Parveen Kumar

Zinc-finger transcription factors are associated with guanine quadruplex motifs in human, chimpanzee, mouse and rat promoters genome-wide

Function of non-B DNA structures are poorly understood though several bioinformatics studies predict role of the G-quadruplex DNA structure in transcription. Earlier, using transcriptome profiling we found evidence of widespread G-quadruplex-mediated gene regulation. Herein, we asked whether potential G-quadruplex (PG4) motifs associate with transcription factors (TF). This was analyzed using 220 position weight matrices [designated as transcription factor binding sites (TFBS)], representing 187 unique TF, in >75u2009000 genes in human, chimpanzee, mouse and rat. Results show binding sites of nine TFs, including that of AP-2, SP1, MAZ and VDR, occurred significantly within 100 bases of the PG4 motif (Pu2009<u20091.24E-10). PG4–TFBS combinations were conserved in ‘orthologously’ related promoters across all four organisms and were associated with >850 genes in each genome. Remarkably, seven of the nine TFs were zinc-finger binding proteins indicating a novel characteristic of PG4 motifs. To test these findings, transcriptome profiles from human cell lines treated with G-quadruplex-specific molecules were used; 66 genes were significantly differentially expressed across both cell-types, which also harbored conserved PG4 motifs along with one/more of the nine TFBS. In addition, genes regulated by PG4–TFBS combinations were found to be co-regulated in human tissues, further emphasizing the regulatory significance of the associations.

Immobilization of enzyme on long period grating fibers for sensitive glucose detection.

Glucose oxidase (GOD) immobilized long period grating (LPG) fibers have been proposed for the specific and sensitive detection of glucose. The treatment of LPG fibers with aminopropyl triethoxysilane has induced biding sites for the subsequent GOD immobilization. Field emission scanning electron microscopy, confocal laser scanning microscopy, infrared spectroscopy and Raman spectroscopy have provided detailed evidences about the effectiveness of the adopted biofunctionalization methodology. The enzyme activity is conserved during the immobilization step. Fabricated LPG sensor was tested on different glucose solutions to record the transmission spectra on an optical spectrum analyzer. The wavelength shifts in the transmission spectra are linearly correlated with the glucose concentration in the range of 10-300 mg dL(-1). The fabricated sensor gives fast response and is demonstrated to be of practical utility by determining glucose contents in blood samples. Proposed technique can further be extended to develop LPG fiber based novel, sensitive and label free nanosensors for disease diagnosis and clinical analysis.

A universal solid support for the synthesis of 3'-thiol group containing oligonucleotides

Abstract Use of a derivatised polymer support 5 involving the 4,4′-dimethoxytrityloxypentyl-3-mercaptopropionamide group allows the automated synthesis of oligonucleotides bearing thiol group at their 3′-termini.

Synthesis and conjugation of ZnO nanoparticles with bovine serum albumin for biological applications

Semiconductor nanomaterials tagged with biomarkers may be used for an early fluorescence-based detection of breast cancer. ZnO nanoparticles are water-soluble, non-toxic, photo-chemically stable with highly fluorescence applicability and are regarded for their possible biocompatibility. As a long-term research planning, we are aiming to use QDs conjugated with serum-biomarker for the diagnosis of breast cancer. The present work is a part in the said direction and reports preliminary observations on the synthesis and conjugation of ZnO nanoparticles with a representative protein marker.

Recovery of Pure ZnO Nanoparticles from Spent Zn-Mno2 Alkaline Batteries

The recovery of pure ZnO (zinc oxide) nanoparticles from spent Zn-Mn dry alkaline batteries is reported. Spent batteries were dismantled to separate the contained valuable metals of the cell electrodes in the form of black powder. Treatment of this black powder with 5 mol L(-1) HCl produced leach liquor, primarily containing 2.90 g L(-1) Zn and 2.02 g L(-1) Mn. Selective and quantitative liquid-liquid extraction of Zn(II) was then carried out in three counter current steps by using Cyanex 923 (0.10 mol L(-1) in n-hexane). Zn(II) distributed in the organic phase as complex ZnCl(2)·2R (R = Cyanex 923 molecule). The metal loaded organic phase was subjected to combust at 600 °C to yield pure ZnO nanoparticles (40-50 nm). Important characteristics of the synthesized nanoparticles were investigated by field emission scanning electron microscopy (FESEM), energy dispersive X-ray spectroscopy (EDX), X-ray diffraction spectroscopy (XRD), and atomic force microscopy (AFM).

Metastases suppressor NME2 associates with telomere ends and telomerase and reduces telomerase activity within cells

Analysis of chromatin-immunoprecipitation followed by sequencing (ChIP-seq) usually disregards sequence reads that do not map within binding positions (peaks). Using an unbiased approach, we analysed all reads, both that mapped and ones that were not included as part of peaks. ChIP-seq experiments were performed in human lung adenocarcinoma and fibrosarcoma cells for the metastasis suppressor non-metastatic 2 (NME2). Surprisingly, we identified sequence reads that uniquely represented human telomere ends in both cases. In vivo presence of NME2 at telomere ends was validated using independent methods and as further evidence we found intranuclear association of NME2 and the telomere repeat binding factor 2. Most remarkably, results demonstrate that NME2 associates with telomerase and reduces telomerase activity in vitro and in vivo, and sustained NME2 expression resulted in reduced telomere length in aggressive human cancer cells. Anti-metastatic function of NME2 has been demonstrated in human cancers, however, mechanisms are poorly understood. Together, findings reported here suggest a novel role for NME2 as a telomere binding protein that can alter telomerase function and telomere length. This presents an opportunity to investigate telomere-related interactions in metastasis suppression.

Highly Sensitive Glucose Sensing With Multi-Walled Carbon Nanotubes – Polyaniline Composite

Multi-walled carbon nanotubes (MWCNTs) have been carboxylated and then immobilized with glucose oxidase (GOx) by amine coupling through EDC-NHS chemistry. These functionalized MWCNTs have been introduced into polyaniline matrix by electrochemical method. The different involved steps have been characterized with molecular and electronic spectroscopy. Prepared thin films preserved the enzymatic activity of GOx and their average electrical conductivity was measured as 3.78 × 10−1 S cm−1. Observed response time was 5 s and a linear pattern of current vs. concentration was recorded for 0.5–22 mM glucose.

A facile chemical route for recovery of high quality zinc oxide nanoparticles from spent alkaline batteries

Recycling of spent domestic batteries has gained a great environmental significance. In the present research, we propose a new and simple technique for the recovery of high-purity zinc oxide nanoparticles from the electrode waste of spent alkaline Zn-MnO2 batteries. The electrode material was collected by the manual dismantling and mixed with 5M HCl for reaction with a phosphine oxide reagent Cyanex 923® at 250°C for 30min. The desired ZnO nanoparticles were restored from the Zn-Cyanex 923 complex through an ethanolic precipitation step. The recovered particle product with about 5nm diameter exhibited fluorescent properties (emission peak at 400nm) when excited by UV radiation (excitation energy of 300nm). Thus, the proposed technique offered a simple and efficient route for recovering high purity ZnO nanoparticles from spent alkaline batteries.

Application of MoS2 modified screen-printed electrodes for highly sensitive detection of bovine serum albumin.

The present work reports the application of a new molybdenum disulphide (MoS2)-based electrochemical platform for highly sensitive quantitation of an iron-binding protein, bovine serum albumin (BSA). The gold screen-printed electrodes were modified with MoS2 nanoflakes, followed by bioconjugation with anti-BSA antibodies. Using the above bioelectrode, cyclic voltammetric analysis was carried out in the presence of a Fe(3+)/Fe(2+) redox probe which exhibited a linear response of peak current with varying concentrations of BSA up to 10xa0ng/mL (with a detection limit of 0.006xa0ng/mL). This study is novel in that it shows a considerable enhancement of signal during electrochemical sensing of a protein.

Bioconjugation of InGaP quantum dots for molecular sensing.

Fluorescence-based molecular sensing and cellular imaging are commonly carried out with the application of organic dyes. Quantum dots (QDs) are now recognized as better tools because they are brighter, size tunable, and more photostable than dyes. Most of the proposed QD-based biosensing systems involve elements of known toxicity. The present work reports the functionalization of biocompatible InGaP/ZnS core-shell QDs with anti-bovine serum albumin (anti-BSA) to exploit them as fluorescent probes for antigen detection. Successful bioconjugation was characterized with the absorption and emission spectra showing blue shifts of around 40 and 30 nm, respectively. Gel electrophoresis and particle size distribution studies further confirmed the mass increment of QDs after their functionalization with anti-BSA. Surface plasmon resonance spectrometry has been used to study the affinity of QD-(anti-BSA) probes for bovine serum albumin (BSA). Photoluminescence quenching of the developed probe is observed in the presence of BSA.