<p>IPW interactome and comparison with existing annotation databases (a) IPW-Only protein-p... more <p>IPW interactome and comparison with existing annotation databases (a) IPW-Only protein-protein functional interaction network, (b) Comparative analysis of IPW-Only proteins and interaction with existing manually curated databases, Ring represents all interactions and proteins in IPW displaying the subsets which are obtained from other manually curated databases (b1) Comparative analysis of IPW-Only interactions to that of existing manually curated databases (b2) comparative analysis of protein as curated in IPW-Only to that of proteins presents in other manually curated databases (c) TubercuList functional class interaction relation based on the interactions as obtained from IPW-Only. The connectivity (lines) represents the interacting proteins within these classes.</p
The data structure that was used to capture the interactome data
<p>There were 11 annotation fields for reporting annotations. The data is available in PSI ... more <p>There were 11 annotation fields for reporting annotations. The data is available in PSI MITAB format.</p
The list of all the 17 central proteins as predicted from the betweenness centrality of >0.2 through IPW network with their gene products
<p>RvIDs superscripted with asterisk are essential proteins as evidenced by genetic and bio... more <p>RvIDs superscripted with asterisk are essential proteins as evidenced by genetic and biochemical studies.</p
Illustration of 17 putative drug target interaction from IPW interactome depicting the cascade of how the central proteins interact with each other in a spatio-temporal manner under different conditions like growth, stress and survival in macrophages including virulence
<p>Under normal conditions, PknB phosphorylates RshA which inhibits SigH. However, under ox... more <p>Under normal conditions, PknB phosphorylates RshA which inhibits SigH. However, under oxidative stress, RshA is not phosphorylated and this abolishes its binding to SigH, rendering it free. SigH in turn upregulates expression of SigE and SigB which regulates MprA (bacterial persistence regulator). MprA also regulates SigB and SigE. SigB plays important role in adaptation to stationary phase and nutritionally poor conditions and SigE is upregulated in mycobacterial growth within human macrophages and is transcribed from three different promoters under different conditions. sigB is also regulated by SigF, which regulates the expression of genes involved in the biosynthesis and structure of the mycobacterial cell envelope, including complex polysaccharides and lipids, particularly virulence- related sulfolipids and several transcription factors. Rv0516c is an anti-anti sigma factor and regulates anti-sigma factor SigF (upregulated during infection culture of human macrophages and in nutrient starvation condition; regulates transcription of genes involved in cell wall biosynthesis, sulfolipid metabolism, nucleotide metabolism, energy metabolism and several transcription factors) on getting phosphorylated by PknD which in turn is regulated by Rv0020c phosphorylated by PknB and PknE. SigF also regulates sigC and regulates hspx that is also regulated by dosR regulon. dosR regulon in turn is again regulated by PhoP which is a transcription factor for nuoG, eccCb1, esxb/cfp10 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039808#pone.0039808-Sachdeva1" target="_blank">[48]</a>.</p
<p>The C2D annotation approach for manual annotation and curation of Mtb interactome follow... more <p>The C2D annotation approach for manual annotation and curation of Mtb interactome followed by network analysis to predict potential drug targets reported at various sequence and structural level filters. (A) Illustrates the overall approach of crowd sourcing through social network implemented in C2D exercise (B)(a) Mtb Genome (b) Manual collation and sequence/structure based curation for gene annotation (c) Collation of re-annotated genome into comprehensive data structure (d) Construction of protein-protein interaction network based on the annotated data (e) Target identification using network analysis; Sequence level comparison of selected proteins with that of human homologs, human gut flora and human oral flora; systems, sequence and structure level analysis of shortlisted proteins and experimentally validated drug targets.</p
<p>Network parameters (a) Characteristic path length of IPW-Only network and IPWSI network.... more <p>Network parameters (a) Characteristic path length of IPW-Only network and IPWSI network. In both the graphs the x-axis represents the path length whereas the y-axis represents the frequency. 3(b) Log-Log plot of degree distribution of IPW network, the solid line was obtained by fitting the power law for γ = 1.99 and Log-Log plot of degree distribution of IPWSI network, the solid line represents the power law fit with γ = 2.01.</p
Perhaps completely open science seems unsuitable to you, if for example you are engaged in market... more Perhaps completely open science seems unsuitable to you, if for example you are engaged in market-driven R&D that must recoup investments. There are ways to
This article attempts to summarize some of the recently reported cases on intellectual property l... more This article attempts to summarize some of the recently reported cases on intellectual property law to enable readers to understand how the courts have applied the principles of intellectual property law to actual IP disputes. In this article two widely discussed cases, one on trademark law and another on patent law are discussed.
The concepts we read in intellectual property law acquire better clarity when understood in the c... more The concepts we read in intellectual property law acquire better clarity when understood in the context of application of the law by a court to a set of facts in a real life dispute. However, many of the readers of this magazine are scientists and do not get to read the cases. The attempt in this article is to summarize some of the recently decided cases to enable the readers to understand how The Courts have applied the law. Obviously, it is neither practical nor necessary to narrate all of the reported cases. Some cases are chosen as they convey a certain principle. To ensure that readers do not get distracted, the issues other than the main principle being explained in the judgment are left out. This narration is intended only to kindle the interest of a knowledge seeking mind to go through the full text of the cases and is not intended to be a definitive statement of law or a complete summary of the judgments involved.
Every medicinal preparation has an active ingredient, the ingredient that produces the therapeuti... more Every medicinal preparation has an active ingredient, the ingredient that produces the therapeutic effect. The active ingredient, the drug, has a chemical name and a generic name. The chemical name specifies the molecular structure of the drug and is used primarily by researchers. The chemical name is usually long, sometimes may have numbers indicating the molecular structure in them and is therefore difficult to pronounce and remember. For reference purposes, the drug is known by its generic name in the scientific community. The main consideration in assigning the generic name is the usefulness to scientific and medical research, education and medical journals. This international nonproprietary name is important to doctors, pharmacists and other health care providers. As it is a nonproprietary name, it is in public domain and is not protected by exclusive rights. The medicinal preparation containing the drug will have a brand name, chosen by the entity marketing the medicine. The b...
Technological progress, which ushered in new modes of exploitation of copyright works brought in ... more Technological progress, which ushered in new modes of exploitation of copyright works brought in challenges to the copyright regime which had to be periodically modified to ensure adequate return to the authors and access to the public of these works. Most significant of the challenges hitherto has been from digital technologies. In order to update the copyright system the international community drew up two treaties, the WIPO Copyright Treaty (WCT) and the WIPO Performances and Phonograms Treaty (WPPT). In addition to enhancing the rights of the authors the treaties provided legal protection to the technological measures used by the authors in digital transmission. Accession to the Treaties has been rather slow and implementation of technological protection measures has been a hotly debated issue. The US was the first major country to implement the Treaty provisions through its Digital Millennium Copyright Act (DMCA) and the protection of technological measures, particularly antici...
The Copyright Amendment Act, 2012 has been enacted by the Government of India bringing changes to... more The Copyright Amendment Act, 2012 has been enacted by the Government of India bringing changes to the Copyright Act, 1957. The amendments make Indian copyright law compliant with the Internet Treaties, WIPO Copyright Treaty (WCT) and WIPO Performances and Phonograms Treaty (WPPT). The amendments grant performers’ rights to performers. While introducing technological protection measures, the law ensures that fair use survives in the digital era by providing special fair use provisions. The amendments have gone beyond the limited mandate of WCT and WPPT and made many author friendly amendments to streamline business practices, special provisions for disabled, amendments facilitating access to works and other amendments to streamline copyright administration. The purpose of this paper is to narrate the changes made in the Copyright Amendment Act. Wherever possible a brief rationale for the amendment as culled out from the Notes on Clauses of the Copyright Amendment Bill and from the Re...
This Essay outlines how open source methods of working could be applied to the discovery and deve... more This Essay outlines how open source methods of working could be applied to the discovery and development of new medicines. • There are many potential advantages of an open source approach, such as improved efficiency , the quality and relevance of the research, and wider participation by the scientific and patient communities; a blend of traditional and innovative financing mechanisms will have to be adopted. • To evaluate properly the effectiveness of an open source methodology and its potential as an alternative model of drug discovery and development, we recommend that new projects be trialed and existing projects scaled up.
and colleagues call for a comprehensive policy for neglected diseases research in India to foster... more and colleagues call for a comprehensive policy for neglected diseases research in India to foster innovation in drugs, diagnostics, and vaccines, critical for evolving needs of elimination programmes
Collaborative Tools to Accelerate Neglected Disease Research: Open-Source Drug Discovery Model
20.1 Introduction 322 20.2 Semantic Web - based Portal to Link Mind and Machines 323 20.3 Descrip... more 20.1 Introduction 322 20.2 Semantic Web - based Portal to Link Mind and Machines 323 20.3 Description of the Portal: Collaborative Workspaces 324 20.3.1 Single Sign On 325 20.3.2 OpenID Server 325 20.3.3 Portal Backbone 326 20.3.4 Data Store 326 20.3.5 Project ...
<p>IPW interactome and comparison with existing annotation databases (a) IPW-Only protein-p... more <p>IPW interactome and comparison with existing annotation databases (a) IPW-Only protein-protein functional interaction network, (b) Comparative analysis of IPW-Only proteins and interaction with existing manually curated databases, Ring represents all interactions and proteins in IPW displaying the subsets which are obtained from other manually curated databases (b1) Comparative analysis of IPW-Only interactions to that of existing manually curated databases (b2) comparative analysis of protein as curated in IPW-Only to that of proteins presents in other manually curated databases (c) TubercuList functional class interaction relation based on the interactions as obtained from IPW-Only. The connectivity (lines) represents the interacting proteins within these classes.</p
The data structure that was used to capture the interactome data
<p>There were 11 annotation fields for reporting annotations. The data is available in PSI ... more <p>There were 11 annotation fields for reporting annotations. The data is available in PSI MITAB format.</p
The list of all the 17 central proteins as predicted from the betweenness centrality of >0.2 through IPW network with their gene products
<p>RvIDs superscripted with asterisk are essential proteins as evidenced by genetic and bio... more <p>RvIDs superscripted with asterisk are essential proteins as evidenced by genetic and biochemical studies.</p
Illustration of 17 putative drug target interaction from IPW interactome depicting the cascade of how the central proteins interact with each other in a spatio-temporal manner under different conditions like growth, stress and survival in macrophages including virulence
<p>Under normal conditions, PknB phosphorylates RshA which inhibits SigH. However, under ox... more <p>Under normal conditions, PknB phosphorylates RshA which inhibits SigH. However, under oxidative stress, RshA is not phosphorylated and this abolishes its binding to SigH, rendering it free. SigH in turn upregulates expression of SigE and SigB which regulates MprA (bacterial persistence regulator). MprA also regulates SigB and SigE. SigB plays important role in adaptation to stationary phase and nutritionally poor conditions and SigE is upregulated in mycobacterial growth within human macrophages and is transcribed from three different promoters under different conditions. sigB is also regulated by SigF, which regulates the expression of genes involved in the biosynthesis and structure of the mycobacterial cell envelope, including complex polysaccharides and lipids, particularly virulence- related sulfolipids and several transcription factors. Rv0516c is an anti-anti sigma factor and regulates anti-sigma factor SigF (upregulated during infection culture of human macrophages and in nutrient starvation condition; regulates transcription of genes involved in cell wall biosynthesis, sulfolipid metabolism, nucleotide metabolism, energy metabolism and several transcription factors) on getting phosphorylated by PknD which in turn is regulated by Rv0020c phosphorylated by PknB and PknE. SigF also regulates sigC and regulates hspx that is also regulated by dosR regulon. dosR regulon in turn is again regulated by PhoP which is a transcription factor for nuoG, eccCb1, esxb/cfp10 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039808#pone.0039808-Sachdeva1" target="_blank">[48]</a>.</p
<p>The C2D annotation approach for manual annotation and curation of Mtb interactome follow... more <p>The C2D annotation approach for manual annotation and curation of Mtb interactome followed by network analysis to predict potential drug targets reported at various sequence and structural level filters. (A) Illustrates the overall approach of crowd sourcing through social network implemented in C2D exercise (B)(a) Mtb Genome (b) Manual collation and sequence/structure based curation for gene annotation (c) Collation of re-annotated genome into comprehensive data structure (d) Construction of protein-protein interaction network based on the annotated data (e) Target identification using network analysis; Sequence level comparison of selected proteins with that of human homologs, human gut flora and human oral flora; systems, sequence and structure level analysis of shortlisted proteins and experimentally validated drug targets.</p
<p>Network parameters (a) Characteristic path length of IPW-Only network and IPWSI network.... more <p>Network parameters (a) Characteristic path length of IPW-Only network and IPWSI network. In both the graphs the x-axis represents the path length whereas the y-axis represents the frequency. 3(b) Log-Log plot of degree distribution of IPW network, the solid line was obtained by fitting the power law for γ = 1.99 and Log-Log plot of degree distribution of IPWSI network, the solid line represents the power law fit with γ = 2.01.</p
Perhaps completely open science seems unsuitable to you, if for example you are engaged in market... more Perhaps completely open science seems unsuitable to you, if for example you are engaged in market-driven R&D that must recoup investments. There are ways to
This article attempts to summarize some of the recently reported cases on intellectual property l... more This article attempts to summarize some of the recently reported cases on intellectual property law to enable readers to understand how the courts have applied the principles of intellectual property law to actual IP disputes. In this article two widely discussed cases, one on trademark law and another on patent law are discussed.
The concepts we read in intellectual property law acquire better clarity when understood in the c... more The concepts we read in intellectual property law acquire better clarity when understood in the context of application of the law by a court to a set of facts in a real life dispute. However, many of the readers of this magazine are scientists and do not get to read the cases. The attempt in this article is to summarize some of the recently decided cases to enable the readers to understand how The Courts have applied the law. Obviously, it is neither practical nor necessary to narrate all of the reported cases. Some cases are chosen as they convey a certain principle. To ensure that readers do not get distracted, the issues other than the main principle being explained in the judgment are left out. This narration is intended only to kindle the interest of a knowledge seeking mind to go through the full text of the cases and is not intended to be a definitive statement of law or a complete summary of the judgments involved.
Every medicinal preparation has an active ingredient, the ingredient that produces the therapeuti... more Every medicinal preparation has an active ingredient, the ingredient that produces the therapeutic effect. The active ingredient, the drug, has a chemical name and a generic name. The chemical name specifies the molecular structure of the drug and is used primarily by researchers. The chemical name is usually long, sometimes may have numbers indicating the molecular structure in them and is therefore difficult to pronounce and remember. For reference purposes, the drug is known by its generic name in the scientific community. The main consideration in assigning the generic name is the usefulness to scientific and medical research, education and medical journals. This international nonproprietary name is important to doctors, pharmacists and other health care providers. As it is a nonproprietary name, it is in public domain and is not protected by exclusive rights. The medicinal preparation containing the drug will have a brand name, chosen by the entity marketing the medicine. The b...
Technological progress, which ushered in new modes of exploitation of copyright works brought in ... more Technological progress, which ushered in new modes of exploitation of copyright works brought in challenges to the copyright regime which had to be periodically modified to ensure adequate return to the authors and access to the public of these works. Most significant of the challenges hitherto has been from digital technologies. In order to update the copyright system the international community drew up two treaties, the WIPO Copyright Treaty (WCT) and the WIPO Performances and Phonograms Treaty (WPPT). In addition to enhancing the rights of the authors the treaties provided legal protection to the technological measures used by the authors in digital transmission. Accession to the Treaties has been rather slow and implementation of technological protection measures has been a hotly debated issue. The US was the first major country to implement the Treaty provisions through its Digital Millennium Copyright Act (DMCA) and the protection of technological measures, particularly antici...
The Copyright Amendment Act, 2012 has been enacted by the Government of India bringing changes to... more The Copyright Amendment Act, 2012 has been enacted by the Government of India bringing changes to the Copyright Act, 1957. The amendments make Indian copyright law compliant with the Internet Treaties, WIPO Copyright Treaty (WCT) and WIPO Performances and Phonograms Treaty (WPPT). The amendments grant performers’ rights to performers. While introducing technological protection measures, the law ensures that fair use survives in the digital era by providing special fair use provisions. The amendments have gone beyond the limited mandate of WCT and WPPT and made many author friendly amendments to streamline business practices, special provisions for disabled, amendments facilitating access to works and other amendments to streamline copyright administration. The purpose of this paper is to narrate the changes made in the Copyright Amendment Act. Wherever possible a brief rationale for the amendment as culled out from the Notes on Clauses of the Copyright Amendment Bill and from the Re...
This Essay outlines how open source methods of working could be applied to the discovery and deve... more This Essay outlines how open source methods of working could be applied to the discovery and development of new medicines. • There are many potential advantages of an open source approach, such as improved efficiency , the quality and relevance of the research, and wider participation by the scientific and patient communities; a blend of traditional and innovative financing mechanisms will have to be adopted. • To evaluate properly the effectiveness of an open source methodology and its potential as an alternative model of drug discovery and development, we recommend that new projects be trialed and existing projects scaled up.
and colleagues call for a comprehensive policy for neglected diseases research in India to foster... more and colleagues call for a comprehensive policy for neglected diseases research in India to foster innovation in drugs, diagnostics, and vaccines, critical for evolving needs of elimination programmes
Collaborative Tools to Accelerate Neglected Disease Research: Open-Source Drug Discovery Model
20.1 Introduction 322 20.2 Semantic Web - based Portal to Link Mind and Machines 323 20.3 Descrip... more 20.1 Introduction 322 20.2 Semantic Web - based Portal to Link Mind and Machines 323 20.3 Description of the Portal: Collaborative Workspaces 324 20.3.1 Single Sign On 325 20.3.2 OpenID Server 325 20.3.3 Portal Backbone 326 20.3.4 Data Store 326 20.3.5 Project ...
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