A Structural Proteomics Exploration of Synphilin-1 and Alpha-Synuclein Interaction in Pathogenesis of Parkinson's Disease.

Pathological significance of interaction of Synphilin-1 with mutated alpha-synuclein is well known to have serious consequences in causing the formation of inclusion bodies that are linked to Parkinson's disease (PD). Information extracted so far pointed out that specific mutations, A53T, A30P, and E46K, in alpha-synuclein promote such interactions. However, a detailed structural study of this interaction is pending due to the unavailability of the complete structures of the large protein Synphilin-1 of chain length 919 residues and the mutated alpha-synuclein having all the reported specific mutations so far.

Application of sequence semantic and integrated cellular geography approach to study alternative biogenesis of exonic circular RNA.

Background: Concurrent existence of lncRNA and circular RNA at both nucleus and cytosol within a cell at different proportions is well reported. Previous studies showed that circular RNAs are synthesized in nucleus followed by transportation across the nuclear membrane and the export is primarily defined by their length. lncRNAs primarily originated through inefficient splicing and seem to use NXF1 for cytoplasm export.

TemPred: A Novel Protein Template Search Engine to Improve Protein Structure Prediction.

Among new protein structure predictors, the recently developed AlphaFold predictor relies on contact map in line with contact map potential based threading model that basically relies on fold recognition. In parallel, sequence similarity based homology model relies on homologue recognition. Both of these methods rely on sequence-structure or sequence-sequence similarity with protein with known structure in absence of which, as argued in the development of AlphaFold, the structure prediction becomes quite challenging.

ProtPCV: A Fixed Dimensional Numerical Representation of Protein Sequence to Significantly Reduce Sequence Search Time.

Protein sequence is a wealth of experimental information which is yet to be exploited to extract information on protein homologues. Consequently, it is observed from publications that dynamic programming, heuristics and HMM profile-based alignment techniques along with the alignment free techniques do not directly utilize ordered profile of physicochemical properties of a protein to identify its homologue. Also, it is found that these works lack crucial bench-marking or validation in absence of which their incorporation in search engines may appears to be questionable.

APT: An Automated Probe Tracker From Gene Expression Data.

Out of currently available semi-automatic tools for detecting diagnostic probes relevant to a pathophysiological condition, ArrayMining and GEO2R of NCBI are most popular. The shortcomings of ArrayMining and GEO2R are that both tools list the probes ordering them on the basis of their individual statistical level of significances with only difference of statistical methods used by them. While the latest tool GEO2R outputs either top 250 or all genes following its own ranking mechanism, ArrayMining requires number of probes to be inputted by the user.

Synthesis and structure of [(PhP)Cu(μ-SeCHPh)In(SeCHPh)] as a single-source precursor for the preparation of CuInSe nano-materials.

The reaction of freshly prepared Na[In(SeCHCH)] with the mixture of CuCl and triphenylphosphine in methanol yielded [(PPh)CuIn(SeCHCH)]. The X-ray structure of the complex revealed the monomeric form of [(PhP)Cu(μ-SeCHPh)In(SeCHPh)] consisting of tetrahedral Cu(i) and In(iii) centers, bridged by two benzyl selenolate ligands. The complex on pyrolysis in a furnace or in oleylamine/HDA yielded tetragonal CuInSe.

An improved protein structure evaluation using a semi-empirically derived structure property.

Background: In the backdrop of challenge to obtain a protein structure under the known limitations of both experimental and theoretical techniques, the need of a fast as well as accurate protein structure evaluation method still exists to substantially reduce a huge gap between number of known sequences and structures. Among currently practiced theoretical techniques, homology modelling backed by molecular dynamics based optimization appears to be the most popular one. However it suffers from contradictory indications of different validation parameters generated from a set of protein models which are predicted against a particular target protein.

Development of X-ray CCD camera based X-ray micro-CT system.

Availability of microfocus X-ray sources and high resolution X-ray area detectors has made it possible for high resolution microtomography studies to be performed outside the purview of synchrotron. In this paper, we present the work towards the use of an external shutter on a high resolution microtomography system using X-ray CCD camera as a detector. During micro computed tomography experiments, the X-ray source is continuously ON and owing to the readout mechanism of the CCD detector electronics, the detector registers photons reaching it during the read-out period too.

PCV: An Alignment Free Method for Finding Homologous Nucleotide Sequences and its Application in Phylogenetic Study.

Online retrieval of the homologous nucleotide sequences through existing alignment techniques is a common practice against the given database of sequences. The salient point of these techniques is their dependence on local alignment techniques and scoring matrices the reliability of which is limited by computational complexity and accuracy. Toward this direction, this work offers a novel way for numerical representation of genes which can further help in dividing the data space into smaller partitions helping formation of a search tree.

Multiplexed magnetic nanoparticle-antibody conjugates (MNPs-ABS) based prognostic detection of ovarian cancer biomarkers, CA-125, β-2M and ApoA1 using fluorescence spectroscopy with comparison of surface plasmon resonance (SPR) analysis.

A multiplexed MNPs-Abs based fluorescence spectroscopic system in analysis of serum biomarkers; CA-125, β2-M and ApoA1 for the early detection of ovarian cancer was first time proposed. The lowest detection limits measured in multiplexed setup were 0.26 U/mL, 0.

Protein structure validation using a semi-empirical method.

Current practice of validating predicted protein structural model is knowledge-based where scoring parameters are derived from already known structures to obtain decision on validation out of this structure information. For example, the scoring parameter, Ramachandran Score gives percentage conformity with steric-property higher value of which implies higher acceptability. On the other hand, Force-Field Energy Score gives conformity with energy-wise stability higher value of which implies lower acceptability.

A comparative study on PVC based sensors in determination of.

The proposed work described the synthesis of neutral ionophores; 4,8-diaza-3,3,10,10-tetramethyl-1,2-dithiacyclodecane (S1), 5,8-diaza-3,3,10,10-tetramethyl-1,2 dithiacyclodecane-N,N''-diacetic acid (S2) and N,N''-bis(2,2-dimethyl-2-mercaptoethyl)ethylenediamine-N,N-diacetic acid (S3) used for comparative analysis in determination of molybdenum(v) as PVC-based membrane sensors. The best result was obtained with sensor no. 7 based on S3 ionophore with membrane composition (w/w, mg%); 5.

Comparative studies on Tb (III)-selective PVC membrane sensors.

A new terbium selective sensor based on N-(2-hydroxyphenyl)-3-(2-hydroxyphenylhydroxyphenylimino)-N-phenylbutanamidine (L(1)) and N,N'-bis((1H-indole-3-yl)methylene)butane-1,4 diamine (L(2)) as a ionophore is reported. Effect of various plasticizers; 2-nitrophenyloctylether (o-NPOE), dibutyl butylphosphonate (DBBP), chloronaphthelene (CN), dioctylphthalate (DOP) and tri-(2-ethylhexyl)phosphate (TEHP) with anion excluder, potassium tetrakis (p-chloropheny1)borate (KTpClPB) have been studied. The membrane with a composition of ionophore (L(1)):KTpClPB:PVC:o-NPOE (w/w, %) in ratio of 3.

Comparative study on 2-amino-1,4-naphthoquinone derived ligands as indium (III) selective PVC-based sensors.

The three different ligands (Q(2) to Q(4)) based on 2-amino-1,4-naphthoquinone (Q(1)), have been synthesized and explored as neutral ionophores for preparing polyvinyl chloride-based membrane sensors selective to indium (III). The addition of potassium tetrakis(4-chlorophenyl) borate and various plasticizers, viz., o-NPOE, DBP, DBBP, DOP and CN has been found to substantially improve the performance of the sensors.

Gallium(III) selective sensors based on 2-amino-3-(alpha-N-phenylmethyl-2'-amino-1',4'-naphthoquinonyl)-1,4 naphthoquinones in poly (vinyl chloride).

Synthesis and application of 2-amino-3-(alpha-N-phenylmethyl-2'-amino-1',4'-naphthoquinonyl)-1,4 naphthoquinone (S) as a neutral ionophore for the determination of gallium(III) in PVC-based membrane sensors has been described. The sensor based on membrane composition (w/w, mg%); 5.0 (S):30.

Comparative studies of praseodymium(III) selective sensors based on newly synthesized Schiff's bases.

Praseodymium ion selective polyvinyl chloride (PVC) membrane sensors, based on two new Schiff's bases 1,3-diphenylpropane-1,3-diylidenebis(azan-1-ylidene)diphenol (M(1)) and N,N'-bis(pyridoxylideneiminato) ethylene (M(2)) have been developed and studied. The sensor having membrane composition of PVC: o-NPOE: ionophore (M(1)): NaTPB (w/w; mg) of 150: 300: 8: 5 showed best performances in comparison to M(2) based membranes. The sensor based on (M(1)) exhibits the working concentration range 1.

Comparative evaluation of Dy(III) selective poly(vinyl) chloride based membrane electrodes of macrocyclic tetraimine Schiff's bases.

Three different derivatives of macrocyclic tetraimine Schiff's base have been synthesized and explored as a neutral ionophores for preparing poly(vinyl chloride) based membrane sensors selective to Dy(3+). The addition of sodium tetraphenyl borate and various plasticizers, viz., o-NPOE, DBP, DBBP, DOP and CN has been found to substantially improve the performance of the sensors.

Nano level detection of Cd(II) using poly(vinyl chloride) based membranes of Schiff bases.

The construction and performance characteristics of polymeric membrane electrodes based on two neutral ionophores, 2,2'-(1Z,1'Z)-(1E,1'E)-(1,2-phenylenebis(methan-1-yl-1-ylidene))bis(azaan-1-yl-1-ylidene)bis(methylene)bis(azan-1-yl-1-ylidene)bis(methan-1-yl-ylidene)diphenol (L(1)) and 4,4'-(1E,1'E)-(butane-1,4-diylbis(azan-1-yl-1-ylidene))bis(methan-1-yl-1-ylidene)dinaphthalen-1-ol (L(2)) for quantification of cadmium ions, are described. The influences of membrane compositions on the potentiometric response of the electrodes have been found to substantially improve the performance characteristics. The best performance was obtained with the electrode having a membrane composition (w/w) of (L(1)) (2.

Comparative study of Ag(I) selective poly(vinyl chloride) membrane sensors based on newly developed Schiff-base lariat ethers derived from 4,13-diaza-18-crown-6.

The six Schiff-base lariat ether chelates based on 4,13-diaza-18-crown ether, have been synthesized and explored as a neutral ionophores for preparing poly(vinyl chloride) based membrane sensors selective to silver(I). The addition of potassium tetrakis(4-chlorophenyl) borate and various plasticizers, viz., o-NPOE, DBP, DBBP, DOP and CN has been found to substantially improve the performance of the sensors.

Ni(II) selective sensors based on Schiff bases membranes in poly(vinyl chloride).

The two nickel chelates of Schiff bases, 3-hydroxy-N-{2-[(3-hydroxy-N-phenylbutyrimidoyl)-amino]-phenyl}-N'-phenylbutyramidine (M(1)) and bis-4-(ethyliminomethyl)naphthalene-1-ol (M(2)), have been synthesized and explored as ionophores for preparing PVC-based membrane sensors selective to nickel ion. The influences of membrane compositions on the potentiometric response of the electrodes have been found to substantially improve the performance characteristics. The best performance was obtained with the electrode having a membrane composition (w/w; mg) of (M(1)): PVC:NaTPB:CN in the ratio 5:150:5:150.