Archive for May 2014
The 3,000 rice genomes project: new opportunities and challenges for future rice research
Corresponding author: Robert S Zeigler r.zeigler@irri.org
International Rice Research Institute, DAPO 7777, Metro Manila 1301, Philippines
GigaScience 2014, 3:8 doi:10.1186/2047-217X-3-8
Abstract
Rice is the world’s most important staple grown by millions of small-holder farmers. Sustaining rice production relies on the intelligent use of rice diversity. The 3,000 Rice Genomes Project is a giga-dataset of publically available genome sequences (averaging 14× depth of coverage) derived from 3,000 accessions of rice with global representation of genetic and functional diversity. The seed of these accessions is available from the International Rice Genebank Collection. Together, they are an unprecedented resource for advancing rice science and breeding technology. Our immediate challenge now is to comprehensively and systematically mine this dataset to link genotypic variation to functional variation with the ultimate goal of creating new and sustainable rice varieties that can support a future world population that will approach 9.6 billion by 2050.
Keywords: Oryza sativa; Genetic resources; Genome diversity; Phenomics; Sequencing
The electronic version of this article is the complete one and can be found online at: http://www.gigasciencejournal.com/content/3/1/8
#image source: http://tuebingen.mpg.de/en/news-press/press-releases/detail/getting-to-the-bottom-of-rice.html
International Rice Research Institute, DAPO 7777, Metro Manila 1301, Philippines
GigaScience 2014, 3:8 doi:10.1186/2047-217X-3-8
Abstract
Rice is the world’s most important staple grown by millions of small-holder farmers. Sustaining rice production relies on the intelligent use of rice diversity. The 3,000 Rice Genomes Project is a giga-dataset of publically available genome sequences (averaging 14× depth of coverage) derived from 3,000 accessions of rice with global representation of genetic and functional diversity. The seed of these accessions is available from the International Rice Genebank Collection. Together, they are an unprecedented resource for advancing rice science and breeding technology. Our immediate challenge now is to comprehensively and systematically mine this dataset to link genotypic variation to functional variation with the ultimate goal of creating new and sustainable rice varieties that can support a future world population that will approach 9.6 billion by 2050.
Keywords: Oryza sativa; Genetic resources; Genome diversity; Phenomics; Sequencing
The electronic version of this article is the complete one and can be found online at: http://www.gigasciencejournal.com/content/3/1/8
#image source: http://tuebingen.mpg.de/en/news-press/press-releases/detail/getting-to-the-bottom-of-rice.html
How England win World Cup 2014? Listen how Prof. Stephen Hawking says:
When I was a kid, I learnt football (soccer ball) is a sphere...
# image source: www.englandfootballblog.com
Now I know how England can win in WorldCup 2014 from Prof. Stephen Hawking ...
For full report, go to
Stephen Hawking's formula on how England cold win the World Cup
Stephen Hawking's formula on how England can score penalities
# image source: www.englandfootballblog.com
Can't see through the mind of a mathematician? try this - Encyclopedia of Mathematics, a completely free online tool
If you find mathematics is necessary...
If you find mathematics is too difficult...
If you find you have a mathematical examination tomorrow...
I suggest you a good free online tool - Encyclopedia of Mathematics
http://www.encyclopediaofmath.org/index.php/Main_Page
screenshot 01: homepage of Encyclopedia of Mathematics
screenshot 02: a comprehensive list of theories and equations
# image source: http://lookslikescience.tumblr.com/post/24878710516/i-am-bradley-k-oconnor-mathematician-phd
Career in R&D - Hong Kong
Beside universities, where you can find a R&D career, especially in Hong Kong?
Nano and Advanced materials Institute Limited
http://www.nami.org.hk/en/nami/careers.html
Hong Kong Applied Science and Technology Research Institute Company Limited
http://www.astri.org/main/?contentnamespace=careers:home
Hong Kong Science & Technology Parks - Member Companies
https://talent.hkstp.org/jsk_main.php
Hong Kong Science & Technology Parks
http://www.hkstp.org/en-US/Career/Job-Vacancies.aspx#.U4L0CnKSyVM
Hong Kong Cyberport Management Company Limited
http://www.cyberport.hk/en/ict_connect/ict-jobs
#image source: http://www.campusexplorer.com/
Nano and Advanced materials Institute Limited
http://www.nami.org.hk/en/nami/careers.html
Hong Kong Applied Science and Technology Research Institute Company Limited
http://www.astri.org/main/?contentnamespace=careers:home
Hong Kong Science & Technology Parks - Member Companies
https://talent.hkstp.org/jsk_main.php
Hong Kong Science & Technology Parks
http://www.hkstp.org/en-US/Career/Job-Vacancies.aspx#.U4L0CnKSyVM
Hong Kong Cyberport Management Company Limited
http://www.cyberport.hk/en/ict_connect/ict-jobs
#image source: http://www.campusexplorer.com/
Tag :
job,
Startup Highlights - KickStarter Projects
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Let's see some cool ideas from KickStarter:
Niwa: The world’s first smartphone-controlled growing system
http://kck.st/1l417HB
ARKYD: A Space Telescope for Everyone
OpenBCI: An Open Source Brain-Computer Interface For Makers
Ring : Shortcut Everything
#Image Source: http://compliancex.com/this-crazy-idea-just-may-work-lets-tie-pay-performance
Suggested Youtube Videos Introducing Bioengineering
It is always hard to imagine how bioengineering will grow in the next 10 years, right?
 |
Let's take 5 minutes to understand what is bioengineering by professors from Stanford University.
Bioengineering: Transforming Human Health - Stanford University
You can also go to the department website: http://bioengineering.stanford.edu
#Image Source: http://bioengineer.org/wp-content/uploads/2014/02/New-Heart-Liver-Kidney-or-Eye-in-under-2-hours-Bioprinting.jpg
Suggested Youtube Videos Introducing Chemical Engineering
Chemical Engineering is far beyond a chemical plant!
 |
Chemical Engineer - Profiles of Scientists and Engineers - National Science Foundation
Free Online Tools - Calculators
Are you using these online tools in your research? Unit Converter
http://www.unitconverters.net/
Oligo Calc: Oligonucleotide Properties Calculator
http://www.basic.northwestern.edu/biotools/OligoCalc.html
RNA secondary structure prediction
http://www.genebee.msu.su/services/rna2_reduced.html
RNAfold web server
http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi
Aragorn, tRNA (and tmRNA) detection
http://130.235.46.10/ARAGORN/
Metal-Oxide-Semiconductor Calculator Applet
http://jas.eng.buffalo.edu/education/mos/moscalc/index.html
Building Mass and Energy Balances
http://www.ce.utexas.edu/bmeb/
Enthalpy and Gibbs Free Energy Calculator
http://www.shodor.org/unchem/advanced/thermo/thermocalc.html
Calculator Edge
http://www.calculatoredge.com/
Tag :
general,
online tools,
Suggested Youtube Videos Introducing Electrical Engineering
It is always amazing to see cable towers, but this is not the only reason to study electrical engineering, right?
 |
The Future of Electrical Engineering - Boeing
Image Source: http://www.electricalengineerworld.com/
G-protein-coupled Receptors
Synonyms
Seven transmembrane helix receptors; Heptahelical receptors; Serpentine receptors
Definition
G-protein-coupled receptors (GPCRs) are a large family of plasma membrane receptors. Upon binding its agonist, a GPCR activates an intracellular heterotrimeric guanine nucleotide regulatory protein (G protein). The activated G protein modulates the activity of one or more enzymes or ion channels. G protein independent signaling pathways have also been identified for several receptors.
Basic Characteristics
Cells receive much of the information about their external environment by way of receptor proteins that span the plasma membrane. GPCRs are the largest family of plasma membrane receptors. They mediate response to the majority of hormones and neurotransmitters as well as the senses of sight, smell, and taste. These receptors have in common a seven transmembrane topology and functional interactions with heterotrimeric guanine nucleotide binding proteins (G proteins). GPCRs respond to a large variety of stimuli ranging from photons, ions, amino acids, and small organic molecules to peptide and protein hormones.
Analysis of the human genome reveals over 800 unique GPCRs [1]. The functional role for many of these GPCRs has not yet been determined and these have been designated as orphan GPCRs. GPCRs can be divided into five families based on sequence homology: the rhodopsin family, the secretin receptor family, the glutamate receptor family, the adhesion receptor family, and the frizzled/TAS2 receptor family. The rhodopsin family is by far the largest with over 700 members. Of these 460 belong to the subfamily of odorant receptors, and the rest are receptors for hormones and neurotransmitters.
GPCRs as a group constitute the largest family of targets for pharmacological intervention. They are critically involved in virtually every physiological system. A partial list of natural GPCR ligands includes protons, calcium, glutamate, GABA, acetylcholine, histamine, GTP/ATP, adenosine, cAMP, melatonin, epinephrine, serotonin, and dopamine. Peptide hormone GPCR activators include angiotensin, vasopressin, bradykinin, calcitonin, FSH, glucagon, somatostatin and a host of chemokines, opioids, and cannabinoids. Olfactory and gustatory sensory transduction involves GPCRs responsive to a large array of odorants and pheromones, and vision depends on the light-activated ligand retinal covalently bound to its own GPCR rhodopsin.
The electronic version of this article is the complete one and can be found online at: http://www.springerreference.com/docs/html/chapterdbid/137855.html
Antimicrobial resistance: a global view from the 2013 World Healthcare-Associated Infections Forum
Corresponding author: Didier Pittet didier.pittet@hcuge.ch
Infection Control Programme and WHO Collaborating Centre on Patient Safety, University Hospitals of Geneva, Rue Gabrielle-Perret-Gentil 4, 1205, Geneva, Switzerland
Antimicrobial Resistance and Infection Control 2013, 2:31 doi:10.1186/2047-2994-2-31
Abstract
Antimicrobial resistance (AMR) is now a global threat. Its emergence rests on antimicrobial overuse in humans and food-producing animals; globalization and suboptimal infection control facilitate its spread. While aggressive measures in some countries have led to the containment of some resistant gram-positive organisms, extensively resistant gram-negative organisms such as carbapenem-resistant enterobacteriaceae and pan-resistant Acinetobacter spp. continue their rapid spread. Antimicrobial conservation/stewardship programs have seen some measure of success in reducing antimicrobial overuse in humans, but their reach is limited to acute-care settings in high-income countries. Outside the European Union, there is scant or no oversight of antimicrobial administration to food-producing animals, while evidence mounts that this administration leads directly to resistant human infections. Both horizontal and vertical infection control measures can interrupt transmission among humans, but many of these are costly and essentially limited to high-income countries as well. Novel antimicrobials are urgently needed; in recent decades pharmaceutical companies have largely abandoned antimicrobial discovery and development given their high costs and low yield. Against this backdrop, international and cross-disciplinary collaboration appears to be taking root in earnest, although specific strategies still need defining. Educational programs targeting both antimicrobial prescribers and consumers must be further developed and supported. The general public must continue to be made aware of the current scale of AMR’s threat, and must perceive antimicrobials as they are: a non-renewable and endangered resource.
The electronic version of this article is the complete one and can be found online at: http://www.aricjournal.com/content/2/1/31
# Image Source: http://greenwatchbd.com
Infection Control Programme and WHO Collaborating Centre on Patient Safety, University Hospitals of Geneva, Rue Gabrielle-Perret-Gentil 4, 1205, Geneva, Switzerland
Antimicrobial Resistance and Infection Control 2013, 2:31 doi:10.1186/2047-2994-2-31
 |
Abstract
Antimicrobial resistance (AMR) is now a global threat. Its emergence rests on antimicrobial overuse in humans and food-producing animals; globalization and suboptimal infection control facilitate its spread. While aggressive measures in some countries have led to the containment of some resistant gram-positive organisms, extensively resistant gram-negative organisms such as carbapenem-resistant enterobacteriaceae and pan-resistant Acinetobacter spp. continue their rapid spread. Antimicrobial conservation/stewardship programs have seen some measure of success in reducing antimicrobial overuse in humans, but their reach is limited to acute-care settings in high-income countries. Outside the European Union, there is scant or no oversight of antimicrobial administration to food-producing animals, while evidence mounts that this administration leads directly to resistant human infections. Both horizontal and vertical infection control measures can interrupt transmission among humans, but many of these are costly and essentially limited to high-income countries as well. Novel antimicrobials are urgently needed; in recent decades pharmaceutical companies have largely abandoned antimicrobial discovery and development given their high costs and low yield. Against this backdrop, international and cross-disciplinary collaboration appears to be taking root in earnest, although specific strategies still need defining. Educational programs targeting both antimicrobial prescribers and consumers must be further developed and supported. The general public must continue to be made aware of the current scale of AMR’s threat, and must perceive antimicrobials as they are: a non-renewable and endangered resource.
The electronic version of this article is the complete one and can be found online at: http://www.aricjournal.com/content/2/1/31
# Image Source: http://greenwatchbd.com
HIV integrase and the swan song of the CD4 T cells?
Corresponding author: Jérôme Estaquier estaquier@yahoo.fr
CNRS FRE 3235, Université Paris Descartes, Paris, France
Retrovirology 2013, 10:149 doi:10.1186/1742-4690-10-149
Abstract
T cell apoptosis represents one pathophysiological mechanism associated with AIDS. Herein, we discuss the recent report published by A. Cooper et al. in Nature (June 2013) regarding HIV viral DNA integration-mediated apoptosis.
The electronic version of this article is the complete one and can be found online at: http://www.retrovirology.com/content/10/1/149
CNRS FRE 3235, Université Paris Descartes, Paris, France
Retrovirology 2013, 10:149 doi:10.1186/1742-4690-10-149
Abstract
T cell apoptosis represents one pathophysiological mechanism associated with AIDS. Herein, we discuss the recent report published by A. Cooper et al. in Nature (June 2013) regarding HIV viral DNA integration-mediated apoptosis.
The electronic version of this article is the complete one and can be found online at: http://www.retrovirology.com/content/10/1/149
Will we cure cancer by sequencing thousands of genomes?
Correspondence: Joshua M Nicholson jmn@vt.edu
Virginia Tech, Department of Biological Sciences, 1981 Kraft Dr, Blacksburg, VA 24060, USA
Molecular Cytogenetics 2013, 6:57 doi:10.1186/1755-8166-6-57
Abstract
The promise to understand cancer and develop efficacious therapies by sequencing thousands of cancers has not occurred. Mutations in specific genes termed oncogenes and tumor suppressor genes are extremely heterogeneous amongst the same type of cancer as well as between cancers. They provide little selective advantage to the cancer and in functional tests have yet to be shown to be sufficient for transformation. Here I discuss the karyotyptic theory of cancer and ask if it is time for a new approach to understanding and ultimately treating cancer.
The electronic version of this article is the complete one and can be found online at: http://www.molecularcytogenetics.org/content/6/1/57
#Image Source: http://cdn.knowcancer.com
Virginia Tech, Department of Biological Sciences, 1981 Kraft Dr, Blacksburg, VA 24060, USA
Molecular Cytogenetics 2013, 6:57 doi:10.1186/1755-8166-6-57
 |
Abstract
The promise to understand cancer and develop efficacious therapies by sequencing thousands of cancers has not occurred. Mutations in specific genes termed oncogenes and tumor suppressor genes are extremely heterogeneous amongst the same type of cancer as well as between cancers. They provide little selective advantage to the cancer and in functional tests have yet to be shown to be sufficient for transformation. Here I discuss the karyotyptic theory of cancer and ask if it is time for a new approach to understanding and ultimately treating cancer.
The electronic version of this article is the complete one and can be found online at: http://www.molecularcytogenetics.org/content/6/1/57
#Image Source: http://cdn.knowcancer.com
Computational neuroscience in research for depression
Correspondence: Georg Juckel georg.juckel@wkp-lwl.org
Department of Psychiatry, Psychotherapy and Preventive Medicine Ruhr University Bochum, Alexandrinenstr 1-3, 44791 Bochum, Germany
In Silico Pharmacology 2013, 1:19 doi:10.1186/2193-9616-1-19
Abstract
Depression is a common and hazardous mental disorder, which has been pathophysiologically associated with alterations of neurocircuitries involving medial prefrontal cortex, hippocampus and thalamus. Recent progress in computational neuroscience, particularly in the field of in silico psychopharmacology suggests the increasing potential of mathematical modeling in providing insights on the dynamics of these neuronal networks, which in turn may lead to further develop and clarify the present models of the pathophysiology of depression. Moreover, computational approaches provide well-defined non-invasive frameworks for investigation of the clinically common poly-pharmacological treatment strategies, which take us one step closer to the development of novel agents that will potentially result in diagnostic and prognostic indicators to be used in individualized treatment strategies.
The electronic version of this article is the complete one and can be found online at: http://www.in-silico-pharmacology.com/content/1/1/19
#Image Source: http://www.kuramamagazine.com
Department of Psychiatry, Psychotherapy and Preventive Medicine Ruhr University Bochum, Alexandrinenstr 1-3, 44791 Bochum, Germany
In Silico Pharmacology 2013, 1:19 doi:10.1186/2193-9616-1-19
 |
Depression is a common and hazardous mental disorder, which has been pathophysiologically associated with alterations of neurocircuitries involving medial prefrontal cortex, hippocampus and thalamus. Recent progress in computational neuroscience, particularly in the field of in silico psychopharmacology suggests the increasing potential of mathematical modeling in providing insights on the dynamics of these neuronal networks, which in turn may lead to further develop and clarify the present models of the pathophysiology of depression. Moreover, computational approaches provide well-defined non-invasive frameworks for investigation of the clinically common poly-pharmacological treatment strategies, which take us one step closer to the development of novel agents that will potentially result in diagnostic and prognostic indicators to be used in individualized treatment strategies.
The electronic version of this article is the complete one and can be found online at: http://www.in-silico-pharmacology.com/content/1/1/19
#Image Source: http://www.kuramamagazine.com
Zip nucleic acid: a new reliable method to increase the melting temperature of real-time PCR probes
Corresponding author: Fariba Koohdani fkoohdan@sina.tums.ac.ir
Diabetes Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
Journal of Diabetes & Metabolic Disorders 2014, 13:26 doi:10.1186/2251-6581-13-26
Abstract
TaqMan genotyping with real-time PCR is a reliable method for single nucleotide polymorphism detection, which is done by probes. These oligonucleotides should be short enough to avoid mismatch hybridization, as well as having 5–10°C higher melting temperature than the primers of real-time PCR reaction. One approach for these qualities is to conjugate the probe with minor groove binder (MGB). Having no access to MGB probes, we searched for an alternative. In the current study, we used Zip Nucleic Acids (ZNA) as probes to increase its stability and melting temperature. Our aim was to genotype the -265 T/C changes of Apolipoprotein A-2 gene. We set up the real-time PCR reaction with ZNA probes, and by repeating the reactions, we confirmed the reliability of this new approach. It is now recommended to use ZNA probes, as an alternative to MGB probes, to increase the probe Tm value and its binding to target DNA.
The electronic version of this article is the complete one and can be found online at: http://www.jdmdonline.com/content/13/1/26
Diabetes Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
Journal of Diabetes & Metabolic Disorders 2014, 13:26 doi:10.1186/2251-6581-13-26
TaqMan genotyping with real-time PCR is a reliable method for single nucleotide polymorphism detection, which is done by probes. These oligonucleotides should be short enough to avoid mismatch hybridization, as well as having 5–10°C higher melting temperature than the primers of real-time PCR reaction. One approach for these qualities is to conjugate the probe with minor groove binder (MGB). Having no access to MGB probes, we searched for an alternative. In the current study, we used Zip Nucleic Acids (ZNA) as probes to increase its stability and melting temperature. Our aim was to genotype the -265 T/C changes of Apolipoprotein A-2 gene. We set up the real-time PCR reaction with ZNA probes, and by repeating the reactions, we confirmed the reliability of this new approach. It is now recommended to use ZNA probes, as an alternative to MGB probes, to increase the probe Tm value and its binding to target DNA.
The electronic version of this article is the complete one and can be found online at: http://www.jdmdonline.com/content/13/1/26
Do smartphone applications in healthcare require a governance and legal framework? It depends on the application!
Corresponding author: Esmita Charani e.charani@imperial.ac.uk
Centre for Infection Prevention and Management, Imperial College London, Du Cane Road, London W12 0NN, UK
BMC Medicine 2014, 12:29 doi:10.1186/1741-7015-12-29
Abstract
The fast pace of technological improvement and the rapid development and adoption of healthcare applications present crucial challenges for clinicians, users and policy makers. Some of the most pressing dilemmas include the need to ensure the safety of applications and establish their cost-effectiveness while engaging patients and users to optimize their integration into health decision-making. Healthcare organizations need to consider the risk of fragmenting clinical practice within the organization as a result of too many apps being developed or used, as well as mechanisms for app integration into the wider electronic health records through development of governance framework for their use. The impact of app use on the interactions between clinicians and patients needs to be explored, together with the skills required for both groups to benefit from the use of apps. Although healthcare and academic institutions should support the improvements offered by technological advances, they must strive to do so within robust governance frameworks, after sound evaluation of clinical outcomes and examination of potential unintended consequences.
The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1741-7015/12/29
#Image Source: http://chicagohealthonline.com
Centre for Infection Prevention and Management, Imperial College London, Du Cane Road, London W12 0NN, UK
BMC Medicine 2014, 12:29 doi:10.1186/1741-7015-12-29
 |
Abstract
The fast pace of technological improvement and the rapid development and adoption of healthcare applications present crucial challenges for clinicians, users and policy makers. Some of the most pressing dilemmas include the need to ensure the safety of applications and establish their cost-effectiveness while engaging patients and users to optimize their integration into health decision-making. Healthcare organizations need to consider the risk of fragmenting clinical practice within the organization as a result of too many apps being developed or used, as well as mechanisms for app integration into the wider electronic health records through development of governance framework for their use. The impact of app use on the interactions between clinicians and patients needs to be explored, together with the skills required for both groups to benefit from the use of apps. Although healthcare and academic institutions should support the improvements offered by technological advances, they must strive to do so within robust governance frameworks, after sound evaluation of clinical outcomes and examination of potential unintended consequences.
The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1741-7015/12/29
#Image Source: http://chicagohealthonline.com
The impact of harm reduction on HIV and illicit drug use
Corresponding author: Thomas Kerr uhri-tk@cfenet.ubc.ca
Author Affiliations
British Columbia Centre for Excellence in HIV/AIDS, St. Paul’s Hospital, 608 - 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
Harm Reduction Journal 2014, 11:7 doi:10.1186/1477-7517-11-7
ABSTRACT
There has been widespread support for harm reduction programs as an essential component for responding to the HIV and illicit drug use epidemics. However, despite the growing international acceptance of harm reduction, there continues to be strong opposition to this approach, with critics alleging that harm reduction programs enable drug use. Vancouver, Canada provides a compelling case study that demonstrates that many positive impacts of harm reduction can be attained while addiction treatment-related goals are simultaneously supported. While the evidence for harm reduction is clearly mounting, it is unfortunate that ideological and political barriers to implementing harm reduction programs in Canada remain. As evidenced by Vancouver and elsewhere, harm reduction programs do not exacerbate drug use and undermine treatment efforts and should thereby occupy a well-deserved space within the continuum of programs and services offered to people who inject drugs.
The electronic version of this article is the complete one and can be found online at: http://www.harmreductionjournal.com/content/11/1/7
#Image Source: http://bioengineer.org
Author Affiliations
British Columbia Centre for Excellence in HIV/AIDS, St. Paul’s Hospital, 608 - 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
Harm Reduction Journal 2014, 11:7 doi:10.1186/1477-7517-11-7
 |
ABSTRACT
There has been widespread support for harm reduction programs as an essential component for responding to the HIV and illicit drug use epidemics. However, despite the growing international acceptance of harm reduction, there continues to be strong opposition to this approach, with critics alleging that harm reduction programs enable drug use. Vancouver, Canada provides a compelling case study that demonstrates that many positive impacts of harm reduction can be attained while addiction treatment-related goals are simultaneously supported. While the evidence for harm reduction is clearly mounting, it is unfortunate that ideological and political barriers to implementing harm reduction programs in Canada remain. As evidenced by Vancouver and elsewhere, harm reduction programs do not exacerbate drug use and undermine treatment efforts and should thereby occupy a well-deserved space within the continuum of programs and services offered to people who inject drugs.
The electronic version of this article is the complete one and can be found online at: http://www.harmreductionjournal.com/content/11/1/7
#Image Source: http://bioengineer.org
Drug-target and disease networks: polypharmacology in the post-genomic era
Corresponding author: Ali Masoudi-Nejad amasoudin@ibb.ut.ac.ir
Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
In Silico Pharmacology 2013, 1:17 doi:10.1186/2193-9616-1-17
Abstract
With the growing understanding of complex diseases, the focus of drug discovery has shifted away from the well-accepted “one target, one drug” model, to a new “multi-target, multi-drug” model, aimed at systemically modulating multiple targets. Identification of the interaction between drugs and target proteins plays an important role in genomic drug discovery, in order to discover new drugs or novel targets for existing drugs. Due to the laborious and costly experimental process of drug-target interaction prediction, in silico prediction could be an efficient way of providing useful information in supporting experimental interaction data. An important notion that has emerged in post-genomic drug discovery is that the large-scale integration of genomic, proteomic, signaling and metabolomic data can allow us to construct complex networks of the cell that would provide us with a new framework for understanding the molecular basis of physiological or pathophysiological states. An emerging paradigm of polypharmacology in the post-genomic era is that drug, target and disease spaces can be correlated to study the effect of drugs on different spaces and their interrelationships can be exploited for designing drugs or cocktails which can effectively target one or more disease states. The future goal, therefore, is to create a computational platform that integrates genome-scale metabolic pathway, protein–protein interaction networks, gene transcriptional analysis in order to build a comprehensive network for multi-target multi-drug discovery.
The electronic version of this article is the complete one and can be found online at: http://www.in-silico-pharmacology.com/content/1/1/17
Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
In Silico Pharmacology 2013, 1:17 doi:10.1186/2193-9616-1-17
Abstract
With the growing understanding of complex diseases, the focus of drug discovery has shifted away from the well-accepted “one target, one drug” model, to a new “multi-target, multi-drug” model, aimed at systemically modulating multiple targets. Identification of the interaction between drugs and target proteins plays an important role in genomic drug discovery, in order to discover new drugs or novel targets for existing drugs. Due to the laborious and costly experimental process of drug-target interaction prediction, in silico prediction could be an efficient way of providing useful information in supporting experimental interaction data. An important notion that has emerged in post-genomic drug discovery is that the large-scale integration of genomic, proteomic, signaling and metabolomic data can allow us to construct complex networks of the cell that would provide us with a new framework for understanding the molecular basis of physiological or pathophysiological states. An emerging paradigm of polypharmacology in the post-genomic era is that drug, target and disease spaces can be correlated to study the effect of drugs on different spaces and their interrelationships can be exploited for designing drugs or cocktails which can effectively target one or more disease states. The future goal, therefore, is to create a computational platform that integrates genome-scale metabolic pathway, protein–protein interaction networks, gene transcriptional analysis in order to build a comprehensive network for multi-target multi-drug discovery.
The electronic version of this article is the complete one and can be found online at: http://www.in-silico-pharmacology.com/content/1/1/17
Retrotransposition in tumors and brains
Correspondence: John L Goodier jgoodier@jhmi.edu
Author Affiliations
McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
Mobile DNA 2014, 5:11 doi:10.1186/1759-8753-5-11
Abstract
LINE-1s (L1s), the only currently active autonomous mobile DNA in humans, occupy at least 17% of human DNA. Throughout evolution, the L1 has also been responsible for genomic insertion of thousands of processed pseudogenes and over one million nonautonomous retrotransposons called SINEs (mainly Alus and SVAs). The 6-kb human L1 has a 5′- untranslated region (UTR) that functions as an internal promoter, two open reading frames—ORF1, which encodes an RNA-binding protein, and ORF2, which expresses endonuclease and reverse transcriptase activities—and a 3′-UTR which ends in a poly(A) signal and tail. Most L1s are molecular fossils: truncated, rearranged or mutated. However, 80 to 100 remain potentially active in any human individual, and to date 101 de novo disease-causing germline retrotransposon insertions have been characterized. It is now clear that significant levels of retrotransposition occur not only in the human germline but also in some somatic cell types. Recent publications and new investigations under way suggest that this may especially be the case for cancers and neuronal cells. This commentary offers a few points to consider to aid in avoiding misinterpretation of data as these studies move forward.
The electronic version of this article is the complete one and can be found online at: http://www.mobilednajournal.com/content/5/1/11
Author Affiliations
McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
Mobile DNA 2014, 5:11 doi:10.1186/1759-8753-5-11
Abstract
LINE-1s (L1s), the only currently active autonomous mobile DNA in humans, occupy at least 17% of human DNA. Throughout evolution, the L1 has also been responsible for genomic insertion of thousands of processed pseudogenes and over one million nonautonomous retrotransposons called SINEs (mainly Alus and SVAs). The 6-kb human L1 has a 5′- untranslated region (UTR) that functions as an internal promoter, two open reading frames—ORF1, which encodes an RNA-binding protein, and ORF2, which expresses endonuclease and reverse transcriptase activities—and a 3′-UTR which ends in a poly(A) signal and tail. Most L1s are molecular fossils: truncated, rearranged or mutated. However, 80 to 100 remain potentially active in any human individual, and to date 101 de novo disease-causing germline retrotransposon insertions have been characterized. It is now clear that significant levels of retrotransposition occur not only in the human germline but also in some somatic cell types. Recent publications and new investigations under way suggest that this may especially be the case for cancers and neuronal cells. This commentary offers a few points to consider to aid in avoiding misinterpretation of data as these studies move forward.
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