Phytic acid dynamics during seed development and it’s composition in yellow and black Indian soybean (<Emphasis Type="Italic">Glycine max</Emphasis> L.) genotypes through a modified extraction and HPLC method

Identifying or designing low phytic acid soybean demands an improved understanding of its dynamics and a need for a reliable and accurate phytate quantification method and hence an improved quantitative technique for accurate and rapid quantification of phytic acid (PA) using high-performance liquid chromatography is proposed in this paper. A rapid PA extraction method utilizing sonication of sample in 0.78 M HCl for 3 min followed by mechanical agitation and separation using strong anion exchange column in a vacuum manifold was optimized. The elution of PA was performed using a RP-C₁₈ column with an isocratic mobile phase [Acetonitrile, 35 mM formic acid and tetrabutylammonium hydroxide (4.8: 5.1: 0.1, v/v/v)]. The modified method was rapid, accurate, precise, and reproducible with relative standard deviation of 1.80 and 3.01 % (n = 10, for 1 mg ml^?1) for within and between days respectively with linearity (R² = 0.999, P < 0.05), low limit of detection (LOD = 7.8 μg ml^?1) and limit of quantification (LOQ = 31.25 μg ml^?1). PA dynamics was found increased in a linear trend from initial to later developing stages until maturity in both yellow (DS-9814) and black (DS-MM-64) genotypes. The PA content ranged from 2.38–4.72 g 100g^?1 in the 20 soybean genotypes screened and the variability in PA content was more in black genotypes (P < 0.0001). The black soybean genotypes JS 76-205 (2.38 g 100g^?1), Kalitur (2.50 g 100g^?1) and UPSL 652 (2.54 g 100g^?1), inherently rich in anthocyanin, contains the lowest PA content and hence can serve as potential genotypes with nutraceutical benefits.

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Graphical Abstract Pictorial representation of phytic acid extraction and quantification from soybean flour by the modified high performance liquid chromatography (HPLC) method.

     

Opportunities to improve the prevention and treatment of cervical cancer

Human papillomavirus (HPV) is a causal agent for approximately 5.3% of cancers worldwide, including cervical cancer, and subsets of genital and head and neck cancer. Persistent HPV infection is a necessary, but not sufficient, cause of cervical cancer. Of the >100 HPV genotypes, only about a dozen, termed "high-risk", are associated with cancer. HPV-16 is present in approximately 50% of all cervical cancers and HPV-16, HPV-18, HPV-31 and HPV-45 together account for approximately 80%. Most high-risk HPV infections are subclinical, and are cleared by the host's immune system. The remainder produces low or high-grade squamous intraepithelial lesions (SILs), also called cervical intraepithelial neoplasia (CIN), which also may regress spontaneously. However persistent high grade SIL represents the precursor lesion of cervical cancer and carcinogenic progression is associated with integration of the viral DNA, loss of E2 and upregulation of viral oncogene expression, and chromosomal rearrangements like 3q gain. Cytologic screening of the cervix for SIL and intervention has reduced the incidence of cervical cancer in the US by an estimated 80% and HPV viral DNA and other molecular tests may improve screening further. The licensure of a preventive HPV vaccine ushers in a new era, but issues remain, including: protection restricted to a few oncogenic HPV types, access in low resource settings and impact on current cytologic screening protocols. Importantly, preventive HPV vaccination does not help with current HPV infection or disease. Here we examine the potential of second-generation preventive HPV vaccines and therapeutic HPV vaccination to address these outstanding issues.     

iTRAQ reagent-based quantitative proteomic analysis on a linear ion trap mass spectrometer

For proteomic analysis using tandem mass spectrometry, linear ion trap instruments provide unsurpassed sensitivity but unreliably detect low mass peptide fragments, precluding their use with iTRAQ reagent-labeled samples. Although the popular LTQ linear ion trap supports analyzing iTRAQ reagent-labeled peptides via pulsed Q dissociation, PQD, its effectiveness remains questionable. Using a standard mixture, we found careful tuning of relative collision energy necessary for fragmenting iTRAQ reagent-labeled peptides, and increasing microscan acquisition and repeat count improves quantification but identifies somewhat fewer peptides. We developed software to calculate abundance ratios via summing reporter ion intensities across spectra matching to each protein, thereby providing maximized accuracy. Testing found that results closely corresponded between analysis using optimized LTQ-PQD settings plus our software and using a Qstar instrument. Thus, we demonstrate the effectiveness of LTQ-PQD analyzing iTRAQ reagent-labeled peptides, and provide guidelines for successful quantitative proteomic studies.     

Immune upregulation of novel antibacterial proteins from silkmoths (Lepidoptera) that resemble lysozymes but lack muramidase activity

Study on immune proteins in domesticated and wild silkmoths Bombyx mori and Antheraea mylitta, respectively, led to identification of a new class of antimicrobial proteins. We designated them as lysozyme-like proteins (LLPs) owing to their partial similarity with lysozymes. However, lack of characteristic catalytic amino acid residues essential for muramidase activity in LLPs puts them functionally apart from classical lysozymes. Two LLPs, one from B. mori (BLLP1) and the other from A. mylitta (ALLP1) expressed in a recombinant system, exhibited a broad-spectrum antibacterial action. Further investigation of the antibacterial mechanism revealed that BLLP1 is bacteriostatic rather than bactericidal against Escherichia coli and Micrococcus luteus. Substantial increase in hemolymph bacterial load was observed in B. mori upon RNA interference mediated in vivo knockdown of BLLP1. We demonstrate that the antibacterial mechanism of this protein depends on peptidoglycan binding unlike peptidoglycan hydrolysis or membrane permeabilization as observed with lysozymes and most other antimicrobial peptides. To our knowledge, this is the first report on functional analysis of novel, non-catalytic lysozyme-like family of antibacterial proteins that are quite apart functionally from classical lysozymes. The present analysis holds promise for functional annotation of similar proteins from other organisms.     

Comparative codon and amino acid composition analysis of Tritryps-conspicuous features of Leishmania major

Comparative analyses of codon/amino acid usage in Leishmania major, Trypanosoma brucei and Trypanosoma cruzi reveal that gene expressivity and GC-bias play key roles in shaping the gene composition of all three parasites, and protein composition of L. major only. In T. brucei and T. cruzi, the major contributors to the variation in protein composition are hydropathy and/or aromaticity. Principle of Cost Minimization is followed by T. brucei, disregarded by T. cruzi and opposed by L. major. Slowly evolving highly expressed gene-products of L. major bear signatures of relatively AT-rich ancestor, while faster evolution under GC-bias has characterized the lowly expressed genes of the species by higher GC12-content.     

A method for production of recombinant mCD1d protein in insect cells

CD1 proteins constitute a third class of antigen-presenting molecules. They are cell surface glycoproteins, expressed as approximately 50-kDa glycosylated heavy chains that are noncovalently associated with beta2-microglobulin. They bind lipids rather than peptides. Although their structure confirms the similarity of CD1 proteins to MHC class I and class II antigen presenting molecules, the mCD1d groove is relatively narrow, deep, and highly hydrophobic and it has two binding pockets instead of the several shallow pockets described for the classical MHC-encoded antigen-presenting molecules. Based upon their amino acid sequences, such a hydrobphobic groove provides an ideal environment for the binding of lipid antigens. The Natural Killer T (NKT) cells use their TCR to recognize glycolipids bound to or presented by CD1d. T cells reactive to lipids presented by CD1 have been involved in the protection against autoimmune and infectious diseases and in tumor rejection. Thus, the ability to identify, purify , and track the response of CD1-reactive NKT cell is of great importance . The generation of tetramers of alpha Galactosyl ceramide (a-Galcer) with CD1d has significant insight into the biology of NKT cells. Tetramers constructed from other CD1 molecules have also been generated and these new reagents have greatly expanded the knowledge of the functions of lipid-reactive T cells, with potential use in monitoring the response to lipid-based vaccines and in the diagnosis of autoimmune diseases and other treatments.     

Cloning and Characterization of Full-length Triticin cDNA and Genes from Wheat Varieties K-68 and Chinese Spring

Full-length cDNA and genes for triticin protein were cloned and characterized from wheat varieties K-68 and Chinese Spring differing considerably in grain colour, total protein content, grain hardness, milling behaviour and baking characteristics. Wheat variety K-68 possesses excellent chapatti (unleavened bread) making quality in contrast to Chinese Spring. The nucleotide and deduced amino acid sequences of the full-length triticin cDNA and genes were compared with those of other legumin genes. Although minor variations in the nucleotide sequences were observed when compared with the published sequence of the partial triticin cDNA clone λTri-25, the deduced amino acid sequence of the full-length triticin cDNA clone (Tri-cK68) revealed large variation in the Hyper Variable Region. The deduced amino acid sequence of the full-length triticin cDNA clone Tri-cK68 revealed two lysine-rich regions in the triticin protein. Comparative analysis of the nucleotide sequences of the triticin genes with the cDNA clone λTri-25 revealed the presence of a stretch of 31 nucleotides in the 5′ UTR of λTri-25 having exact complementarity with a stretch of nucleotides of the same length in the 3′ UTR of the full length triticin genes cloned from the wheat varieties K-68 (Tri-gK68) and Chinese Spring (Tri-gCS). Analysis of the nucleotide sequence of triticin promoter (Tri-pK68) revealed the presence of several elements responsible for seed-specific expression and responsiveness to light.     

Nano-bio-chips for high performance multiplexed protein detection: Determinations of cancer biomarkers in serum and saliva using quantum dot bioconjugate labels

The integration of semiconductor nanoparticle quantum dots (QDs) into a modular, microfluidic biosensor for the multiplexed quantitation of three important cancer markers, carcinoembryonic antigen (CEA), cancer antigen 125 (CA125), and Her-2/Neu (C-erbB-2) was achieved. The functionality of the integrated sample processing, analyte capture and detection modalities was demonstrated using both serum and whole saliva specimens. Here, nano-bio-chips that employed a fluorescence transduction signal with QD-labeled detecting antibody were used in combination with antigen capture by a microporous agarose bead array supported within a microfluidics ensemble so as to complete the sandwich-type immunoassay. The utilization of QD probes in this miniaturized biosensor format resulted in signal amplification 30 times relative to that of standard molecular fluorophores as well as affording a reduction in observed limits of detection by nearly 2 orders of magnitude (0.02 ng/mL CEA; 0.11 pM CEA) relative to enzyme-linked immunosorbent assay (ELISA). Assay validation studies indicate that measurements by the nano-bio-chip system correlate to standard methods at R² = 0.94 and R² = 0.95 for saliva and serum, respectively. This integrated nano-bio-chip assay system, in tandem with next-generation fluorophores, promises to be a sensitive, multiplexed tool for important diagnostic and prognostic applications.