Introduction to the 'IIOAB Letters'

The Institute of Integrative Omics and Applied Biotechnology (IIOAB), India (www.iioab.webs.com / www.iioab.ac.in) is a non-profit scientific organization that aims to provide a global platform for multidisciplinary research and advocacy. Other aspects of the organization are promotion of higher education, R&D, and to serve science, society, and the mankind. To fulfil its mission, IIOAB is now introducing a new open access, preer-reviewed, scientific international journal- the “IIOAB Letters” that will publish articles covering all aspects of biological sciences.  The journal is dedicated to students, who are our future, and will provide a platform to all scientific community to publish their articles.The journal is a collaborative effore of IIOAB and University Library Sysltem (ULS), Office of Scholarly Communication, Publishing and Web Services from University of Pittsburgh, USA. for puting their all valuable efforts in successfully launch the journal using Open Journal System (OJS).The journal will publish basic and applied research articles, invited review articles, interviews, letters, reports etc. This journal will also provide a global forum for ethical and business knowledge exchange through publishing papers from all over the world. Another aspect of the journal is rapid review and fast publication.  The journal will be indexed in well known indexing agencies soon.As an open access journal, the journal will be highly dynamic and interactive and all article will be available freely immediately after publication. Therefore, all published article will be visible to researchers, teachers, students, and scientific community and industry people without delay.We are simply convinced that this is the right time for introduction of this new journal and we are confident that the IIAOB Letters will be a very successful new launch and will be essential to all scientific community.  Comments, suggestions and criticisms are always welcome.Success of any journal depends on strong international and dedicated Editorial Board and fortunately, we have a respectable board consisting of highly qualified personalities from multidisciplinary Biological Science background and from across the geographal regions. During the end of this year, IIOAB Letters also will invite distinguished members for Editorial Board expansion. In the near future our efforts will be focused to increase the publication of high quality research papers and to get a good impact factor as soon as possible. The Institute of Integrative Omics and Applied Biotechnology (IIOAB), India (www.iioab.webs.com / www.iioab.ac.in) is a non-profit scientific organization that aims to provide a global platform for multidisciplinary research and advocacy. Other aspects of the organization are promotion of higher education, R&D, and to serve science, society, and the mankind. To fulfil its mission, IIOAB is now introducing a new open access, preer-reviewed, scientific international journal- the “IIOAB Letters” that will publish articles covering all aspects of biological sciences.  The journal is dedicated to students, who are our future, and will provide a platform to all scientific community to publish their articles. The journal is a collaborative effore of IIOAB and University Library Sysltem (ULS), Office of Scholarly Communication, Publishing and Web Services from University of Pittsburgh, USA. for puting their all valuable efforts in successfully launch the journal using Open Journal System (OJS). The journal will publish basic and applied research articles, invited review articles, interviews, letters, reports etc. This journal will also provide a global forum for ethical and business knowledge exchange through publishing papers from all over the world. Another aspect of the journal is rapid review and fast publication.  The journal will be indexed in well known indexing agencies soon.As an open access journal, the journal will be highly dynamic and interactive and all article will be available freely immediately after publication. Therefore, all published article will be visible to researchers, teachers, students, and scientific community and industry people without delay.  We are simply convinced that this is the right time for introduction of this new journal and we are confident that the IIAOB Letters will be a very successful new launch and will be essential to all scientific community.  Comments, suggestions and criticisms are always welcome. Success of any journal depends on strong international and dedicated Editorial Board and fortunately, we have a respectable board consisting of highly qualified personalities from multidisciplinary Biological Science background and from across the geographal regions. During the end of this year, IIOAB Letters also will invite distinguished members for Editorial Board expansion. In the near future our efforts will be focused to increase the publication of high quality research papers and to get a good impact factor as soon as possible

Genomic Target Database (GTD): A database of potential targets in human pathogenic bacteria

A Genomic Target Database (GTD) has been developed having putative genomic drug targets for human bacterial pathogens. The selected pathogens are either drug resistant or vaccines are yet to be developed against them. The drug targets have been identified using subtractive genomics approaches and these are subsequently classified into Drug targets in pathogen specific unique metabolic pathways,Drug targets in host-pathogen common metabolic pathways, andMembrane localized drug targets. HTML code is used to link each target to its various properties and other available public resources. Essential resources and tools for subtractive genomic analysis, sub-cellular localization, vaccine and drug designing are also mentioned. To the best of authors knowledge, no such database (DB) is presently available that has listed metabolic pathways and membrane specific genomic drug targets based on subtractive genomics. Listed targets in GTD are readily available resource in developing drug and vaccine against the respective pathogen, its subtypes, and other family members. Currently GTD contains 58 drug targets for four pathogens. Shortly, drug targets for six more pathogens will be listed

In silico identification of essential proteins in Corynebacterium pseudotuberculosis based on protein-protein interaction networks

Background Corynebacterium pseudotuberculosis (Cp) is a gram-positive bacterium that is classified into equi and ovis serovars. The serovar ovis is the etiological agent of caseous lymphadenitis, a chronic infection affecting sheep and goats, causing economic losses due to carcass condemnation and decreased production of meat, wool, and milk. Current diagnosis or treatment protocols are not fully effective and, thus, require further research of Cp pathogenesis. Results Here, we mapped known protein-protein interactions (PPI) from various species to nine Cp strains to reconstruct parts of the potential Cp interactome and to identify potentially essential proteins serving as putative drug targets. On average, we predict 16,669 interactions for each of the nine strains (with 15,495 interactions shared among all strains). An in silico sanity check suggests that the potential networks were not formed by spurious interactions but have a strong biological bias. With the inferred Cp networks we identify 181 essential proteins, among which 41 are non-host homologous. Conclusions The list of candidate interactions of the Cp strains lay the basis for developing novel hypotheses and designing according wet-lab studies. The non-host homologous essential proteins are attractive targets for therapeutic and diagnostic proposes. They allow for searching of small molecule inhibitors of binding interactions enabling modern drug discovery. Overall, the predicted Cp PPI networks form a valuable and versatile tool for researchers interested in Corynebacterium pseudotuberculosis

MapRepeat: an approach for effective assembly of repetitive regions in prokaryotic genomes

The newest technologies for DNA sequencing have led to the determination of the primary structure of the genomes of organisms, mainly prokaryotes, with high efficiency and at lower costs. However, the presence of regions with repetitive sequences, in addition to the short reads produced by the Next-Generation Sequencing (NGS) platforms, created a lot of difficulty in reconstructing the original genome in silico. Thus, even today, genome assembly continues to be one of the major challenges in bioinformatics specifically when repetitive sequences are considered. In this paper, we present an approach to assemble repetitive regions in prokaryotic genomes. Our methodology enables (i) the identification of these regions through visual tools, (ii) the characterization of sequences on the extremities of gaps and (iii) the extraction of consensus sequences based on mapping of raw data to a reference genome. We also present a case study on the assembly of regions that encode ribosomal RNAs (rRNA) in the genome of Corynebacterium ulceransFRC11, in order to show the efficiency of the strategies presented here. The proposed methods and tools will help in finishing genome assemblies, besides reducing the running time and associated costs. Availability All scripts are available at http://github.com/dcbmariano/maprepea

Implementation of a Noise Filter for Grouping in Bibliographic Databases using Latent Semantic Indexing

Clustering algorithms can assist in scientific research by presenting themes related to some topics from which we can extract information more easily. However, it is common for many of these clusters to have documents that have no relevance to the topic of interest, thereby reducing the quality of the information. We can manage the reduced quality of information of clusters for a bibliographic database by dealing with noise in the semantic space that represents the relations between the grouped documents. In this work, we sustain the hypothesis of using the Latent Semantic Indexing (LSI) technique as an efficient instrument to reduce noise and promote better group quality. Using a database of 90 scientific publications from different areas, we pre-processed the documents by LSI and grouped them using six clustering algorithms. The results were significantly improved compared to our initial results that did not use LSI-based pre-processing. From the perspective of individual performance of the algorithms demonstrating the best results, CMeans was the one that got the highest average gain, with approximately 25%, followed by K-Means and SKmeans, with 17% each; PAM, with 16.5%; and EM, with 15%. The conclusion is that Latent Semantic Indexing has proven to be a helpful tool for noise reduction. We recommend its use to improve the cluster quality of bibliographic databases significantly

Long Term Suboxone™ Emotional Reactivity As Measured by Automatic Detection in Speech

Addictions to illicit drugs are among the nation’s most critical public health and societal problems. The current opioid prescription epidemic and the need for buprenorphine/naloxone (Suboxone®; SUBX) as an opioid maintenance substance, and its growing street diversion provided impetus to determine affective states (“true ground emotionality”) in long-term SUBX patients. Toward the goal of effective monitoring, we utilized emotion-detection in speech as a measure of “true” emotionality in 36 SUBX patients compared to 44 individuals from the general population (GP) and 33 members of Alcoholics Anonymous (AA). Other less objective studies have investigated emotional reactivity of heroin, methadone and opioid abstinent patients. These studies indicate that current opioid users have abnormal emotional experience, characterized by heightened response to unpleasant stimuli and blunted response to pleasant stimuli. However, this is the first study to our knowledge to evaluate “true ground” emotionality in long-term buprenorphine/naloxone combination (Suboxone™). We found in long-term SUBX patients a significantly flat affect (p<0.01), and they had less self-awareness of being happy, sad, and anxious compared to both the GP and AA groups. We caution definitive interpretation of these seemingly important results until we compare the emotional reactivity of an opioid abstinent control using automatic detection in speech. These findings encourage continued research strategies in SUBX patients to target the specific brain regions responsible for relapse prevention of opioid addiction.United States. Dept. of Defense. Assistant Secretary of Defense for Research & Engineering (Air Force Contract FA8721-05-C-0002

Hypothesizing Synergy between Acupuncture/ Auriculotherapy and Natural Activation of Mesolimbic Dopaminergic Pathways: Putative Natural Treatment Modalities for the Reduction of Drug Hunger and Relapse

Acupuncture is a very ancient form of healing which predates recorded history. The philosophy is rooted in the Taoist tradition which goes back over 8000 years. To date this practice although used world-wide to treat addictive behaviors has not been generally accepted or scientifically proven. There are however many positive reports in the literature in its effectiveness in reducing symptoms of withdrawal from alcohol, heroin and cocaine. In addition, due to known neuro-chemical mechanisms associated with acupuncture, especially its role in pain relief and endogenous opioid function, clinical benefits in reward dependence behaviors seem parsimonious. In this review article we are hypothesizing synergy between acupuncture/auriculotherapy and natural activation of mesolimbic dopaminergic pathways to reduce drug hunger and prevent relapse. Following a review of the literature involving both of these modalities the scientific and clinical community is encouraged to carry out translational research in large randomized double-blinded placebo controlled investigations coupling these two anti-craving treatment modalities

Novel aromatase inhibitors selection using induced fit docking and extra precision methods: Potential clinical use in ER-alpha-positive breast cancer

This article aims to identify new molecules which could block or suppress the activity of aromatase enzyme by molecular docking studies using Schrödinger-Maestro v9.3