In silico selection of an aptamer to estrogen receptor alpha using computational docking employing estrogen response elements as aptamer-alike molecules

Aptamers, the chemical-antibody substitute to conventional antibodies, are primarily discovered through SELEX technology involving multi-round selections and enrichment. Circumventing conventional methodology, here we report an in silico selection of aptamers to estrogen receptor alpha (ERα) using RNA analogs of human estrogen response elements (EREs). The inverted repeat nature of ERE and the ability to form stable hairpins were used as criteria to obtain aptamer-alike sequences. Near-native RNA analogs of selected single stranded EREs were modelled and their likelihood to emerge as ERα aptamer was examined using AutoDock Vina, HADDOCK and PatchDock docking. These in silico predictions were validated by measuring the thermodynamic parameters of ERα -RNA interactions using isothermal titration calorimetry. Based on the in silico and in vitro results, we selected a candidate RNA (ERaptR4; 5′-GGGGUCAAGGUGACCCC-3′) having a binding constant (Ka) of 1.02 ± 0.1 × 108 M−1 as an ERα-aptamer. Target-specificity of the selected ERaptR4 aptamer was confirmed through cytochemistry and solid-phase immunoassays. Furthermore, stability analyses identified ERaptR4 resistant to serum and RNase A degradation in presence of ERα. Taken together, an efficient ERα-RNA aptamer is identified using a non-SELEX procedure of aptamer selection. The high-affinity and specificity can be utilized in detection of ERα in breast cancer and related diseases

Clinical outcome after high dose rate intracavitary brachytherapy with traditional point ‘A’ dose prescription in locally advanced carcinoma of uterine cervix: dosimetric analysis from the perspective of computed tomography imaging-based 3-dimensional treatment planning

Objective To analyze tumour response and toxicity with respect to cumulative radiotherapy dose to target and organs at risk (OARs) with computed tomography (CT)-based image guided adaptive brachytherapy planning for locally advanced carcinoma cervix. Methods Patients were treated with two-dimensional concurrent chemoradiotherapy to whole pelvis followed by intracavitary brachytherapy (ICBT) with dose prescription to point ‘A’. CT image-based delineation of high-risk clinical target volume (HR-CTV), urinary bladder, rectum and sigmoid colon was done with generation of dose-volume histogram (DVH) data and optimization of doses to target and OARs. Follow up assessments were done for response of disease and toxicity with generation of data for statistical analysis. Results One hundred thirty-six patients were enrolled in the study. Delineated volume of HR-CTV ranged from 20.9 to 37.1 mL, with median value of 30.2 mL. The equivalent dose in 2 Gy per fraction (EQD2) for point ‘A’ ranged from 71.31 to 79.75 Gy with median value of 75.1 Gy and EQD2 HR-CTV D90 ranged from 71.9 to 89.7 Gy with median value of 85.1 Gy. 69.2% of patients showed complete response and after median follow-up of 25 months, 50 patients remained disease free, of whom, 74.0% had received ≥85 Gy to HR-CTV D90 versus 26.0% receiving <85 Gy to HR-CTV D90. Conclusions Amidst the unavailability of magnetic resonance imaging facilities in low middle income countries, incorporation of CT-image based treatment planning into routine practice for ICBT provides the scope to delineate volumes of target and OARs and to generate DVH data, which can prove to be a better surrogate for disease response and toxicity

Grazing incidence x-ray diffraction studies of lipid-peptide mixed monolayers during shear flow

Grazing Incidence X-ray Diffraction (GIXD) studies of monolayers of biomolecules at the air-water interface give quantitative information of in-plane packing, coherence lengths of the ordered diffracting crystalline domains and the orientation of hydrocarbon chains. Rheo-GIXD measurements revel quantitative changes in the monolayer under shear. Here we report GIXD studies of monolayers of Alamethicin peptide, DPPC lipid and their mixtures at the air-water interface under the application of steady shear stresses. The Alamethicin monolayer and the mixed monolayer show flow jamming transition. On the other hand, pure DPPC monolayer under the constant stress flows steadily with a notable enhancement of area/molecule, coherence length, and the tilt angle with increasing stress, suggesting fusion of nanocrystallites during flow. The DPPC-Alamethicin mixed monolayer shows no significant change in the area/DPPC molecule or in the DPPC chain tilt but the coherence length of both phases (DPPC and Alamethicin) increases suggesting that the crystallites of individual phases are merging to bigger size promoting more separation of phases in the system during flow. Our results show that Rheo-GIXD has the potential to explore in-situ molecular structural changes under rheological conditions for a diverse range of confined biomolecules at the interfaces.Comment: 21 pages, 11 figures, 2 table

Deregulation of LIMD1-VHL-HIF-1α-VEGF pathway is associated with different stages of cervical cancer.

To understand the mechanism of cellular stress in basal-parabasal layers of normal cervical epithelium and during different stages of cervical carcinoma, we analyzed the alterations (expression/methylation/copy number variation/mutation) of HIF-1α and its associated genes LIMD1, VHL and VEGF in disease-free normal cervix (n = 9), adjacent normal cervix of tumors (n = 70), cervical intraepithelial neoplasia (CIN; n = 32), cancer of uterine cervix (CACX; n = 174) samples and two CACX cell lines. In basal-parabasal layers of normal cervical epithelium, LIMD1 showed high protein expression, while low protein expression of VHL was concordant with high expression of HIF-1α and VEGF irrespective of HPV-16 (human papillomavirus 16) infection. This was in concordance with the low promoter methylation of LIMD1 and high in VHL in the basal-parabasal layers of normal cervix. LIMD1 expression was significantly reduced while VHL expression was unchanged during different stages of cervical carcinoma. This was in concordance with their frequent methylation during different stages of this tumor. In different stages of cervical carcinoma, the expression pattern of HIF-1α and VEGF was high as seen in basal-parabasal layers and inversely correlated with the expression of LIMD1 and VHL. This was validated by demethylation experiments using 5-aza-2'-deoxycytidine in CACX cell lines. Additional deletion of LIMD1 and VHL in CIN/CACX provided an additional growth advantage during cervical carcinogenesis through reduced expression of genes and associated with poor prognosis of patients. Our data showed that overexpression of HIF-1α and its target gene VEGF in the basal-parabasal layers of normal cervix was due to frequent inactivation of VHL by its promoter methylation. This profile was maintained during different stages of cervical carcinoma with additional methylation/deletion of VHL and LIMD1.This work was supported by CSIR (Council of Scientific and Industrial Research, Government of India)-JRF/NET grant [File No.09/030(0059)/2010-EMR-I] to Mr. C.Chakraborty, grant [Sr. No. 2121130723] from UGC (University Grants Commission, Government of India) to Mr. Sudip Samadder, grant [SR/SO/HS-116/2007] from DST (Department of Science and Technology, Government of India) to Dr. C. K. Panda and grant [ No. 60(0111)/14/EMR-II of dt.03/11/2014] from CSIR (Council of Scientific and Industrial Research, Government of India) to Dr. C. K. Pand

A mild and versatile synthesis of bis(indolyl)methanes and tris(indolyl)alkanes catalyzed by antimony trichloride

1402-1406Antimony trichloride is found to be a mild and efficient catalyst for electrophilic substitution reaction at 3-position of 3-unsubstituted indole derivatives with a variety of carbonyl compounds in acetonitrile to afford the corresponding bis(indolyl)methanes in excellent yields. ⍺,β -Unsaturated carbonyl compounds give tris(indolyl)alkanes under the same reaction conditions. The versatility of this method has been proved with a wide range of aromatic aldehydes with various stereo-electronic factors. This method shows much better selectivity between aldehydes and ketones as well as greater reactivity towards the electron deficient over the electron rich aromatic aldehydes, which are in contrast to the existing methods

Synthesis of polyarylether sulphone by nitro displacement polymerization

63-68<span style="font-size:11.0pt;line-height: 115%;font-family:Calibri;mso-fareast-font-family:" times="" new="" roman";mso-bidi-font-family:="" "times="" roman";mso-ansi-language:en-us;mso-fareast-language:en-us;="" mso-bidi-language:ar-sa"="" lang="EN-US">Polyarylether sulphone has been synthesized by the sulphone activated nitrodisplacement polymerization from dinitrodiphenyl sulphone and bisphenol A dianion prepared by various methods. The use of pressure increases the rate of polymerization and the molecular weight of the polymer. The n of the polymer has been computed from the PMR analysis. The polymers obtained have low inherent viscosities and are amorphous and soluble in polar solvents.</span

Synthesis and curing of bis[4(3'-ethynyl phenyl amino)- 3-nitrophenyl]sulphone

1023-1028A new acetylene terminated nitrophenyl sulphone (ATNPS) has been synthesized by nucleophilic displacement reaction between bis(4-chloro-3-nitrophenyl)sulphone and 3-ethynyl aniline. ATNPS is characterized by elemental analysis, IR and 1H-NMR spectroscopies. On heating at ca. 250ᵒC or above ATNPS becomes cross linked due to the presence of the acetylenic end group. The thermal behavior has been studied by DSC and DTA techniques. The kinetic study of the curing has been carried out by both differential and integral methods by use of a computational programming

Polysulphide amide synthesized by activated nucleophilic displacement polymerization

81-86<span style="font-size:11.0pt;line-height:115%; font-family:" calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-fareast-font-family:="" "times="" new="" roman";mso-fareast-theme-font:minor-fareast;mso-hansi-theme-font:="" minor-latin;mso-bidi-font-family:arial;mso-ansi-language:en-us;mso-fareast-language:="" en-us;mso-bidi-language:ar-sa"="">Polysulphide amide (PSA) is synthesized by the displacement polymerization between 4, 4'-bis (pchlorophenyl carbonyl amino) diphenyl ether and anhydrous sodium sulphide in NMP at 200°C. PSA is soluble in aprotic solvents and is characterized by elemental analysis, IR and 1H-NMR spectroscopy, and viscometry. Thermal behaviour of PSA is studied by TGA, DSC and TMA. The polymer shows good thermal stability and LOI value of about 44. X-ray analysis reveals that PSA is crystalline and has similar orthorhombic unit cell parameters to those of PPS and PEEK. The chain symmetry pattern of these three polymers is also very similar. The higher thermal stability of PSA appears to be due to higher degree of crystallinity and hydrogen bonding.</span

A Note on the Possibility of Decentralization in a Model of Allocation of Resources

The decomposition algorithm for the solution of large-scale linear programmes has been interpreted by Baumol and Fabian (Management Science, September, 1964) as a procedure for decentralized decision by the multi-division company or the multi-sector economy. While commenting on the possibility of decentralization in this context, they maintain that an economy's optimum point will not in general yield a sectoral optimum. The present note demonstrates that this contention is not valid.