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1.
J Food Sci Technol ; 60(1): 252-261, 2023 Jan.
Article in English | MEDLINE | ID: mdl-36349282

ABSTRACT

Acute lung injury (ALI), is a severe inflammatory lung disease. We tested the prophylactic effect of a functional food mix comprising three anti-inflammatory plant products: turmeric, amla, and black pepper (TAB) against lipopolysaccharide (LPS)-induced ALI in rats. Two-month-old male Wistar rats were randomly divided into three groups: control (C), LPS (5 mg/kg), and LPS with TAB (TAB). After 6 h of LPS injection, the rats were sacrificed by cervical decapitation to collect the lung tissue. Results showed that TAB partially ameliorated LPS-induced increase in circulating inflammatory cytokines (TNFα and IL6) and significantly prevented lung histopathological changes. TAB also suppressed LPS-activated ER stress markers (GRP78, pIRE1, and CHOP) and apoptotic markers (caspase-3 and - 12) in the lung. The anti-inflammatory effects of the TAB support its potential use as an adjuvant to mitigate ALI. Importantly, TAB's ingredients have been used for centuries as part of the diet with limited or no toxic effects.

2.
Curr Genomics ; 22(2): 137-152, 2021 Feb.
Article in English | MEDLINE | ID: mdl-34220300

ABSTRACT

BACKGROUND: Sorghum, the C4 dry-land cereal, important for food, fodder, feed and fuel, is a model crop for abiotic stress tolerance with smaller genome size, genetic diversity, and bio-energy traits. The heat shock proteins/chaperonin 60s (HSP60/Cpn60s) assist the plastid proteins, and participate in the folding and aggregation of proteins. However, the functions of HSP60s in abiotic stress tolerance in Sorghum remain unclear. METHODS: Genome-wide screening and in silico characterization of SbHSP60s were carried out along with tissue and stress-specific expression analysis. RESULTS: A total of 36 HSP60 genes were identified in Sorghum bicolor. They were subdivided into 2 groups, the HSP60 and HSP10 co-chaperonins encoded by 30 and 6 genes, respectively. The genes are distributed on all the chromosomes, chromosome 1 being the hot spot with 9 genes. All the HSP60s were found hydrophilic and highly unstable. The HSP60 genes showed a large number of introns, the majority of them with more than 10. Among the 12 paralogs, only 1 was tandem and the remaining 11 segmental, indicating their role in the expansion of SbHSP60s. Majority of the SbHSP60 genes expressed uniformly in leaf while a moderate expression was observed in the root tissues, with the highest expression displayed by SbHSP60-1. From expression analysis, SbHSP60-3 for drought, SbHSP60-9 for salt, SbHSP60-9 and 24 for heat and SbHSP60-3, 9 and SbHSP10-2 have been found implicated for cold stress tolerance and appeared as the key regulatory genes. CONCLUSION: This work paves the way for the utilization of chaperonin family genes for achieving abiotic stress tolerance in plants.

3.
Mol Biol Rep ; 47(10): 7379-7390, 2020 Oct.
Article in English | MEDLINE | ID: mdl-32880065

ABSTRACT

The DnaJ/Hsp40s, are important components in the chaperone machine, and play pivotal roles in plant growth, development and stress tolerance. Sorghum, the semi-arid crop, is the drought resilient, model C4 crop. However, no reports of DnaJs have been available. Genome-wide analysis of Sorghum bicolor revealed 113 DnaJ/Hsp40 genes, classified into four groups; 8 genes in SbDnaJ-A class, 10 in SbDnaJ-B, 82 in SbDnaJ-C and 13 in SbDnaJ-D distributed unevenly on all the 10 chromosomes. Chromosomes 1 and 3 were found hot spots with 22 and 20 genes respectively. All genes displayed large number of introns, with an exception of 11 of the SbDnaJ-C which is devoid of introns. Out of 36 paralogous duplications, 7 tandem and 29 segmental duplications were noticed, indicating the major role of segmental duplications in the expansion. Analysis of digital data revealed tissue and stage-specific expressions. Transcriptional profiling of 12 selected genes representing all 4 classes revealed highly significant expression in leaf followed by root tissues. No expression was noticed in stems with an exception of SbDnaJ-C76. The SbDnaJ-A1, D1, and C subgroup genes displayed upregulation in roots, stems and leaves under cold, inferring the involvement of Hsp40s for cellular protection during cold stress. The results demonstrate that C76 and D1 are the candidate genes associated with multiple abiotic stresses. Present research furnishes valuable information about the role of sorghum DnaJs in abiotic stress response and establishes a foundation for understanding the molecular mechanisms associated with plant development and stress tolerance.


Subject(s)
Gene Expression Regulation, Viral , HSP40 Heat-Shock Proteins , HSP70 Heat-Shock Proteins , Multigene Family , Plant Proteins , Sorghum , Genome-Wide Association Study , HSP40 Heat-Shock Proteins/biosynthesis , HSP40 Heat-Shock Proteins/genetics , HSP70 Heat-Shock Proteins/biosynthesis , HSP70 Heat-Shock Proteins/genetics , Plant Proteins/biosynthesis , Plant Proteins/genetics , Sorghum/genetics , Sorghum/metabolism
4.
Int J Biol Macromol ; 142: 822-834, 2020 Jan 01.
Article in English | MEDLINE | ID: mdl-31622710

ABSTRACT

The small heat shock proteins (sHsps/Hsp20s) are the molecular chaperones that maintain proper folding, trafficking and disaggregation of proteins under diverse abiotic stress conditions. In the present investigation, a genome-wide scan revealed the presence of a total of 47 sHsps in Sorghum bicolor (SbsHsps), distributed across 10 subfamilies, the major subfamily being P (plastid) group with 17 genes. Chromosomes 1 and 3 appear as the hot spot regions for SbsHsps, and majority of them were found acidic, hydrophilic, unstable and intron less. Interestingly, promoter analysis indicated that they are associated with both biotic and abiotic stresses, as well as plant development. Sorghum sHsps exhibited 15 paralogous and 20 orthologous duplications. Expression analysis of 15 genes selected from different subfamilies showed high transcript levels in roots and leaves implying that they are likely to participate in the developmental processes. SbsHsp genes were highly induced by diverse abiotic stresses inferring their critical role in mediating the environmental stress responses. Gene expression data revealed that SbsHsp-02 is a candidate gene expressed in all the tissues under varied stress conditions tested. Our results contribute to the understanding of the complexity of SbsHsp genes and help to analyse them further for functional validation.


Subject(s)
Gene Expression Regulation, Plant/physiology , Heat-Shock Proteins, Small/genetics , Plant Proteins/genetics , Sorghum/genetics , Stress, Physiological/physiology , Base Sequence , Computer Simulation , Gene Expression Profiling , Genome, Plant , Heat-Shock Proteins, Small/metabolism , Multigene Family/genetics , Phylogeny , Plant Leaves/genetics , Plant Proteins/metabolism , Plant Roots/genetics , Transcriptome
5.
PLoS One ; 14(9): e0222203, 2019.
Article in English | MEDLINE | ID: mdl-31536532

ABSTRACT

Members of the plant Heme Activator Protein (HAP) or NUCLEAR FACTOR Y (NF-Y) are trimeric transcription factor complexes composed of the NF-YA, NF-YB and NF-YC subfamilies. They bind to the CCAAT box in the promoter regions of the target genes and regulate gene expressions. Plant NF-Ys were reported to be involved in adaptation to several abiotic stresses as well as in development. In silico analysis of Sorghum bicolor genome resulted in the identification of a total of 42 NF-Y genes, among which 8 code for the SbNF-YA, 19 for SbNF-YB and 15 for the SbNF-YC subunits. Analysis was also performed to characterize gene structures, chromosomal distribution, duplication status, protein subcellular localizations, conserved motifs, ancestral protein sequences, miRNAs and phylogenetic tree construction. Phylogenetic relationships and ortholog predictions displayed that sorghum has additional NF-YB genes with unknown functions in comparison with Arabidopsis. Analysis of promoters revealed that they harbour many stress-related cis-elements like ABRE and HSE, but surprisingly, DRE and MYB elements were not detected in any of the subfamilies. SbNF-YA1, 2, and 6 were found upregulated under 200 mM salt and 200 mM mannitol stresses. While NF-YA7 appeared associated with high temperature (40°C) stress, NF-YA8 was triggered by both cold (4°C) and high temperature stresses. Among NF-YB genes, 7, 12, 15, and 16 were induced under multiple stress conditions such as salt, mannitol, ABA, cold and high temperatures. Likewise, NF-YC 6, 11, 12, 14, and 15 were enhanced significantly in a tissue specific manner under multiple abiotic stress conditions. Majority of the mannitol (drought)-inducible genes were also induced by salt, high temperature stresses and ABA. Few of the high temperature stress-induced genes are also induced by cold stress (NF-YA2, 4, 6, 8, NF-YB2, 7, 10, 11, 12, 14, 16, 17, NF-YC4, 6, 12, and 13) thus suggesting a cross talk among them. This work paves the way for investigating the roles of diverse sorghum NF-Y proteins during abiotic stress responses and provides an insight into the evolution of diverse NF-Y members.


Subject(s)
CCAAT-Binding Factor/genetics , Genes, Plant/genetics , Plant Proteins/genetics , Sorghum/genetics , Chromosome Mapping , Gene Expression Regulation, Plant , Genome-Wide Association Study , Phylogeny , Real-Time Polymerase Chain Reaction , Transcriptome
6.
Int J Biol Macromol ; 140: 17-32, 2019 Nov 01.
Article in English | MEDLINE | ID: mdl-31419556

ABSTRACT

The SPX gene family, ubiquitous in all vascular plants, plays a critical role in plant development and growth as well as in response to phosphorus stress. Based on genomic census, 46 TaSPX genes were identified in the wheat genome. All of them are evenly distributed on 13 of the 21 wheat chromosomes and chromosome 7A contains the largest members. As many as 57 gene specific SSRs were discovered among genomic sequences of identified TaSPXs. MicroRNA target analysis revealed that TaSPX genes were targeted by 9 different miRNAs including tae-miR1120a, tae-miR1120b-3p, tae-miR1120c-5p, tae-miR1122b-3p, tae-miR1122c-3p, tae-miR1130a, tae-miR1130b-3p, tae-miR1137a, and tae-miR1137b-5p. Expression profiles derived from transcriptome data and real-time quantitative PCR revealed that TaSPX genes were significantly induced by Pi starvation. The modeled 3D structure of wheat SPX proteins shared high level of homology with template structures, providing information to understand their functions at proteomic level. We have also refined the modeled 3D structures on 10 ns using molecular dynamics simulations for conformational stability. The discovered members of SPX gene family and their targeting miRNAs may provide resource for genetic improvement and promote P use efficiency in cereals.


Subject(s)
Chromosomes, Plant , Gene Expression Regulation, Plant , Plant Proteins , Transcriptome , Triticum , Chromosomes, Plant/genetics , Chromosomes, Plant/metabolism , Gene Expression Profiling , Genome-Wide Association Study , MicroRNAs/biosynthesis , MicroRNAs/genetics , Plant Proteins/biosynthesis , Plant Proteins/genetics , RNA, Plant/biosynthesis , RNA, Plant/genetics , Triticum/genetics , Triticum/metabolism
7.
PLoS One ; 14(1): e0209980, 2019.
Article in English | MEDLINE | ID: mdl-30650107

ABSTRACT

Late embryogenesis abundant (LEA) proteins, the space fillers or molecular shields, are the hydrophilic protective proteins which play an important role during plant development and abiotic stress. The systematic survey and characterization revealed a total of 68 LEA genes, belonging to 8 families in Sorghum bicolor. The LEA-2, a typical hydrophobic family is the most abundant family. All of them are evenly distributed on all 10 chromosomes and chromosomes 1, 2, and 3 appear to be the hot spots. Majority of the S. bicolor LEA (SbLEA) genes are intron less or have fewer introns. A total of 22 paralogous events were observed and majority of them appear to be segmental duplications. Segmental duplication played an important role in SbLEA-2 family expansion. A total of 12 orthologs were observed with Arabidopsis and 13 with Oryza sativa. Majority of them are basic in nature, and targeted by chloroplast subcellular localization. Fifteen miRNAs targeted to 25 SbLEAs appear to participate in development, as well as in abiotic stress tolerance. Promoter analysis revealed the presence of abiotic stress-responsive DRE, MYB, MYC, and GT1, biotic stress-responsive W-Box, hormone-responsive ABA, ERE, and TGA, and development-responsive SKn cis-elements. This reveals that LEA proteins play a vital role during stress tolerance and developmental processes. Using microarray data, 65 SbLEA genes were analyzed in different tissues (roots, pith, rind, internode, shoot, and leaf) which show clear tissue specific expression. qRT-PCR analysis of 23 SbLEA genes revealed their abundant expression in various tissues like roots, stems and leaves. Higher expression was noticed in stems compared to roots and leaves. Majority of the SbLEA family members were up-regulated at least in one tissue under different stress conditions. The SbLEA3-2 is the regulator, which showed abundant expression under diverse stress conditions. Present study provides new insights into the formation of LEAs in S. bicolor and to understand their role in developmental processes under stress conditions, which may be a valuable source for future research.


Subject(s)
Gene Expression Regulation, Plant , Plant Proteins/genetics , Sorghum/genetics , Stress, Physiological , Amino Acid Sequence , Chromosome Mapping , Gene Expression Regulation, Developmental , Genome, Plant , MicroRNAs/genetics , Phylogeny , Plant Proteins/analysis , Sorghum/chemistry , Sorghum/growth & development , Sorghum/physiology , Transcriptome
8.
Genes (Basel) ; 9(5)2018 May 03.
Article in English | MEDLINE | ID: mdl-29751546

ABSTRACT

Na⁺ transporters play an important role during salt stress and development. The present study is aimed at genome-wide identification, in silico analysis of sodium-proton antiporter (NHX) and sodium-proton exchanger (NHE)-type transporters in Sorghum bicolor and their expression patterns under varied abiotic stress conditions. In Sorghum, seven NHX and nine NHE homologs were identified. Amiloride (a known inhibitor of Na⁺/H⁺ exchanger activity) binding motif was noticed in both types of the transporters. Chromosome 2 was found to be a hotspot region with five sodium transporters. Phylogenetic analysis inferred six ortholog and three paralog groups. To gain an insight into functional divergence of SbNHX/NHE transporters, real-time gene expression was performed under salt, drought, heat, and cold stresses in embryo, root, stem, and leaf tissues. Expression patterns revealed that both SbNHXs and SbNHEs are responsive either to single or multiple abiotic stresses. The predicted protein⁻protein interaction networks revealed that only SbNHX7 is involved in the calcineurin B-like proteins (CBL)- CBL interacting protein kinases (CIPK) pathway. The study provides insights into the functional divergence of SbNHX/NHE transporter genes with tissue specific expressions in Sorghum under different abiotic stress conditions.

9.
Biotechnol Rep (Amst) ; 16: 18-20, 2017 Dec.
Article in English | MEDLINE | ID: mdl-29062722

ABSTRACT

Sclerospora graminicola pathogen is the most important biotic production constraints of pearl millet in India, Africa and other parts of the world. We report a de novo whole genome assembly and analysis of pathotype 1, one of the most virulent pathotypes of S. graminicola from India. The draft genome assembly contained 299,901,251 bp with 65,404 genes. This study may help understand the evolutionary pattern of pathogen and aid elucidation of effector evolution for devising effective durable resistance breeding strategies in pearl millet.

10.
Methods Enzymol ; 577: 185-212, 2016.
Article in English | MEDLINE | ID: mdl-27498639

ABSTRACT

Adenosine triphosphate (ATP)-binding cassette (ABC) transporters are ubiquitous ATP-dependent membrane proteins involved in translocations of a wide variety of substrates across cellular membranes. To understand the chemomechanical coupling mechanism as well as functional asymmetry in these systems, a quantitative description of how ABC transporters hydrolyze ATP is needed. Complementary to experimental approaches, computer simulations based on combined quantum mechanical and molecular mechanical (QM/MM) potentials have provided new insights into the catalytic mechanism in ABC transporters. Quantitatively reliable determination of the free energy requirement for enzymatic ATP hydrolysis, however, requires substantial statistical sampling on QM/MM potential. A case study shows that brute force sampling of ab initio QM/MM (AI/MM) potential energy surfaces is computationally impractical for enzyme simulations of ABC transporters. On the other hand, existing semiempirical QM/MM (SE/MM) methods, although affordable for free energy sampling, are unreliable for studying ATP hydrolysis. To close this gap, a multiscale QM/MM approach named reaction path-force matching (RP-FM) has been developed. In RP-FM, specific reaction parameters for a selected SE method are optimized against AI reference data along reaction paths by employing the force matching technique. The feasibility of the method is demonstrated for a proton transfer reaction in the gas phase and in solution. The RP-FM method may offer a general tool for simulating complex enzyme systems such as ABC transporters.


Subject(s)
ATP-Binding Cassette Transporters/metabolism , Adenosine Triphosphate/metabolism , Molecular Dynamics Simulation , Quantum Theory , Thermodynamics , ATP-Binding Cassette Transporters/chemistry , Animals , Humans , Hydrolysis
11.
Curr Genomics ; 16(4): 279-91, 2015 Aug.
Article in English | MEDLINE | ID: mdl-27006630

ABSTRACT

A genome-wide scanning of Sorghum bicolor resulted in the identification of 25 SbHsf genes. Phylogenetic analysis shows the ortholog genes that are clustered with only rice, representing a common ancestor. Promoter analysis revealed the identification of different cis-acting elements that are responsible for abiotic as well as biotic stresses. Hsf domains like DBD, NLS, NES, and AHA have been analyzed for their sequence similarity and functional characterization. Tissue specific expression patterns of Hsfs in different tissues like mature embryo, seedling, root, and panicle were studied using real-time PCR. While Hsfs4 and 22 are highly expressed in panicle, 4 and 9 are expressed in seedlings. Sorghum plants were exposed to different abiotic stress treatments but no expression of any Hsf was observed when seedlings were treated with ABA. High level expression of Hsf1 was noticed during high temperature as well as cold stresses, 4 and 6 during salt and 5, 6, 10, 13, 19, 23 and 25 during drought stress. This comprehensive analysis of SbHsf genes will provide an insight on how these genes are regulated in different tissues and also under different abiotic stresses and help to determine the functions of Hsfs during drought and temperature stress tolerance.

12.
Indian J Crit Care Med ; 19(11): 690-2, 2015 Nov.
Article in English | MEDLINE | ID: mdl-26730125

ABSTRACT

Cerebrospinal fluid (CSF) diversion procedure has been used for long to treat hydrocephalus in children. The principle of shunting is to establish a communication between the CSF and a drainage cavity (peritoneum, right atrium, and pleura). Ventriculoperitoneal shunt is used most commonly, followed secondly by ventriculopleural shunt (VPLS). Hydrothorax due to excessive CSF accumulation is a rare complication following both the type of shunts and is more frequently seen with VPLS. We report a case of a 6-year-old female child presenting with massive CSF hydrothorax with respiratory failure following VPLS. The aim of the article is to highlight early recognition of this rare and life-threatening condition, which could easily be missed if proper history is not available.

13.
Bioorg Med Chem Lett ; 22(13): 4314-7, 2012 Jul 01.
Article in English | MEDLINE | ID: mdl-22668451

ABSTRACT

A new class of hybrid chalcones (17a-l &18a-l) was synthesized by Claisen-Schmidt condensation. All compounds were characterized by (1)H NMR, IR and mass spectral analysis and tested for their cytotoxic activity against PC-3 (prostate cancer), HT-29 (colon cancer), B-16 (mouse macrophages) and NCI-H460 (lung cancer) cell lines. Three compounds 18i, 18j and 18l (IC(50)=8.4, 7.9 & 5.9 µM) showed significant activity against PC-3 cell line.


Subject(s)
Antineoplastic Agents/chemical synthesis , Chalcone/analogs & derivatives , Animals , Antineoplastic Agents/therapeutic use , Antineoplastic Agents/toxicity , Apoptosis/drug effects , Cell Line, Tumor , Chalcone/therapeutic use , Chalcone/toxicity , Drug Screening Assays, Antitumor , Humans , Male , Mice , Prostatic Neoplasms/drug therapy , Structure-Activity Relationship
14.
Br J Cancer ; 105(9): 1313-21, 2011 Oct 25.
Article in English | MEDLINE | ID: mdl-21952626

ABSTRACT

BACKGROUND: Phosphatase and tensin homologue deleted on chromosome 10 (PTEN) regulation of the Rho-like GTPase Cdc42 has a central role in epithelial polarised growth, but effects of this molecular network on apoptosis remain unclear. METHODS: To investigate the role of Cdc42 in PTEN-dependent cell death, we used flow cytometry, in vitro pull-down assays, poly(ADP ribose) polymerase (PARP) cleavage and other immunoblots in isogenic PTEN-expressing and -deficient colorectal cells (HCT116PTEN(+/+), HCT116PTEN(-/-), Caco2 and Caco2 ShPTEN cells) after transfection or treatment strategies. RESULTS: The PTEN knockout or suppression by short hairpin RNA or small interfering RNA (siRNA) inhibited Cdc42 activity, PARP cleavage and/or apoptosis in flow cytometry assays. Transfection of cells with wild-type or constitutively active Cdc42 enhanced PARP cleavage, whereas siRNA silencing of Cdc42 inhibited PARP cleavage and/or apoptosis. Pharmacological upregulation of PTEN by sodium butyrate (NaBt) treatment enhanced Cdc42 activity, PARP cleavage and apoptosis, whereas Cdc42 siRNA suppressed NaBt-induced PARP cleavage. Cdc42-dependent signals can suppress glycogen synthase kinase-ß (GSK3ß) activity. Pharmacological inhibition of GSK3ß by lithium chloride treatment mimicked effects of Cdc42 in promotion of PARP cleavage and/or apoptosis. CONCLUSION: Phosphatase and tensin homologue deleted on chromosome 10 may influence apoptosis in colorectal epithelium through Cdc42 signalling, thus providing a regulatory framework for both polarised growth and programmed cell death.


Subject(s)
Cell Cycle Proteins/metabolism , PTEN Phosphohydrolase/metabolism , RNA-Binding Proteins/metabolism , Apoptosis , Caco-2 Cells , Gene Knockout Techniques , HCT116 Cells , Humans , Poly(ADP-ribose) Polymerases/metabolism , RNA Splicing Factors , RNA, Small Interfering/pharmacology , Signal Transduction
15.
J Mol Model ; 17(7): 1801-16, 2011 Jul.
Article in English | MEDLINE | ID: mdl-21080017

ABSTRACT

The effect of alkyl substitution (CH3, C2H5, n-C3H7, i-C3H7, and t-C4H9) on the hydrogen bond strengths (H-bond) of substituted amide-alcohol complexes has been systematically explored. B3LYP/aug-cc-pVDZ method was applied to a total of 215 alkyl substituted amide-alcohol complexes to delineate the effect of substitution on the H-bond strength; formamide-water complex is taken as reference point. Complexes are classified into five types depending on the hydrogen donor, acceptor and the site of alkyl substitution (Type-IA, Type-IIA, Type-IB, Type-IIB and Type-III). The strength of H-bond was correlated with geometrical parameters such as proton-acceptor (H∙∙∙∙Y) distance, the length of proton donating bond (X-H). In all the complexes N-H and O-H stretching frequencies are red-shifted. The effect of alkyl substitution on N-H and O-H stretching frequencies were analyzed. Topological parameters like electron density at H∙∙∙∙Y and X-H bond critical points as derived from atom in molecules (AIM) theory was also evaluated. When C = O group is participating in H-bond, the strength of H-bond decreases with increasing size of alcohols except for methanol (Type-IA, Type-III and Type-IB complexes). But it increases with increasing size of alkyl groups on amide and decreases with bulky groups. In the case of N-H group as H-bond donor, the strength of H-bond increases with increasing size of alcohols (Type-IIA and Type-IIB complexes) whereas decreases with increasing size of alkyl groups on amide. Type-IA, IIA, IB and IIB complexes exhibit good correlations among IE, H-bond distance and electron density at bcp. In Type-III complexes, average H-bond distance and sum of electron densities shows better correlation with IEs than the corresponding individuals. The correlation of IE less with electron density at RCP compared to sum of electron densities.


Subject(s)
Alcohols/chemistry , Amides/chemistry , Hydrogen Bonding , Models, Molecular , Molecular Structure
16.
J Phys Chem A ; 113(34): 9533-42, 2009 Aug 27.
Article in English | MEDLINE | ID: mdl-19655710

ABSTRACT

Quantum chemical calculations and molecular dynamics simulations are carried out to study the host-guest inclusion complexes of cyclodextrins (alpha-, beta-, and gamma-CDs) with small guest molecules such as H(2)O, NH(3), NH(4)(+), C(6)H(6), and bisimidazolyl compounds. The uptake ability of the CDs to accommodate the small molecules inside the cavity is examined by the sequential addition of 10 molecules of water or ammonia using the semiempirical (PM3) method. In the case of benzene, this was done up to six molecules. PM3 calculations indicate that alpha-, beta-, and gamma-CD can accommodate three, seven, and nine water molecules, respectively. In the case of NH(3) as guest molecule, alpha-, beta-, and gamma-CDs can accommodate up to two, five, and six molecules, respectively. Semiempirical calculations indicate that two benzene molecules can be accommodated in the alpha-CD cavity, whereas beta- and gamma-CD cavities adopt three and four benzene molecules, respectively. Molecular dynamics simulations were carried out for 1.0 ns on benzene and bisimidazolyl complexes of CDs in explicit solvent (TIP3P water model). The interaction energies calculated by the MM/PBSA method reveal that ligand 1,6-bis(imidazol-l-lyl) hexane (B) and 1,4-bis(imidazol-l-lylmethyl) benzene (C) molecules prefer to form 1:1 complexes with alpha-, beta-, and gamma-CDs. However, C preferentially forms 1:2 complexes with alpha-CDs. Ligands 1,10-bis(imidazol-l-lyl) decane (A) and 4,4'-(bis(imidazol-l-ylmethylene))biphenyl (D) form 1:2 complexes with alpha-, beta-, and gamma-CDs in head-to-head (HH) orientation of CDs. The stability of inclusion compounds depends on the type of CD and the physicochemical properties of the involved guest. Both of these methods (semiempirical and MD simulations) reveal that beta-CDs form more stable complexes compared with alpha- and gamma-CDs with C, D, NH(4)(+), and C(6)H(6), whereas alpha-CD forms more stable complexes with A and B.


Subject(s)
Cyclodextrins/chemistry , Molecular Dynamics Simulation , Quantum Theory , Molecular Structure
17.
J Comput Aided Mol Des ; 19(12): 857-70, 2005 Dec.
Article in English | MEDLINE | ID: mdl-16741831

ABSTRACT

This study sheds new light on the role of acidic residues present in the active site cavity of human aromatase. Eight acidic residues (E129, D222, E245, E302, D309, E379, D380 and D476) lining the cavity are identified and studied using comparative modeling, docking, molecular dynamics as well as statistical techniques. The structural environment of these acidic residues is studied to assess the stability of the corresponding carboxylate anions. Results indicate that the environment of the residues E245, E302 and D222 is most suitable for carboxylate ion formation in the uncomplexed form. However, the stability of D309, D222 and D476 anions is seen to increase on complexation to steroidal substrates. In particular, the interaction between D309 and T310, which assists proton transfer, is found to be formed following androgen/nor-androgen complexation. The residue D309 is found to be clamped in the presence of substrate which is not observed in the case of the other residues although they exhibit changes in properties following substrate binding. Information entropic analysis indicates that the residues D309, D222 and D476 have more conformational flexibility compared to E302 and E245 prior to substrate binding. Interaction similar to that between D476 and D309, which is expected to assist androgen aromatization, is proposed between E302 and E245. The inhibition of aromatase activity by 4-hydroxy androstenedione (formestane) is attributed to a critical hydrogen bond formation between the hydroxy moiety and T310/D309 as well as the large distance from D476. The results corroborate well with earlier site directed mutagenesis studies.


Subject(s)
Amino Acids, Acidic/chemistry , Amino Acids, Acidic/metabolism , Aromatase/chemistry , Aromatase/metabolism , Breast Neoplasms/enzymology , Models, Molecular , Amino Acids, Acidic/genetics , Aromatase/genetics , Binding Sites/genetics , Breast Neoplasms/drug therapy , Computer Simulation , Enzyme Stability/genetics , Female , Humans , Substrate Specificity/genetics
18.
Inorg Chem ; 42(21): 6604-6, 2003 Oct 20.
Article in English | MEDLINE | ID: mdl-14552610

ABSTRACT

A novel chainlike coordination polymer [Cu(II)(2,2'-bipy)(H(2)O)(2)Al(OH)(6)Mo(6)O(18)](n)()(n)()(-), formed from a heteropolyanion [Al(OH)(6)Mo(6)O(18)](3)(-) as a building unit and a copper(II) complex fragment, [Cu(II)(2,2'-bipy)(H(2)O)(2)](2+), as a linker, provides the first example of an extended structure based on an Anderson type of polyanion and a transition metal complex with organic ligand. The intra- and interchain O-H.O hydrogen-bonding interactions are seemingly responsible for the spiral shape of this chain. Crystal data: triclinic space group Ponemacr;, a = 11.2253(18) A, b = 14.5194(17) A, c = 15.2672(10) A, alpha = 112.191(8) degrees, beta = 106.693(9) degrees, gamma = 93.916(13) degrees, and Z = 2.

19.
Ann Surg Oncol ; 7(2): 120-4, 2000 Mar.
Article in English | MEDLINE | ID: mdl-10761790

ABSTRACT

BACKGROUND: Sentinel lymph node (SLN) mapping for melanoma and breast cancer has greatly enhanced the identification of micrometastases in many patients, thereby upstaging a subset of these patients. The purpose of this study was to see if SLN mapping technique could be used to identify SLNs in colorectal cancer and to assess its impact on pathological staging and treatment. METHODS: At the time of surgery, 1 ml of Lymphazurin 1% was injected subserosally around the tumor without injecting into the lumen. The first to fourth blue nodes identified were considered the SLNs, which have the highest probability to contain metastases. A standard oncological resection of the bowel was then performed. Multilevel microsections of the SLNs, including a detailed pathological examination of the entire specimen, was performed. RESULTS: SLN was successfully identified in 85 (98.8%) of 86 patients. In 85 patients, there were 1,367 (16 per patient) lymph nodes examined, of which 140 (1.6 per patient) were identified as SLNs. In 53 (95%) of 56, of whom the SLNs were without metastases (negative), all other non-SLNs also were negative. In 29 (34% of 85) patients, SLNs were positive for metastases; in 14 of the 29 patients, other non-SLNs also were positive in addition to the SLNs. In the other 15 of the 29 patients (18% of 85 patients), SLNs were the only site of metastases, and all other non-SLNs were negative. In 7 patients (8.2% of 85 patients), micrometastases were identified only in 1 or 2 of the 10 sections of a single SLN. In five of seven patients, such micrometastases were detected by hematoxylin and eosin staining and immunohistochemistry; in the other two patients, it was detected only by immunohistochemistry. In patients with negative SLNs, the rate of occurrence of micrometastases in non-SLNs was 5 (0.4%) of 1,184 lymph nodes. CONCLUSIONS: SLN mapping can be performed easily in colorectal cancer patients, with an accuracy of more than 95%. The identification of submicroscopic lymph node metastases by this technique may have upstaged these patients (18%) from stage I/II to stage III disease, who may then benefit from further adjuvant chemotherapy.


Subject(s)
Colonic Neoplasms/pathology , Lymph Nodes/diagnostic imaging , Lymph Nodes/pathology , Rectal Neoplasms/pathology , Chemotherapy, Adjuvant , Colonic Neoplasms/drug therapy , Humans , Immunohistochemistry , Lymphatic Metastasis/diagnostic imaging , Neoplasm Staging , Prospective Studies , Radionuclide Imaging , Rectal Neoplasms/drug therapy , Rosaniline Dyes
20.
Am J Gastroenterol ; 90(10): 1881-3, 1995 Oct.
Article in English | MEDLINE | ID: mdl-7572915

ABSTRACT

Appendiceal endometriosis is a very uncommon clinical entity. We describe a 33-yr-old white female who presented with painless profuse rectal bleeding. Emergency colonoscopy revealed bleeding from the appendiceal opening. An emergency appendectomy was performed which controlled her bleeding. The histopathological examination demonstrated appendiceal endometriosis. Painless bleeding from appendiceal endometriosis is extremely rare; however, it should be considered when evaluating young women of reproductive age who present with rectal bleeding.


Subject(s)
Appendix , Endometriosis/complications , Gastrointestinal Hemorrhage/etiology , Adult , Appendectomy , Appendix/pathology , Cecal Diseases/complications , Cecal Diseases/pathology , Cecal Diseases/surgery , Endometriosis/pathology , Endometriosis/surgery , Female , Humans , Rectum
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