In vitro regeneration of Brahmi (Bacopa monnieri (Linn.) Pennell) - an important medicinal herb through nodal segment culture

An efficient and cost effective in vitro plant regeneration protocol through nodalsegment culture was achieved in the medicinally important herb Bacopa monnieri (L.)Pennell, the Memory Plus plant through axillary shoot proliferation in Murashige and Skooge medium augmented with varying concentrations of 6-benzylaminopurine (BAP)1 - 5 mg/l. BAP at 2 mg/l was the most effective in multiple shoot induction and mean number of leaves, which gave an average of 17 shoots and 31.11 leaves, compared toother concentrations of the hormone tried in 35 days of culture. Regarding mean shoot length and number of nodes, basal MS giving 2.66 cm long shoots with 7.44 nodes is thebest. MS basal medium, even though not promoting shoot multiplication, gave highershoot length with elongated internodes. Healthy rooting of the in vitro developed shootswas achieved in half and full strength MS basal solid medium without the addition ofany hormones. The healthy and vigorous in vitro regenerated micro shoots wereseparated out and were hardened on transfer to plastic cups with sterile soil and sandand were successfully acclimatized ex vitro in pots with potting mixture under greenhouse conditions for 3 weeks. The survival rate was 100% and the plants establishedwell in green house resembled the mother plants in habitat without any morphological variations. The very simple and cost effective protocol developed can be used to produceelite stable clones for en masse propagation for the large-scale cultivation of this very important medicinal herb

In vitro propagation of Lesser Galangal (Alpinia calcarata Rosc.) - a commercially important medicinal plant through rhizome bud culture

An efficient protocol has been established for clonal propagation of Alpinia calcarata, a commercially important medicinal plant on Murashige and Skooge medium usingrhizome bud explants. Of the different concentrations of 6-benzylaminopurine (BAP) andBAP in combination with different levels of kinetin, the best response of axillary shootproliferation was achieved in a combination of 1.5 mg/l of kinetin in combination with 0.5mg/l of BAP producing 13.6 shoots per explant in 6-8 weeks of culture followed by 2 mg/lkinetin and 0.5 mg/l BAP with an average of 6.2 shoot buds from each of the explants.Rooting of the shoots also occurred in the same medium in 3 weeks of subculture. Shootstransferred to half strength MS medium with 0.5 mg/l IBA was optimum for healthyrooting. The healthy in vitro rooted plants were hardened on plastic cups in sterile sand andwere transferred to pots containing potting mixture under green house conditions for 3-4weeks for acclimatization. The survival rate was 87-90% and the plants established well inthe field and developed rhizomes after 4-6 weeks of growth under shade house. Thisprotocol proves its utility for rapid propagation of A. calcarata, which can be exploited forpharmaceutical and commercial purpose

Effect of TiO₂ nanotube length and lateral tubular spacing on photovoltaic properties of back illuminated dye sensitized solar cell

The main objective of this study is to show the effect of TiO2 nanotube length, diameter and intertubular lateral spacings on the performance of back illuminated Dye Sensitized Solar Cells (DSSCs). The present study shows that processing short TiO2 nanotubes with good lateral spacings could significantly improve the performance of back illuminated DSSCs. Vertically aligned, uniform sized diameter TiO2 nanotube arrays of different tube lengths have been fabricated on Ti plates by a controlled anodization technique at different times of 24, 36, 48 and 72 h using ethylene glycol and ammonium fluoride as an electrolyte medium. Scanning Electron Microscopy (SEM) showed formation of nanotube arrays spread uniformly over a large area. X-ray Diffraction (XRD) of TiO2 nanotube layer revealed the presence of crystalline anatase phases. By employing the TiO2 nanotube array anodized at 24 h showing a diameter ∼80 nm and length ∼1•5 μm as the photo-anode for back illuminated DSSCs, a full-sun conversion efficiency (η) of 3•5% was achieved, the highest value reported for this length of nanotubes

HIV/AIDS Education for Adolescents

BackgroundAmong adolescents, girls are particularly vulnerable not only because they are more likely to be coerced for unprotected sex but also because they are more susceptible biologically to sexually transmitted diseases (STDs), including HIV infection. This study was carried out to determine the effectiveness of an educational intervention programme aimed at girls focusing on knowledge of and attitude to HIV/AIDS. MethodAn educational intervention study was carried out among 791 rural girls (16-19 years) randomly selected using stratified cluster sampling from coastal villages in Udupi Taluk, Karnataka, Southern India. They were educated regarding HIV/AIDS and their awareness levels were evaluated immediately and one month following intervention. Results Around 35-50% of the girls had misconceptions regarding the modes of transmission which significantly reduced to about 8 % after intervention (95% CI of difference in proportion = (9.2, 17.9);

Fermentation, Isolation, Structure, and antidiabetic activity of NFAT-133 produced by Streptomyces strain PM0324667

Type-2 diabetes is mediated by defects in either insulin secretion or insulin action. In an effort to identify extracts that may stimulate glucose uptake, similar to insulin, a high throughput-screening assay for measuring glucose uptake in skeletal muscle cells was established. During the screening studies to discover novel antidiabetic compounds from microbial resources a Streptomyces strain PM0324667 (MTCC 5543, the Strain accession number at Institute of Microbial Technology, Chandigarh, India), an isolate from arid soil was identified which expressed a secondary metabolite that induced glucose uptake in L6 skeletal muscle cells. By employing bioactivity guided fractionation techniques, a tri-substituted simple aromatic compound with anti-diabetic potential was isolated. It was characterized based on MS and 2D NMR spectral data and identified as NFAT-133 which is a known immunosuppressive agent that inhibits NFAT-dependent transcription in vitro. Our investigations revealed the antidiabetic potential of NFAT-133. The compound induced glucose uptake in differentiated L6 myotubes with an EC50 of 6.3 ± 1.8 μM without activating the peroxisome proliferator-activated receptor-γ. Further, NFAT-133 was also efficacious in vivo in diabetic animals and reduced systemic glucose levels. Thus it is a potential lead compound which can be considered for development as a therapeutic for the treatment of type-2 diabetes. We have reported herewith the isolation of the producer microbe, fermentation, purification, in vitro, and in vivo antidiabetic activity of the compound

SeekFusion - A Clinically Validated Fusion Transcript Detection Pipeline for PCR-Based Next-Generation Sequencing of RNA

Detecting gene fusions involving driver oncogenes is pivotal in clinical diagnosis and treatment of cancer patients. Recent developments in next-generation sequencing (NGS) technologies have enabled improved assays for bioinformatics-based gene fusions detection. In clinical applications, where a small number of fusions are clinically actionable, targeted polymerase chain reaction (PCR)-based NGS chemistries, such as the QIAseq RNAscan assay, aim to improve accuracy compared to standard RNA sequencing. Existing informatics methods for gene fusion detection in NGS-based RNA sequencing assays traditionally use a transcriptome-based spliced alignment approach or a de-novo assembly approach. Transcriptome-based spliced alignment methods face challenges with short read mapping yielding low quality alignments. De-novo assembly-based methods yield longer contigs from short reads that can be more sensitive for genomic rearrangements, but face performance and scalability challenges. Consequently, there exists a need for a method to efficiently and accurately detect fusions in targeted PCR-based NGS chemistries. We describe SeekFusion, a highly accurate and computationally efficient pipeline enabling identification of gene fusions from PCR-based NGS chemistries. Utilizing biological samples processed with the QIAseq RNAscan assay and in-silico simulated data we demonstrate that SeekFusion gene fusion detection accuracy outperforms popular existing methods such as STAR-Fusion, TOPHAT-Fusion and JAFFA-hybrid. We also present results from 4,484 patient samples tested for neurological tumors and sarcoma, encompassing details on some novel fusions identified

Transcriptomic signatures reveal immune dysregulation in human diabetic and idiopathic gastroparesis

Abstract Background Cellular changes described in human gastroparesis have revealed a role for immune dysregulation, however, a mechanistic understanding of human gastroparesis and the signaling pathways involved are still unclear. Methods Diabetic gastroparetics, diabetic non-gastroparetic controls, idiopathic gastroparetics and non-diabetic non-gastroparetic controls underwent full-thickness gastric body biopsies. Deep RNA sequencing was performed and pathway analysis of differentially expressed transcripts was done using Ingenuity®. A subset of differentially expressed genes in diabetic gastroparesis was validated in a separate cohort using QT-PCR. Results 111 genes were differentially expressed in diabetic gastroparesis and 181 in idiopathic gastroparesis with a log2fold difference of | ≥ 2| and false detection rate (FDR) < 5%. Top canonical pathways in diabetic gastroparesis included genes involved with macrophages, fibroblasts and endothelial cells in rheumatoid arthritis, osteoarthritis pathway and differential regulation of cytokine production in macrophages and T helper cells by IL-17A and IL-17F. Top canonical pathways in idiopathic gastroparesis included genes involved in granulocyte adhesion and diapedesis, agranulocyte adhesion and diapedesis, and role of macrophages, fibroblasts and endothelial cells in rheumatoid arthritis. Sixty-five differentially expressed genes (log2fold difference | ≥ 2|, FDR < 5%) were common in both diabetic and idiopathic gastroparesis with genes in the top 5 canonical pathways associated with immune signaling. 4/5 highly differentially expressed genes (SGK1, APOLD1, CXCR4, CXCL2, and FOS) in diabetic gastroparesis were validated in a separate cohort of patients using RT-PCR. Immune profile analysis revealed that genes associated with M1 (pro inflammatory) macrophages were enriched in tissues from idiopathic gastroparesis tissues compared to controls (p < 0.05). Conclusions Diabetic and idiopathic gastroparesis have both unique and overlapping transcriptomic signatures. Innate immune signaling likely plays a central role in pathogenesis of human gastroparesis.https://deepblue.lib.umich.edu/bitstream/2027.42/145193/1/12920_2018_Article_379.pd

Transcriptomic signatures reveal immune dysregulation in human diabetic and idiopathic gastroparesis

Abstract Background Cellular changes described in human gastroparesis have revealed a role for immune dysregulation, however, a mechanistic understanding of human gastroparesis and the signaling pathways involved are still unclear. Methods Diabetic gastroparetics, diabetic non-gastroparetic controls, idiopathic gastroparetics and non-diabetic non-gastroparetic controls underwent full-thickness gastric body biopsies. Deep RNA sequencing was performed and pathway analysis of differentially expressed transcripts was done using Ingenuity®. A subset of differentially expressed genes in diabetic gastroparesis was validated in a separate cohort using QT-PCR. Results 111 genes were differentially expressed in diabetic gastroparesis and 181 in idiopathic gastroparesis with a log2fold difference of | ≥ 2| and false detection rate (FDR) < 5%. Top canonical pathways in diabetic gastroparesis included genes involved with macrophages, fibroblasts and endothelial cells in rheumatoid arthritis, osteoarthritis pathway and differential regulation of cytokine production in macrophages and T helper cells by IL-17A and IL-17F. Top canonical pathways in idiopathic gastroparesis included genes involved in granulocyte adhesion and diapedesis, agranulocyte adhesion and diapedesis, and role of macrophages, fibroblasts and endothelial cells in rheumatoid arthritis. Sixty-five differentially expressed genes (log2fold difference | ≥ 2|, FDR < 5%) were common in both diabetic and idiopathic gastroparesis with genes in the top 5 canonical pathways associated with immune signaling. 4/5 highly differentially expressed genes (SGK1, APOLD1, CXCR4, CXCL2, and FOS) in diabetic gastroparesis were validated in a separate cohort of patients using RT-PCR. Immune profile analysis revealed that genes associated with M1 (pro inflammatory) macrophages were enriched in tissues from idiopathic gastroparesis tissues compared to controls (p < 0.05). Conclusions Diabetic and idiopathic gastroparesis have both unique and overlapping transcriptomic signatures. Innate immune signaling likely plays a central role in pathogenesis of human gastroparesis.https://deepblue.lib.umich.edu/bitstream/2027.42/145193/1/12920_2018_Article_379.pd

TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data

Summary: TREAT (Targeted RE-sequencing Annotation Tool) is a tool for facile navigation and mining of the variants from both targeted resequencing and whole exome sequencing. It provides a rich integration of publicly available as well as in-house developed annotations and visualizations for variants, variant-hosting genes and host-gene pathways