Research Interests: Humans, Computer Simulation, Microbial genetic and drug resistance, Anti-Bacterial Agents, Penicillin-Binding Proteins, and 10 moreBeta Lactams, Microbial Sensitivity Tests, Amino Acid Sequence, Cell Wall, Protein Binding, Molecular Sequence Data, Sequence homology, Ceftazidime, Neisseria meningitidis, and Penicillins
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Extracellular vesicles (EVs) are spherical bilayered proteolipids, harboring various bioactive molecules. Due to the complexity of the vesicular nomenclatures and components, online searches for EV-related publications and vesicular... more
Extracellular vesicles (EVs) are spherical bilayered proteolipids, harboring various bioactive molecules. Due to the complexity of the vesicular nomenclatures and components, online searches for EV-related publications and vesicular components are currently challenging. We present an improved version of EVpedia, a public database for EVs research. This community web portal contains a database of publications and vesicular components, identification of orthologous vesicular components, bioinformatic tools and a personalized function. EVpedia includes 6879 publications, 172 080 vesicular components from 263 high-throughput datasets, and has been accessed more than 65 000 times from more than 750 cities. In addition, about 350 members from 73 international research groups have participated in developing EVpedia. This free web-based database might serve as a useful resource to stimulate the emerging field of EV research. Availability and implementation: The web site was implemented in P...
Research Interests: Engineering, Bioinformatics, Computer Science, Computational Biology, Medicine, and 11 moreDatabases, Database Management Systems, Biological Sciences, Software, Humans, Biomedical Research, Mathematical Sciences, Exosomes, Computer User Interface Design, Extracellular Space, and Extracellular Vesicles
Publisher Summary In an effort to document the composition of the membranes of the Golgi complex and compare and contrast this organelle with the rough endoplasmic reticulum, this chapter describes a subcellular-fractionation procedure... more
Publisher Summary In an effort to document the composition of the membranes of the Golgi complex and compare and contrast this organelle with the rough endoplasmic reticulum, this chapter describes a subcellular-fractionation procedure for rat myeloma cells that effectively eliminates rough microsomes from Golgi-enriched fractions. The differential and isopycnic-sedimentation protocol yields Golgi-enriched fractions of considerable purity. The chapter develops a novel density perturbation procedure to eliminate these plasma membrane contaminants. This protocol makes use of the specific interaction of the plant lectin, wheat germ agglutinin (WGA), with carbohydrates on the surface of intact cells. This lectin is known to bind oligosaccharides with nonreducing terminal D-GlcNAc and clustered sialic acid residues. The binding of the lectin conjugate to the cell surface makes it possible to achieve, during subcellular fractionation, extensive sedimentation of alkaline phosphatase activity, the lectin conjugate itself, and iodinated cell surface proteins to the mitochondrial pellet.
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Discrimination of Lysosomal membrane proteins (LMP's) from folding types of globular (GPs) and other membrane proteins (OtMPs) is an important task both for identifying LMPs from genomic sequences and for... more
Discrimination of Lysosomal membrane proteins (LMP's) from folding types of globular (GPs) and other membrane proteins (OtMPs) is an important task both for identifying LMPs from genomic sequences and for the successful prediction of their secondary and tertiary structures. We have systematically analyzed the amino acid frequencies as well as dipeptide count of GPs, LMPs and OtMPs. Based on the above calculated single amino acid frequency combined with dipeptide count information, we statistically discriminated LMPs from GPs and OtMPs. This approach correctly classified the LMPs with an accuracy of 95 %. On the other hand, the amino acid frequency alone can discriminate LMPs with an accuracy of only 79 %. Similarly dipeptide count alone has an accuracy of 87 % for the discrimination of LMPs. Thus the combined information of both amino acid frequencies and dipeptide composition gives us significant high accurate results.
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Recent advances in the field of luminescent nano-crystals have ushered in a new area of research in fluorescent labeling by semiconductor Quantum dots for biological tagging and detection suitable for biomedical investigations.... more
Recent advances in the field of luminescent nano-crystals have ushered in a new area of research in fluorescent labeling by semiconductor Quantum dots for biological tagging and detection suitable for biomedical investigations. Nanophosphors with remarkable chemical stability may be conveniently coated with 40 nm-nanogold particles to permit density perturbation-based purification of specific biological membranes from a host of contaminant membranes. Apart from their use as nano-immunoconjugates, these nanophosphors can also be effectively employed in drug delivery to appropriate cellular or subcellular targets and are potentially quite attractive for tumor treatment. Functionalized multifunctional and multiplex nanoparticles hold promise for personalized and tailored cancer treatment. In this chapter, we will review preparative methods of nanophosphors, their protein-conjugates and various physical characterization to evaluate their possible use in membrane isolation and nanotherapeutics. Despite the limitation of Quantum dots for bio-tagging, strategies for surface functionalization to conjugate with biomolecules and make suitable biolabels are also discussed.
Research Interests: Biology, Medicine, Humans, Fluorescence in situ hybridization, von Willebrand factor, and 13 moreAnimals, Cattle, European, Molecular cloning, Amino Acids, Tandem Repeats, Short Tandem Repeat, Amino Acid Sequence, Mucins, Biochemistry and cell biology, Molecular Sequence Data, Restriction Mapping, and Medical biochemistry and metabolomics
Many plasma membrane proteins, including Thy-1, are anchored by a carboxyl terminal glycophospholipid. This unit is absent from the Thy-1 of several lymphoma mutants that synthesize the Thy-1 polypeptide but fail to express it at the cell... more
Many plasma membrane proteins, including Thy-1, are anchored by a carboxyl terminal glycophospholipid. This unit is absent from the Thy-1 of several lymphoma mutants that synthesize the Thy-1 polypeptide but fail to express it at the cell surface. Recessive mutants of complementation groups A to C, E, and F contain Thy-1 mRNA of normal size, which suggests that their Thy-1 polypeptide is normal. To identify possible metabolic lesions, each mutant was grown with various supplements. The class F and B mutants exhibited a reversible induction of surface lipid anchored Thy-1 when grown with the aminoglycoside G418. Other aminoglycosides, sugars, and ethanolamine were inactive. These unexpected observations are discussed in the context of lipid anchor biosynthesis.
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Abstract A new flavone, asplenetin, has been isolated from Launea asplenifolia and characterized as 5,7,3′,4′,5′-pentahydroxy-3-(3-methylbutyl)flavone. Its glycoside, asplenetin 5- O -neohesperidoside, is also reported.
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Cold shock proteins (CSPs) are ancient nucleic acid-binding proteins and well conserved from bacteria to animals as well as plants. In prokaryotes, CSPs possess a single cold shock domain (CSD) while animal CSPs, flanked by N- and... more
Cold shock proteins (CSPs) are ancient nucleic acid-binding proteins and well conserved from bacteria to animals as well as plants. In prokaryotes, CSPs possess a single cold shock domain (CSD) while animal CSPs, flanked by N- and C-terminal domains, are commonly named Y-box proteins. Interestingly, the plants CSPs contain auxiliary C-terminal domains in addition to their N-terminal CSD. The CSPs have been shown to play important role in development and stress adaptation in various plant species. The objective of this study was to find out the possible nucleic acid-binding affinities of whole CSP as well as independent domains, so that role of each individual domain may be revealed in Arabidopsis thaliana, the model plant species. The structure of CSP 3 protein from A. thaliana was modeled by homology-based approach and docking was done with different nucleic acid types.
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This work presents a dynamic artificial neural network methodology, which classifies the proteins into their classes from their sequences alone: the lysosomal membrane protein classes and the various other membranes protein classes. In... more
This work presents a dynamic artificial neural network methodology, which classifies the proteins into their classes from their sequences alone: the lysosomal membrane protein classes and the various other membranes protein classes. In this paper, neural networks-based lysosomal-associated membrane protein type prediction system is proposed. Different protein sequence representations are fused to extract the features of a protein sequence, which includes seven feature sets; amino acid (AA) composition, sequence length, hydrophobic group, electronic group, sum of hydrophobicity, R-group, and dipeptide composition. To reduce the dimensionality of the large feature vector, we applied the principal component analysis. The probabilistic neural network, generalized regression neural network, and Elman regression neural network (RNN) are used as classifiers and compared with layer recurrent network (LRN), a dynamic network. The dynamic networks have memory, i.e. its output depends not only on the input but the previous outputs also. Thus, the accuracy of LRN classifier among all other artificial neural networks comes out to be the highest. The overall accuracy of jackknife cross-validation is 93.2% for the data-set. These predicted results suggest that the method can be effectively applied to discriminate lysosomal associated membrane proteins from other membrane proteins (Type-I, Outer membrane proteins, GPI-Anchored) and Globular proteins, and it also indicates that the protein sequence representation can better reflect the core feature of membrane proteins than the classical AA composition.