Bioinformation

The aim of this study was to present integrated mass spectrometric methods for the structural characterization and identification of flavonoid glycoconjugates. During the liquid chromatography/mass spectrometry analyses, TriVersa NanoMate chip-based system with nanoelectrospray ionization and fraction collection was combined to a quadrupole time-of-flight mass spectrometer. In the extract samples prepared from green leaves of wheat plantlets, 41 flavonoid derivatives were recognized. Part of the target natural products had the full structure being characterized after the registration of mass spectra, where m/z values for protonated [M + H] + and deprotonated molecules [M À H] À were annotated. MS 2 and pseudo-MS 3 experiments were performed for [M + H] + or [M À H] À and aglycone ions (Y 0 +/À -type), respectively. It should be underlined that pseudo-MS 3 mass spectra were registered for aglycone product ions in the mass spectra of O-glycosides present in the extract samples. In many cases, only tentative structural identification of aglycones was possible, mainly because of the presence of numerous C-monoglycoside or C-diglycoside in the samples. Acylation of the sugar moiety and/or methylation of the aglycone in the flavonoid glycosides under study was observed. The existence of isobaric and/or isomeric compounds was demonstrated in the extract studied. The collision-induced dissociation mass spectra registered for C,O-diglycosides and C,C-diglycosides did not permit to draw complete structural conclusions about the compounds studied. For the investigated class of natural products, unambiguous classification of sugar moieties linked to the aglycones from the recorded mass spectra was not possible. Registration of the positive and negative ion mass spectra did not lead to the precise conclusion about the glycosylation position at C-6 or C-8, and O-4 0 or O-7 atoms. It was possible, on the basis of the collected MS 2 spectra, to differentiate between O-glycosides and C-glycosides present in the samples analyzed.

We describe a database named MIC database containing 2-dimensional structures of synthesized compounds/antibiotics, IUPAC name, smiles notation and the MIC values / zone of inhibition against a particular organism, strain and culture conditions. The data was collected from various literature sources such as

Despite the increasing advocacy towards the “openness” of science and research data, it is still far from being a widespread practice. The goal of this paper is to identify the most pressing obstacles (in terms of funding, technology, Intellectual Property Rights, contracts, data protection, and social norms), which are hindering the development of Open Science and Open Research Data, with particular attention to the situation of developing countries. The innovative aim of this paper, which is the first essay of a broader research, is to prepare the epistemological basis for a Law and Technology theory of “Open Bioinformation” (OB), where bioinformation stands for research data in life sciences. We argue that so far the literature has addressed the promotion of openness in science and research data only in a sectorial manner, taking into account just one or a few of the factors affecting openness as if they were not related or mutually influenced. Therefore, the suggested solutions are limited to a single perspective and fail to consider the dynamics of information control. In our view, a holistic approach, that tries to zoom out from the specific disciplines and take into account the whole picture, would contribute to determining an effective policy for promoting OB. For this reason, we have to consider the technological, legal, and sociological aspects, in order to assess whether and how changes in one domain might affect the others.

Solanum lycopersicum and Solanum tuberosum are agriculturally important crop species as they are rich sources of starch, protein, antioxidants, lycopene, beta-carotene, vitamin C, and fiber. The genomes of S. lycopersicum and S. tuberosum are currently available. However the linear strings of nucleotides that together comprise a genome sequence are of limited significance by themselves. Computational and bioinformatics approaches can be used to exploit the genomes for fundamental research for improving their varieties. The comparative genome analysis, Pfam analysis of predicted reviewed paralogous proteins was performed. It was found that S. lycopersicum proteins belong to more families, domains and clans in comparison with S. tuberosum. It was also found that mostly intergenic regions are conserved in two genomes followed by exons, intron and UTR. This can be exploited to predict regions between genomes that are similar to each other and to study the evolutionary relationship betwe...

The emergence of multidrug-resistant strain of community-acquired methicillin resistant Staphylococcus aureus (CA-MRSA) strain has highlighted the urgent need for the alternative and effective therapeutic approach to combat the menace of this nosocomial pathogen. In the present work novel potential therapeutic drug targets have been identified through the metabolic pathways analysis. All the gene products involved in different metabolic pathways of CA-MRSA in KEGG database were searched against the proteome of Homo sapiens using the BLASTp program and the threshold of E-value was set to as 0.001. After database searching, 152 putative targets were identified. Among all 152 putative targets, 39 genes encoding for putative targets were identified as the essential genes from the DEG database which are indispensable for the survival of CA-MRSA. After extensive literature review, 7 targets were identified as potential therapeutic drug target. These targets are Fructose-bisphosphate aldolase, Phosphoglyceromutase, Purine nucleoside phosphorylase, Uridylate kinase, Tryptophan synthase subunit beta, Acetate kinase and UDP-N-acetylglucosamine 1-carboxyvinyltransferase. Except Uridylate kinase all the identified targets were involved in more than one metabolic pathways of CA-MRSA which underlines the importance of drug targets. These potential therapeutic drug targets can be exploited for the discovery of novel inhibitors for CA-MRSA using the structure based drug design (SBDD) strategy.

The rich wealth of Citrus genetic resources makes India to enjoy a remarkable position in the "Citrus belt of the world". We have developed CIBMAN, a unique database on Citrus biodiversity of Manipur which comprises 33 accessions collected through extensive survey for more than three years. CIBMAN provides integrated access to Citrus species through sophisticated web interface which has following capabilities a) morphological details, b) socio-economic details, c) taxonomic details and d) geographical distribution. Morphological variability among Citrus accessions is due to variance in their genome which contributes to diverse agronomical traits and diverse bioactive compounds of high value. This diverse gene pool can be potential source for genetic improvement of existing cultivars and rootstocks. Systematic collection, characterization and conservation of the underutilized or lesser exploited varieties is required for incorporating in breeding program and conserve the germplasm from ever going on genetic erosion. This database will be useful for scientific validations and updating of traditional wisdom in bioprospecting aspects especially industrialization of Citrus found in the state. Further, the features will be suited for detailed investigation on potential medicinal and edible Citrus that make CIBMAN a powerful tool for sustainable management. Availability: http://ibsd.gov.in/cibman ISSN 0973-2063 (online) 0973-8894 (print) Bioinformation 8(17): 838-840 (2012) 840

Multiple sequence alignment (MSA) is essential in phylogenetic, evolutionary and functional analysis. Several MSA tools are available in the literature. Here, we use several MSA tools such as ClustalX, Align-m, T-Coffee, SAGA, ProbCons, MAFFT, MUSCLE and DIALIGN to illustrate comparative phylogenetic trees analysis for two datasets. Results show that there is no single MSA tool that consistently outperforms the rest in producing reliable phylogenetic trees. Background: Several multiple sequence alignment (MSA) methods are available in the literature. McClure and colleagues tested the ability of MSA methods to identify short motifs found in four datasets of homologous proteins [1]. Henikoff and Henikoff evaluated the ability of multiple alignments in identifying new family members in database search [2]. Thompson and colleagues presented a systematic analysis and comparison of several alignment programs using the BaliBASE reference alignments as test cases [3]. Despite these comparison studies, choosing an alignment method which produces the nearest phylogenetic test tree (TT) to the reference tree (RT) is still open for discussion. Multiple sequence alignment is a crucial step in phylogenetic analysis essentially for highly divergent data sets (<30% of sequence identity) that are difficult to align. Different methods produce non-identical alignments leading to variation in the constructed phylogenetic trees for a single dataset. Here, we perform the evaluation of eight alignment methods, namely ClustalX 1.81 [4], Align-m 2.3 [5], T-Coffee 3.93 [6], SAGA 0.95 [7], ProbCons 1.08 [8], MAFFT 5.743 [9], MUSCLE 3.6 [10] and DIALIGN 2.2.1 [11] to test their ability to generate similar phylogenetic test trees with respect to reference.