DEVELOPMENT OF MESALAZINE MICROSPHERES FOR COLON TARGETING

Objective: The present work was aimed at preparation of mesalazine microspheres by a non-aqueous solvent evaporation method using eudragit S 100 and eudragit L 100 as pH dependent polymers for colon targeting. Methods: The ratio of drug to polymer was varied and the effect of formulation variables revolutions per minute (RPM) (1000, 1500, 2000 and 2500) and concentration of span 80 (1%, 1.5%, 2% and 2.5%) were studied. Prepared microspheres were evaluated for particle size, percent drug entrapment, granular analysis, in vitro drug release studies, Fourier transformed infrared spectroscopy (FT-IR) Differential Scanning Calorimetry (DSC), X-ray diffraction (XRD) and scanning electron microscopy (SEM) studies. Results: Particle size has decreased and percent drug entrapment had increased with increase in RPM in all formulations. When the span 80 concentration increased, the particle size of the microsphere formulations increased and percent drug entrapment decreased in eudragit S 100 microspheres; whereas in eudragit L 100 microspheres, as the concentration of span 80 increased, the particle size of the microsphere formulations decreased. The prepared microspheres sustained the drug release over a period of 12 h. Conclusion: Thus eudragit S 100 and eudragit L 100 microspheres could constitute a promising approach for colon-specific and sustained delivery of mesalazine for the treatment of inflammatory bowel disease

Classical generalized constant coupling model for geometrically frustrated antiferromagnets

A generalized constant coupling approximation for classical geometrically frustrated antiferromagnets is presented. Starting from a frustrated unit we introduce the interactions with the surrounding units in terms of an internal effective field which is fixed by a self consistency condition. Results for the magnetic susceptibility and specific heat are compared with Monte Carlo data for the classical Heisenberg model for the pyrochlore and kagome lattices. The predictions for the susceptibility are found to be essentially exact, and the corresponding predictions for the specific heat are found to be in very good agreement with the Monte Carlo results.Comment: 4 pages, 3 figures, 2 columns. Discussion about the zero T value of the pyrochlore specific heat correcte

Association of Gene with Cytoplasmic Male Sterility in Pigeonpea

Cytoplasmic male sterility (CMS) has been exploited in the commercial pigeonpea [Cajanus cajan (L.) Millsp.] hybrid breeding system; however, the molecular mechanism behind this system is unknown. To understand the underlying molecular mechanism involved in A4 CMS system derived from C. cajanifolius (Haines) Maesen, 34 mitochondrial genes were analyzed for expression profiling and structural variation analysis between CMS line (ICRISAT Pigeonpea A line, ICPA 2039) and its cognate maintainer (ICPB 2039). Expression profiling of 34 mitochondrial genes revealed nine genes with significant fold differential gene expression at P ≤ 0.01, including one gene, nad4L, with 1366-fold higher expression in CMS line as compared with the maintainer. Structural variation analysis of these mitochondrial genes identified length variation between ICPA 2039 and ICPB 2039 for nad7a (subunit of nad7 gene). Sanger sequencing of nad4L and nad7a genes in the CMS and the maintainer lines identified two single nucleotide polymorphisms (SNPs) in upstream region of nad4L and a deletion of 10 bp in nad7a in the CMS line. Protein structure evaluation showed conformational changes in predicted protein structures for nad7a between ICPA 2039 and ICPB 2039 lines. All above analyses indicate association of nad7a gene with the CMS for A4 cytoplasm in pigeonpea. Additionally, one polymerase chain reaction (PCR) based Indel marker (nad7a_del) has been developed and validated for testing genetic purity of A4 derived CMS lines to strengthen the commercial hybrid breeding program in pigeonpea

NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data

Rapid popularity and adaptation of next generation sequencing (NGS) approaches have generated huge volumes of data. High throughput platforms like Illumina HiSeq produce terabytes of raw data that requires quick processing. Quality control of the data is an important component prior to the downstream analyses. To address these issues, we have developed a quality control pipeline, NGS-QCbox that scales up to process hundreds or thousands of samples. Raspberry is an in-house tool, developed in C language utilizing HTSlib (v1.2.1) (http://htslib.org), for computing read/base level statistics. It can be used as stand-alone application and can process both compressed and uncompressed FASTQ format files. NGS-QCbox integrates Raspberry with other open-source tools for alignment (Bowtie2), SNP calling (SAMtools) and other utilities (bedtools) towards analyzing raw NGS data at higher efficiency and in high-throughput manner. The pipeline implements batch processing of jobs using Bpipe (https://github.com/ssadedin/bpipe) in parallel and internally, a fine grained task parallelization utilizing OpenMP. It reports read and base statistics along with genome coverage and variants in a user friendly format. The pipeline developed presents a simple menu driven interface and can be used in either quick or complete mode. In addition, the pipeline in quick mode outperforms in speed against other similar existing QC pipeline/tools. The NGS-QCbox pipeline, Raspberry tool and associated scripts are made available at the URL https://github.com/CEG-ICRISAT/NGS-QCbox and https://github.com/ CEG-ICRISAT/Raspberry for rapid quality control analysis of large-scale next generation sequencing (Illumina) data

Prioritization of candidate genes in "QTL-hotspot" region for drought tolerance in chickpea (Cicer arietinum L.)

A combination of two approaches, namely QTL analysis and gene enrichment analysis were used to identify candidate genes in the "QTL-hotspot" region for drought tolerance present on the Ca4 pseudomolecule in chickpea. In the first approach, a high-density bin map was developed using 53,223 single nucleotide polymorphisms (SNPs) identified in the recombinant inbred line (RIL) population of ICC 4958 (drought tolerant) and ICC 1882 (drought sensitive) cross. QTL analysis using recombination bins as markers along with the phenotyping data for 17 drought tolerance related traits obtained over 1-5 seasons and 1-5 locations split the "QTL-hotspot" region into two subregions namely "QTL-hotspot_a" (15 genes) and "QTL-hotspot_b" (11 genes). In the second approach, gene enrichment analysis using significant marker trait associations based on SNPs from the Ca4 pseudomolecule with the above mentioned phenotyping data, and the candidate genes from the refined "QTL-hotspot" region showed enrichment for 23 genes. Twelve genes were found common in both approaches. Functional validation using quantitative real-time PCR (qRT-PCR) indicated four promising candidate genes having functional implications on the effect of "QTL-hotspot" for drought tolerance in chickpea.Sandip M Kale, Deepa Jaganathan, Pradeep Ruperao, Charles Chen, Ramu Punna, Himabindu Kudapa, Mahendar Thudi, Manish Roorkiwal, Mohan AVSK Katta, Dadakhalandar Doddamani, Vanika Garg, P B Kavi Kishor, Pooran M Gaur, Henry T Nguyen, Jacqueline Batley, David Edwards, Tim Sutton and Rajeev K Varshne

Matrix-assisted laser desorption ionization hydrogen/deuterium exchange studies to probe peptide conformational changes

AbstractHydrogen/deuterium (H/D) exchange chemistry monitored by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry is used to study solution phase conformational changes of bradykinin, α-melanocyte stimulating hormone, and melittin as water is added to methanol-d4, acetonitrile, and isopropanol-d8 solutions. The results are interpreted in terms of a preference for the peptides to acquire more compact conformations in organic solvents as compared to the random conformations. Our interpretation is supported by circular dichroism spectra of the peptides in the same solvent systems and by previously published structural data for the peptides. These results demonstrate the utility of MALDI-TOF as a method to monitor the H/D exchange chemistry of peptides and investigations of solution-phase conformations of biomolecules

On the interaction of vortices with mixing layers

We describe the perturbations introduced by two counter-rotating vortices - in a two-dimensional configuration - or by a vortex ring - in an axisymmetric configuration - to the mixing layer between two counterflowing gaseous fuel and air streams of the same density. The analysis is confined to the near stagnation point region, where the strain rate of the unperturbed velocity field, A0, is uniform. We restrict our attention to cases where the typical distance 2r0 between the vortices - or the characteristic vortex ring radius r0 - is large compared to both the thickness, δv, of the vorticity core and the thickness, δm∼(ν/A0)1/2, of the mixing layer. In addition, we consider that the ratio, Γ/ν, of the vortex circulation, Γ, to the kinematic viscosity, ν, is large compared to unity. Then, during the interaction time, A0,-1, the viscous and diffusion effects are confined to the thin vorticity core and the thin mixing layer, which, when seen with the scale r0, appears as a passive interface between the two counterflowing streams when they have the same density. In this case, the analysis provides a simple procedure to describe the displacement and distortion of the interface, as well as the time evolution of the strain rate imposed on the mixing layer, which are needed to calculate the inner structure of the reacting mixing layer as well as the conditions for diffusion flame extinction and edge-flame propagation along the mixing layer. Although in the reacting case variable density effects due to heat release play an important role inside the mixing layer, in this paper the analysis of the inner structure is carried out using the constant density model, which provides good qualitative understanding of the mixing layer response

Whole Genome Sequencing and Comparative Genomic Analysis Reveal Allelic Variations Unique to a Purple Colored Rice Landrace (Oryza sativa ssp. indica cv. Purpleputtu)

Purpleputtu (Oryza sativa ssp. indica cv. Purpleputtu) is a unique rice landrace from southern India that exhibits predominantly purple color. This study reports the underlying genetic complexity of the trait, associated domestication and de-domestication processes during its coevolution with present day cultivars. Along-with genome level allelic variations in the entire gene repertoire associated with the purple, red coloration of grain and other plant parts. Comparative genomic analysis using ‘a panel of 108 rice lines’ revealed a total of 3,200,951 variants including 67,774 unique variations in Purpleputtu (PP) genome. Multiple sequence alignment uncovered a 14 bp deletion in Rc (Red colored, a transcription factor of bHLH class) locus of PP, a key regulatory gene of anthocyanin biosynthetic pathway. Interestingly, this deletion in Rc gene is a characteristic feature of the present-day white pericarped rice cultivars. Phylogenetic analysis of Rc locus revealed a distinct clade showing proximity to the progenitor species Oryza rufipogon and O. nivara. In addition, PP genome exhibits a well conserved 4.5 Mbp region on chromosome 5 that harbors several loci associated with domestication of rice. Further, PP showed 1,387 unique when SNPs compared to 3,023 lines of rice (SNP-Seek database). The results indicate that PP genome is rich in allelic diversity and can serve as an excellent resource for rice breeding for a variety of agronomically important traits such as disease resistance, enhanced nutritional values, stress tolerance, and protection from harmful UV-B rays

Fourier transform ion cyclotron resonance mass spectrometric detection of small Ca2+-induced conformational changes in the regulatory domain of human cardiac troponin C

AbstractTroponin C (TnC), a calcium-binding protein of the thin filament of muscle, plays a regulatory role in skeletal and cardiac muscle contraction. NMR reveals a small conformational change in the cardiac regulatory N-terminal domain of TnC (cNTnC) on binding of Ca2+ such that the total exposed hydrophobic surface area increases very slightly from 3090 ± 86 Å2 for apo-cNTnC to 3108 ± 71 Å2 for Ca2+-cNTnC. Here, we show that measurement of solvent accessibility for backbone amide protons by means of solution-phase hydrogen/deuterium (H/D) exchange followed by pepsin digestion, high-performance liquid chromatography, and electrospray ionization high-field (9.4 T) Fourier transform Ion cyclotron resonance mass spectrometry is sufficiently sensitive to detect such small ligand binding-induced conformational changes of that protein. The extent of deuterium incorporation increases significantly on binding of Ca2+ for each of four proteolytic segments derived from pepsin digestion of the apo- and Ca2+-saturated forms of cNTnC. The present results demonstrate that H/D exchange monitored by mass spectrometry can be sufficiently sensitive to detect and identify even very small conformational changes in proteins, and should therefore be especially informative for proteins too large (or too insoluble or otherwise intractable) for NMR analysis

Identification of Prophages in Bacterial Genomes by Dinucleotide Relative Abundance Difference

BACKGROUND: Prophages are integrated viral forms in bacterial genomes that have been found to contribute to interstrain genetic variability. Many virulence-associated genes are reported to be prophage encoded. Present computational methods to detect prophages are either by identifying possible essential proteins such as integrases or by an extension of this technique, which involves identifying a region containing proteins similar to those occurring in prophages. These methods suffer due to the problem of low sequence similarity at the protein level, which suggests that a nucleotide based approach could be useful. METHODOLOGY: Earlier dinucleotide relative abundance (DRA) have been used to identify regions, which deviate from the neighborhood areas, in genomes. We have used the difference in the dinucleotide relative abundance (DRAD) between the bacterial and prophage DNA to aid location of DNA stretches that could be of prophage origin in bacterial genomes. Prophage sequences which deviate from bacterial regions in their dinucleotide frequencies are detected by scanning bacterial genome sequences. The method was validated using a subset of genomes with prophage data from literature reports. A web interface for prophage scan based on this method is available at http://bicmku.in:8082/prophagedb/dra.html. Two hundred bacterial genomes which do not have annotated prophages have been scanned for prophage regions using this method. CONCLUSIONS: The relative dinucleotide distribution difference helps detect prophage regions in genome sequences. The usefulness of this method is seen in the identification of 461 highly probable loci pertaining to prophages which have not been annotated so earlier. This work emphasizes the need to extend the efforts to detect and annotate prophage elements in genome sequences