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July 31, 2006
Resources for Omics Researchers (Omics Series, 16)
While there are a great many resources for omics researchers, both in print and online, these change rapidly and unpredictably, as do the field themselves. Today's entry includes protocols, open-source software, and a few general collections of research resources in these areas. In addition to the resources listed here (all of which were good links as of July 2006), remember to also check the website for the company that produced your equipment, as many corporations also provide detailed protocols guides.
* ONLINE RESOURCES
ApoptosisWorld, resources for studying cell death: http://www.apoptosisworld.com/
BioDAS (Biological Distributed Annotation System): http://biodas.org/
"This site is the center of development of an Open Source system for exchanging annotations on genomic sequence data."
Bioinformatics.Org: The Open-Access Institute: http://bioinformatics.org/
CPAS: http://cpas.fhcrc.org/
"CPAS is an open source science portal offering web-based bioinformatics and collaboration tools to help scientists store, analyze, and share data from high-throughput experiments and clinical trials. The Fred Hutchinson Cancer Research Center uses CPAS to manage the Computational Proteomics Laboratory (CPL) Proteomics Repository containing over 140 million putative MS2 peptides, growing at 3 million per week. CPAS is available as free, installable software, with source code."
Drug Discovery & Development: Buyer's Guide: http://www.dddmag.com/BuyersGuide.aspx
GenomicWorld, resources for genomics and genetics: http://www.genomicworld.com/
Ion Channel Group: Bioinformatics, Databases and Software for Medicine: http://www.bio-computing.org/
Includes: "The first & only bioinformatics-specific relevancy-powered MEDLINE search." "Hint: Sort by citation score to display the highest impact articles."
Max-Planck-Institute of Immunobiology: Proteomics Protocols: http://www.immunbio.mpg.de/home/facilities/proteomics/protocols/index2.html
MicroarrayWorld, resources for microarrays and expression profiling: http://www.microarrayworld.com/
Molecular Station: Links: Proteomics Protocols: http://www.molecularstation.com/protocol-links/Proteomics_Protocols/
Molecular Station: Molecular Biology Techniques: http://www.molecularstation.com/molecular-biology-techniques/
Molecular Station: Proteomics Protocols: http://www.molecularstation.com/proteomics/proteomics-protocols/
msInspect: http://proteomics.fhcrc.org/CPL/msinspect.html
"msInspect allows you to view mass spectrometry (MS1) data in an mzXML file. You can use msInspect's built-in tools to inspect data, identify peptide features, generate peptide arrays using data from multiple runs, and export data to external applications for further analysis and collaboration."
ProteomicWorld: http://www.proteomicworld.org/
Includes: instruments, protocols, reagents, protein arrays, software, databases and more.
Protocol Online: Index to Protocols: http://www.protocol-online.org/prot/
Sashimi: http://sashimi.sourceforge.net/
"The goal of the project is to provide the scientific community with free open source software tools for the downstream analysis of mass spectrometric data. We hope to develop and distribute analysis tools that will facilitate the ability of labs worldwide to perform proteomics experiments."
* BOOKS IN DENTISTRY LIBRARY
For additional books on this topic, we highly recommend the Science Library and Taubman Medical Library.
Cell cycle control and dysregulation protocols : cyclins, cyclin-dependent kinases, and other factors / edited by Antonio Giordano, Gaetano Romano. QH 605 .C42571 2004
Cytokine protocols / edited by Marc de Ley. QH 506 .M451 v.249
Protein purification protocols. QP 551 .P697561 2004
Recombinant gene expression : reviews and protocols / edited by Paulina Balbás and Argelia Lorence. QH 443 .R361 2004
Short protocols in cell biology : a compendium of methods from Current protocols in cell biology / editorial board, Juan S. Bonifacino ... [et al.]. QH 585.2 .S55 2004
Bone research protocols / edited by Miep H. Helfrich, Stuart H. Ralston. QP 88.2 .B58981 2003
PCR protocols / edited by John M.S. Bartlett and David Stirling. QP 606 .D46 P35951 2003
Protein sequencing protocols / edited by Bryan John Smith. QP 625 .N89 P761 2002
* WANT MORE?
Google search: (omics OR genomics OR proteomics OR nanotechnology OR bioinformatics) (instruments OR protocols OR reagents OR "open source")
Posted by pfa at 12:48 PM | Comments (0)
July 28, 2006
Nanodentistry (Omics Series, 15)
Many of the same interests and factors that have captured attention in dental proteomics also overlap with nanodentistry. Specifically, many of the proteomic sensors for biofilms and oral fluid diagnostics have underlying nanotechnology in the final implementation. For this reason, this blog entry highlights a few articles and events that focus specifically on nanotechnology, however if you are interested in this area, please also refer to our article on dental proteomics.
* RESOURCES & EVENTS
European Dental Materials Conference, September 1-2, 2005: Nanomaterials/Nanotechnology in Dentistry: http://www.ucc.ie/academic/restorative/edmc/programme.html
Foresight Institute: Recent Articles on Medical Nanomaterials, Nanobiotechnology, or "Nanomedicine" / compiled by
Robert A. Freitas Jr.: http://www.foresight.org/Nanomedicine/NanoMedArticles.html
Nature Nanotechnology [forthcoming October 2006]: http://www.nature.com/nnano/index.html
Shahed University Dental Research Center: 1st Seminar on Nanotechnology Application in Dentistry; June 15, 2006: http://www.nano.ir
* ARTICLES
Freitas Jr RA.
Nanodentistry.
J. Amer. Dent. Assoc. 131(November 2000):1559-1566.
http://www.rfreitas.com/Nano/Nanodentistry.htm
http://jada.ada.org/cgi/content/abstract/131/11/1559
Jhaveri HM, Balaji PR
Nanotechnology: The future of dentistry
J Prosthodont 2005 5(1):15-17.
http://www.jprosthodont.com/article.asp?issn=0972-4052;year=2005;volume=5;issue=1;spage=15;epage=17;aulast=Jhaveri
Kong LX, Peng Z, Li SD, Bartold PM.
Nanotechnology and its role in the management of periodontal diseases.
Periodontol 2000. 2006;40:184-96.
PMID: 16398694
http://www.ingentaconnect.com/content/mksg/pe2/2006/00000040/00000001/art00014 [UM login required]
Malamud D, Bau H, Niedbala S, Corstjens P.
Point detection of pathogens in oral samples.
Adv Dent Res. 2005 Jun;18(1):12-6.
PMID: 15998938
http://adr.iadrjournals.org/cgi/content/full/18/1/12
Schleyer TL.
Nanodentistry -- truth or fiction?
J Am Dent Assoc, Vol 131, No 11, 1567-1568.
http://jada.ada.org/cgi/content/full/131/11/1567
* WANT MORE?
Google search: nanodentistry OR ((nano OR nanotechnology OR nanobiotechnology) (dentistry OR saliva OR enamel OR periodontal OR gingival))
Google Scholar search: nanodentistry OR ((nano OR nanotechnology OR nanobiotechnology) (dentistry OR saliva OR enamel OR periodontal OR gingival))
Pubmed search: nanotechnology (dentistry OR saliva OR periodontal OR enamel)
Rollyo: pfa: Nano Search: http://rollyo.com/pfa/nano/
Posted by pfa at 09:43 PM | Comments (0)
July 27, 2006
New Articles from UM SoD Faculty: July 06, part 3
Oh TJ. Shotwell JL. Billy EJ. Wang HL.
Effect of flapless implant surgery on soft tissue profile: a randomized controlled clinical trial.
Journal of Periodontology. 77(5):874-82, 2006 May.
PMID: 16671881
Ramamoorthy A. Thennarasu S. Tan A. Gottipati K. Sreekumar S. Heyl DL. An FY. Shelburne CE.
Deletion of all cysteines in tachyplesin I abolishes hemolytic activity and retains antimicrobial activity and lipopolysaccharide selective binding.
Biochemistry. 45(20):6529-40, 2006 May 23.
PMID: 16700563
Posted by pfa at 07:52 PM | Comments (0)
Dentistry and Proteomics (Omics Series, 14)
Proteomics has quickly become one of the most exciting research frontiers in modern dentistry. The two primary areas in which dental proteomics has really shone are salivary diagnostics (also known as oral fluids diagnostics or oral fluid biomarkers) and proteomics of bone and mineral structures, especially dental enamel. Because these lines of research are still very much cutting edge, the bulk of the online resources are specific articles, and websites for the labs of researchers working in these areas. There are a number of meetings and working groups being initiated in these areas. Aside from research, salivary diagnostics has attracted a great deal of commercial and investor attention, making it challenging to search for information on these topics that is appropriate for the researcher or student. For those of the selected articles listed below which link to PubMed, please note that they require a University of Michigan login to retrieve the articles. Where possible, the link provided goes directly to the article on the publisher's website.
* PROTEOMICS AND ENAMEL
Hu JC. Yamakoshi Y. Yamakoshi F. Krebsbach PH. Simmer JP.
Proteomics and genetics of dental enamel.
Cells Tissues Organs. 181(3-4):219-31, 2005.
PMID: 16612087 [UM login required]
Hubbard M.
Enamel proteomics and protein interactions.
Eur J Oral Sci. 2006 May;114 Suppl 1:285-6. No abstract available.
PMID: 16674700 [UM login required]
Hubbard MJ, Kon JC.
Proteomic analysis of dental tissues.
J Chromatogr B Analyt Technol Biomed Life Sci. 2002 May 5;771(1-2):211-20.
PMID: 12016000 [UM login required]
Kim JW, Seymen F, Lin BP, Kiziltan B, Gencay K, Simmer JP, Hu JC.
ENAM mutations in autosomal-dominant amelogenesis imperfecta.
J Dent Res. 2005 Mar;84(3):278-82.
PMID: 15723871
http://jdr.iadrjournals.org/cgi/content/abstract/84/3/278
Oppenheim, Frank.
Proteomics of Human Acquired Enamel Pellicle (EP)
http://people.bu.edu/wzhang/Proteomics/proteomics.html
Simmer JP, Bartlett JD.
Kallikrein 4 is a secreted protein.
Cancer Res. 2004 Nov 15;64(22):8481-2; author reply 8482-3.
PMID: 15548723
http://cancerres.aacrjournals.org/cgi/content/full/64/22/8481
UM School of Dentistry: Biologic and Materials Science: Division of Prosthodontics: Simmer Lab: Research: Proteomics and Genetics of Enamel and Dentin: http://www.dent.umich.edu/depts/bms/research/simmerlab/research.html
Yao Y, Berg EA, Costello CE, Troxler RF, Oppenheim FG.
Identification of protein components in human acquired enamel pellicle and whole saliva using novel proteomics approaches.
J Biol Chem. 2003 Feb 14;278(7):5300-8.
PMID: 12444093
http://www.jbc.org/cgi/content/full/278/7/5300
* SALIVARY DIAGNOSTICS
Amado FML, Vitorino RMP, Domingues PMDN, Lobo MJC, Duarte JAR.
Analysis of the human saliva proteome
Expert Review of Proteomics Aug 2005 2(4):521-539
http://www.future-drugs.com/doi/abs/10.1586/14789450.2.4.521 [$$ required for article, abstract free]
Anderson JM, Oliveira F, Kamhawi S, Mans BJ, Reynoso D, Seitz AE, Lawyer P, Garfield
M, Pham M, Valenzuela JG.
Comparative salivary gland transcriptomics of sandfly vectors of visceral leishmaniasis.
BMC Genomics. 2006 Mar 15;7:52.
PMID: 16539713
http://www.biomedcentral.com/1471-2164/7/52
CPRMap: Clinical Proteomics: Fluid Proteomics: Salivary Proteomics: Salivary Proteomics Research Map:
http://www.cprmap.com/salivary-proteomics/
Li Y, Denny P, Ho CM, Montemagno C, Shi W, Qi F, Wu B, Wolinsky L, Wong DT.
The Oral Fluid MEMS/NEMS Chip (OFMNC): diagnostic and translational applications.
Adv Dent Res. 2005 Jun;18(1):3-5.
PMID: 16000263
http://adr.iadrjournals.org/cgi/content/full/18/1/3
Li Y, Zhou X, St John MA, Wong DT.
RNA profiling of cell-free saliva using microarray technology.
J Dent Res. 2004 Mar;83(3):199-203.
PMID: 14981119
http://jdr.iadrjournals.org/cgi/content/full/83/3/199
NIH: NIDCR: First Meeting of Salivary Diagnostics Group:
http://www.nidcr.nih.gov/NewsAndReports/E-Newsletters/SalivaryDiagnosticsGroup.htm
Oral-Based Diagnostics: A New York Academy of Sciences Meeting, October 10-13, 2006.
http://www.nyas.org/events/eventDetail.asp?eventID=5754&date=10/10/2006
Tabak LA
A revolution in biomedical assessment: the development of salivary diagnostics
J Dent Educ. 65(12): 1335-1339 2001
http://www.jdentaled.org/cgi/reprint/65/12/1335
Wong DT
Salivary diagnostics powered by nanotechnologies, proteomics and genomics
JADA 137 March 2006
http://www.oralcancerfoundation.org/dental/pdf/JADA%20Saliva%20Dx.pdf
Wong DT.
Towards a simple, saliva-based test for the detection of oral cancer 'oral fluid (saliva), which is the mirror of the body, is a perfect medium to be explored for health and disease surveillance'.
Expert Rev Mol Diagn. 2006 May;6(3):267-72.
PMID: 16706730
http://www.future-drugs.com/doi/abs/10.1586/14737159.6.3.267 [$$ required for article, abstract free]
Xie H, Rhodus NL, Griffin RJ, Carlis JV, Griffin TJ.
A Catalogue of Human Saliva Proteins Identified by Free Flow Electrophoresis-based Peptide Separation and Tandem Mass Spectrometry
Molecular & Cellular Proteomics 4:1826-1830, 2005.
http://www.mcponline.org/cgi/content/abstract/4/11/1826 [UM login required]
* OTHER
Barnett ML, Pihlstrom BL.
Methods for enhancing the efficiency of dental/oral health clinical trials: current status, future possibilities.
J Dent Res. 2004 Oct;83(10):744-50.
PMID: 15381712
http://jdr.iadrjournals.org/cgi/content/abstract/83/10/744
Hing KA.
Bone repair in the twenty-first century: biology, chemistry or engineering?
Philos Transact A Math Phys Eng Sci. 2004 Dec 15;362(1825):2821-50. Review.
PMID: 15539372
http://www.journals.royalsoc.ac.uk/link.asp?id=mu5xd2e1ukhn7x6m
Pappano WN, Steiglitz BM, Scott IC, Keene DR, Greenspan DS.
Use of Bmp1/Tll1 doubly homozygous null mice and proteomics to identify and validate in vivo substrates of bone morphogenetic protein 1/tolloid-like metalloproteinases.
Mol Cell Biol. 2003 Jul;23(13):4428-38.
PMID: 12808086
http://mcb.asm.org/cgi/content/full/23/13/4428?view=long&pmid=12808086
Wright JT, Hart TC.
The genome projects: implications for dental practice and education.
J Dent Educ. 2002 May;66(5):659-71.
PMID: 12056771
http://www.jdentaled.org/cgi/content/abstract/66/5/659
* WANT MORE?
Pubmed search: (proteomics OR biomarkers) (dentistry OR enamel OR pellicle OR "salivary diagnostics" OR "oral fluids")
Posted by pfa at 07:30 PM | Comments (0)
July 26, 2006
Birth Defects and Omics (Omics Series, 13)
There is perhaps an intuitive or obvious connection between dentistry and craniofacial anomalies and birth defects, as well as an intuitive connection between birth defects and genetics / genomics. Birth defects are, in some ways, one of the most significant links between genomics and both public health and dentistry. Much of the overlapping work focuses on cleft lip and palate, but definitely not all. In today's entry we will find local, national and international resources as well as articles that explore the connections between these three concepts.
* MICHIGAN
Michigan Genetics Connection: Birth Defects & Folic Acid: http://www.migeneticsconnection.org/birthdefects.shtml
Michigan Birth Defects Registry: http://www.michigan.gov/mdch/0,1607,7-132-2944_4670---,00.html
Pobojewski, Sally. "U-M scientists find genetic cause of multiple birth defects affecting kidneys, eyes and other organs." May 8, 2006. http://www.med.umich.edu/opm/newspage/2006/nphp.htm
* NATIONAL & INTERNATIONAL
CDC Birth Defects and Developmental Disabilities: http://www.cdc.gov/ncbddd/
CDC Genomics and Disease Prevention: http://www.cdc.gov/genomics/
EUROCRAN: European Collaboration on Cranial Facial Anomalies:
http://www.eurocran.org/
INCLUDES:
Directory of European Resources: http://www.eurocran.org/content.asp?contentID=6&sid=18504
Genetic Databases: http://www.eurocran.org/content.asp?contentID=10&sid=184936
Clinical Outcomes Library or Good Practice Archive (members only)
Speech Project: http://www.eurocran.org/content.asp?contentID=1213&sid=18463
Human Genome Epidemiology Network (HuGENet): http://www.cdc.gov/genomics/hugenet/
International Birth Defects Information Systems (IBIS): http://www.ibis-birthdefects.org/
International Clearinghouse for Birth Defects Monitoring Systems (ICBDMS): International Centre for Birth Defects (ICBD): http://www.icbd.org/icbd.htm
Teratology Society: http://teratology.org/
WHO: International Collaborative Research on Craniofacial Anomalies (IRCRA):
http://www.who.int/entity/genomics/anomalies/en/
WHO: International Database on Craniofacial Anomalies (IDCFA):
http://www.who.int/genomics/anomalies/idcfa/en/
* ARTICLES
Brunner HG, van Driel MA.
From syndrome families to functional genomics.
Nat Rev Genet. 2004 Jul;5(7):545-51.
http://www.nature.com/nrg/journal/v5/n7/abs/nrg1383_fs.html;jsessionid=78D5CB675EF83A5A6477FF83F14B9229
genome.gov: Genomics in Action: Lawrence C. Brody: http://www.genome.gov/13014224
Omenn GS.
Genomics and Public Health
Issues in Science and Technology, Spring 2005
"Potential benefits depend on linking genetic and environmental data in designing research, developing applications, and forging public policies."
http://www.issues.org/21.3/omenn.html
Culiat CT (Oak Ridge National Laboratory)
Modeling Human Craniofacial Birth Defects with ORNL Mouse Mutations: http://lsd.ornl.gov/highlights/culiat.pdf
Le Caignec C, Boceno M, Saugier-Veber P, Jacquemont S, Joubert M, David A, Frebourg T, Rival JM.
Detection of genomic imbalances by array based comparative genomic hybridisation in fetuses with multiple malformations.
J Med Genet. 2005 Feb;42(2):121-8.
http://jmg.bmjjournals.com/cgi/content/full/42/2/121
Pobojewski, Sally. "U-M scientists find genetic cause of multiple birth defects affecting kidneys, eyes and other organs." May 8, 2006. http://www.med.umich.edu/opm/newspage/2006/nphp.htm
Polifka JE, Friedman JM.
Medical genetics: 1. Clinical teratology in the age of genomics.
CMAJ August 6, 2002; 167 (3)
http://www.cmaj.ca/cgi/content/full/167/3/265
Spradling A, Ganetsky B, Hieter P, Johnston M, Olson M, Orr-Weaver T, Rossant J, Sanchez A, Waterston R.
New roles for model genetic organisms in understanding and treating human disease: report from the 2006 Genetics Society of America meeting.
Genetics. 2006 Apr;172(4):2025-32.
http://www.genetics.org/cgi/content/full/172/4/2025
Posted by pfa at 02:05 PM | Comments (0)
July 25, 2006
Dentistry and Omics In "Print" Journals (Omics Series, 12)
If you want to discover more about dentistry and the omics in the professional journal literature, then today's blog entry is for you! It is interesting to see the evolution of the field over time. Below you will find selected fulltext online journal articles both from the dental literature and other life science journals. Following the list of selected articles, are several links to other searches for locating articles in the science literature both online and in print. These will lead you to more of the articles from journals for which the University Libraries have paid subscriptions, as well as print articles held in the library itself.
* 2000
Cobourne MT.
Construction for the modern head: current concepts in craniofacial development.
J Orthod. 2000 Dec;27(4):307-14.
PMID: 11099568
http://jorthod.maneyjournals.org/cgi/content/full/27/4/307
* 2001
Dionne RA.
Pharmacologic advances in orofacial pain: from molecules to medicine.
J Dent Educ. 2001 Dec;65(12):1393-403.
PMID: 11780658
http://www.jdentaled.org/cgi/content/abstract/65/12/1393
Slavkin HC.
The human genome, implications for oral health and diseases, and dental education.
J Dent Educ. 2001 May;65(5):463-79.
PMID: 11425251
http://www.jdentaled.org/cgi/content/abstract/65/5/463
* 2002
Hart TC, Ferrell RE.
Genetic testing considerations for oral medicine.
J Dent Educ. 2002 Oct;66(10):1185-202.
PMID: 12449214
http://www.jdentaled.org/cgi/content/abstract/66/10/1185
Scully C, Challacombe SJ.
Pemphigus vulgaris: update on etiopathogenesis, oral manifestations, and management.
Crit Rev Oral Biol Med. 2002;13(5):397-408.
PMID: 12393759
http://crobm.iadrjournals.org/cgi/content/full/13/5/397
Wright JT, Hart TC
The genome projects: implications for dental practice and education.
J Dent Educ. 2002 May;66(5):659-71.
PMID: 12056771
http://www.jdentaled.org/cgi/content/abstract/66/5/659
* 2003
Gettig E, Hart TC.
Genetics in dental practice: social and ethical issues surrounding genetic testing.
J Dent Educ. 2003 May;67(5):549-62.
PMID: 12809190
http://www.jdentaled.org/cgi/content/abstract/67/5/549
Kuo WP
Overview of Bioinformatics and its Application to Oral Genomics.
Adv Dent Res 17:89-94, December, 2003
PMID: 15126216
http://adr.iadrjournals.org/cgi/content/full/17/1/89
Macarthur DJ, Jacques NA.
Proteome analysis of oral pathogens.
J Dent Res. 2003 Nov;82(11):870-6.
PMID: 14578497
http://jdr.iadrjournals.org/cgi/content/full/82/11/870
Miletich I, Sharpe PT.
Normal and abnormal dental development.
Hum Mol Genet. 2003 Apr 1;12 Spec No 1:R69-73.
PMID: 12668599
http://hmg.oxfordjournals.org/cgi/content/full/12/suppl_1/R69
Nishimura I, Drake TA, Lusis AJ, Lyons KM, Nadeau JH, Zernik J.
ENU large-scale mutagenesis and quantitative trait linkage (QTL) analysis in mice: novel technologies for searching polygenetic determinants of craniofacial abnormalities.
Crit Rev Oral Biol Med. 2003;14(5):320-30.
PMID: 14530301
http://crobm.iadrjournals.org/cgi/content/full/14/5/320
Thyagarajan T, Totey S, Danton MJ, Kulkarni AB.
Genetically altered mouse models: the good, the bad, and the ugly.
Crit Rev Oral Biol Med. 2003;14(3):154-74.
PMID: 12799320
http://crobm.iadrjournals.org/cgi/content/full/14/3/154
* 2004
Collins F, Tabak L
A Call for Increased Education in Genetics for Dental Health Professionals.
(Critical Issues in Dental Education: Genetics Education for Dental Health Professionals)
J Dent Educ 68(8): 807-808 2004
http://www.jdentaled.org/cgi/content/full/68/8/807
Stanier P, Moore GE.
Genetics of cleft lip and palate: syndromic genes contribute to the incidence of non-syndromic clefts.
Hum Mol Genet. 2004 Apr 1;13 Spec No 1:R73-81. Epub 2004 Jan 13.
PMID: 14722155
http://hmg.oxfordjournals.org/cgi/content/full/13/suppl_1/R73
* 2005
Zavras AI
Post-marketing Drug Safety in the Era of Genomic Medicine.
J Dent Res 84(2):105-106, 2005
http://jdr.iadrjournals.org/cgi/content/full/84/2/105
Li Y, Denny P, Ho CM, Montemagno C, Shi W, Qi F, Wu B, Wolinsky L, Wong DT.
The Oral Fluid MEMS/NEMS Chip (OFMNC): diagnostic and translational applications.
Adv Dent Res. 2005 Jun;18(1):3-5.
PMID: 16000263
http://adr.iadrjournals.org/cgi/content/full/18/1/3
Kuratani S.
Craniofacial development and the evolution of the vertebrates: the old problems on a new background.
Zoolog Sci. 2005 Jan;22(1):1-19.
PMID: 15684579
http://www.jstage.jst.go.jp/article/zsj/22/1/22_1/_article
* 2006
Wong DT
Salivary diagnostics powered by nanotechnologies, proteomics and genomics.
J Am Dent Assoc Mar 2006
http://jada.ada.org/cgi/content/abstract/137/3/313
* WANT MORE?
Google Scholar: (genomics OR genome OR proteomics OR bioinformatics OR nanotechnology) (dentistry OR "oral health" OR craniofacial OR "oral microorganisms")
Posted by pfa at 12:04 PM | Comments (0)
New Articles from UM SoD Faculty: July 06, part 2
Wilson EE. Awonusi A. Morris MD. Kohn DH. Tecklenburg MM. Beck LW.
Three structural roles for water in bone observed by solid-state NMR.
Biophysical Journal. 90(10):3722-31, 2006 May 15.
16500963
Hydrogen-bearing species in the bone mineral environment were investigated using solid-state NMR spectroscopy of powdered bone, deproteinated bone, and B-type carbonated apatite. Using magic-angle spinning and cross-polarization techniques three types of structurally-bound water were observed in these materials. Two of these water types occupy vacancies within the apatitic mineral crystal in synthetic carbonated apatite and deproteinated bone and serve to stabilize these defect-containing crystals. The third water was observed at the mineral surface in unmodified bone but not in deproteinated bone, suggesting a role for this water in mediating mineral-organic matrix interactions. Direct evidence of monohydrogen phosphate in a (1)H NMR spectrum of unmodified bone is presented for the first time. We obtained clear evidence for the presence of hydroxide ion in deproteinated bone by (1)H MAS NMR. A (1)H-(31)P heteronuclear correlation experiment provided unambiguous evidence for hydroxide ion in unmodified bone as well. Hydroxide ion in both unmodified and deproteinated bone mineral was found to participate in hydrogen bonding with neighboring water molecules and ions. In unmodified bone mineral hydroxide ion was found, through a (1)H-(31)P heteronuclear correlation experiment, to be confined to a small portion of the mineral crystal, probably the internal portion.
Posted by pfa at 12:03 PM | Comments (0)
July 24, 2006
Dentistry and Genomics Online (Omics Series, 11)
Much of the work to date in dental genomics has focused on oral microorganisms, an area also known as microbial genomics, oral diagnostics (especially with saliva), and forensics. Overviews of the discoveries and potential impact are available for laymen from National Coalition for Health Professional Education in Genetics (NCHPEG) and the Harris National Museum of Dentistry (NMD). NCHPEG has designed a rich Flash-based online exhibit including animations, illustrations, and a nicely selected resource list. The NMD has created the first exhibit examinig the impact of the human genome project on dentistry, with the exhibit due to be completed this year (2006).
National Coalition for Health Professional Education in Genetics (NCHPEG): Genetics, Disease and Dentistry: http://www.nchpeg.org/dental/index.html
Harris National Dental Museum (NMD): Exhibits: Your Spitting Image: http://www.dentalmuseum.umaryland.edu/exhibitions/special/detail.cfm?ID=41
The early planning from NIDCR, from 1999 through the 2002 Scientific Expert Panel, proposed that dental genomics focus on ten organisms -- nine bacteria and one yeast.
NIDCR Panel on Genomics and Proteomics Of Oral, Dental and Craniofacial Diseases -- A Scientific Expert Panel; May 22, 2002: http://www.nidcr.nih.gov/Research/LongRangeResearchOpportunities/PanelOnGenomicsAndProteomics.htm
Bacteria of periodontitis:
Porphyromonas gingivalis
Treponema denticola
Actinobacillus actinomycetemcomitans
Fusobacterium nucleatum
Bacteroides forsythus
Prevotella intermedia
Bacteria of dental caries:
Streptococcus mutans
Bacteria of dental plaque and endocarditis:
Streptococcus gordonii (in process)
Streptococcus sanguis
Yeast causing oral mucositis in the immunocompromised:
Candida albicans
Since that time, almost all of the named organisms have indeed had their genome mapped. A few of these projects have substantial websites with information about the project and organism, usually including the sequencing, assembly, and annotation of the specific genome.
Virginia Commonwealth University: Streptococcus sanguinis Genome Sequencing Project: http://www.sanguis.mic.vcu.edu/
Streptococcus mutans Genome Sequencing: http://www.genome.ou.edu/smutans.html
The Candida Genome Database (CGDTM): http://www.candidagenome.org/
NCBI: GenBank: T. denticola sequence (AE017226): http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi?term=AE017226
Porphyromonas Gingivalis Genome Project / Dr. Robert Fleischmann et al.: http://www.pgingivalis.org/
There are a few major resources that specifically collect microbial genomes for dentristry. TIGR-CMR collects a broad range of microbial and bacterial genomes, with a collection of almost 300 bacteria alone, while ORALGEN and BROP both collect only those relevant to dentistry.
Los Alamos: Oral Pathogen Sequence Databases (ORALGEN): http://www.oralgen.lanl.gov/
INCLUDES:
* Actinobacillus actinomycetemcomitans
* Fusobacterium nucleatum
* Porphyromonas gingivalis
* Prevotella intermedia
* Streptococcus mutans
* Tannerella forsythensis
* Treponema denticola
* Human Herpesvirus 1 HSV-1
* Human Herpesvirus 2 HSV-2
* Human Herpesvirus 5 HCMV
* Human Herpesvirus 8 KSHV
Forsyth Institute: Genome Viewing, Exploring & Analysis Tools: The Bioinformatics Resources for Oral Pathogens (BROP): http://genome.brop.org/
TIGR: Comprehensive Microbial Resource (CMR):
http://www.tigr.org/CMR
Posted by pfa at 09:21 PM | Comments (0)
July 21, 2006
Omics in Michigan (Omics Series, 10)
Where do you go with a quick question or how do you find an expert partner to extend your area of inquiry? There are amazing researchers all over the world, but there are also amazing researchers right next door. Today we are looking at the range of omics resources and research centers within the state of Michigan, at academic and corporate institutions, and within the University of Michigan. Let's explore what our neighbors are doing.
* MICHIGAN GOVERNMENT, ASSOCIATIONS, & OTHER
Michigan Genetics Resource Center: http://www.migeneticsconnection.org/
INCLUDES:
- Michigan Genetics Connection: Genetic Literacy: http://www.migeneticsconnection.org/geneticliteracy.shtml
- Michigan Genetics Connection: Michigan Genetics Support Group Directory: http://www.migeneticsconnection.org/supportdirectory.shtml
- Michigan Genetics Connection: Michigan State Genetics Plan: http://www.migeneticsconnection.org/stateplan.shtml
Michigan Proteome Consortium: http://www.proteomeconsortium.org/
Michigan Public Health Genomics* Program (PHGP): http://www.michigan.gov/mdch/0,1607,7-132-2942_4911_4916-85137--,00.html
State of Michigan: Public Health Genomics Program: http://www.michigan.gov/mdch/0,1607,7-132-2942_4911_4916-85137--,00.html
Michigan SmallTech Association (MISTA): http://www.michigansmalltech.com/
Michigan.org: Life Sciences Corridor: http://www.michigan.org/medc/ttc/LifeSciences/
Nanotechnology International: Usa/Michigan: companies, profiles and links: http://www.nanovip.com/directory/International/Usa/Michigan/index.php
* MICHIGAN UNIVERSITIES & SCHOOLS
EMU: Bioinformatics@emich.edu: http://www.emich.edu/bioinformatics/
MSU: Bioinformatics Services: http://genomics.msu.edu/bioinformatics/Bioinformatics.html
MSU: Genomics: Research Technology Support Facility (RTSF): http://genomics.msu.edu/index.html
MSU: Nanoscale Interdisciplinary Research Team (NIRT): http://nirt.pa.msu.edu/
MSU: Proteomics Database: http://genomics.msu.edu/cgi-bin/proteomics/login.cgi
MSU: Proteomics: http://proteomics.msu.edu/
MSU: The Nanotechnology Site: http://www.pa.msu.edu/cmp/csc/nanotech/
Michigan Technological University (MTU): Nanotechnology: http://nano.mtu.edu/
UM: Bioinformatics: http://www.bioinformatics.med.umich.edu/
UM: Center for Computational Medicine and Biology: http://www.ccmb.med.umich.edu/
UM: Center for Integrative Genomics: http://www.med.umich.edu/cig/index.html
UM: Center for Proteome Studies: http://www.proteomecenter.med.umich.edu/
UM: Michigan Center for Genomics & Public Health: http://www.sph.umich.edu/genomics/
UM: Michigan Nanofabrication Facility: http://www.mnf.umich.edu/
UM: Michigan Nanotechnology Institute for Medicine and Biological Sciences (M-NIMBS): http://nano.med.umich.edu/
UM: Microbial Genomics: http://sitemaker.umich.edu/microbial_genomics
UM: National Nanotechnology Infrastructure Network (Nanotech at UM): http://www.mnf.umich.edu/NNIN/
* WANT MORE?
Posted by pfa at 02:41 PM | Comments (0)
July 20, 2006
New IOM Report on Medication Errors
Hot off the presses, the Institute of Medicine today released a report on "Preventing Medication Errors".
Preventing Medication Errors (Quality Chasm Series): http://www.nap.edu/catalog/11623.html
Key findings of the report are that a quarter of all medication errors are preventable, and that the best prevention is good clinician-patient communication and good intra-institutional communication (between the clinician, pharmacist and other members of the support team).
In an rare but welcome move, the FDA immediately released a statement of support for the report.
FDA Statement on Institute of Medicine's Report on Preventing Medication Errors: http://www.fda.gov/bbs/topics/NEWS/2006/NEW01414.html
The FDA statement outlines a series of resources and actions related to improvements in this area. As a significant part of this, they recommend access to reliable and understandable medication information for the health care consumer, recommending the following resource from the National Library of Medicine.
DailyMed: http://dailymed.nlm.nih.gov/dailymed/about.cfm
"This Web site provides health information providers and the public with a standard, comprehensive, up-to-date, look-up and download resource of medication content and labeling as found in medication package inserts."
Posted by pfa at 05:33 PM | Comments (0)
Genetic and Genomic Information from NLM and the Genetics Home Reference (GHR) (Omics Series, 9)
The United States government, in general, and the National Library of Medicine, in particular, have taken leading roles in providing information, tools, resources, and training for biomedical and life sciences researchers and clinicians, including omics researchers. Very few people make use of the full range of resources they provide. Today, we will survey a few of the broad omics resources available, and then spend a little more time on a specific resource that tends to have information for both dental researchers and clinicians.
This is probably a good time to again mention the forthcoming short course on campus about NCBI resources.
National Center for Biotechnology Information: Short Course, September 7,2006 (Hosted by the Program in Bioinformatics, Department of Human Genetics & Taubman Medical Library): http://www.hg.med.umich.edu/ncbi/
In this course, you will see overviews and demonstrations of how to use many of the databases listed below. NLM and NCBI provide an astonishing number of databases. From their main databases page, you can browse a list of many of their offerings in this area.
NLM: NCBI: Entrez: All Databases: http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi?itool=toolbar
Here are a few of the specific databases, just to give you an idea of what you might find.
3D Domains: domains from Entrez Structure: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Domains
BLAST (Basic Local Alignment Search Tool finds regions of local similarity between sequences): http://www.ncbi.nlm.nih.gov/BLAST/
Cancer Chromosomes: cytogenetic databases: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=CancerChromosomes
CDD: conserved protein domain database: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd
Gene: gene-centered information: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
Genome Project: genome project information: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj
Genome: whole genome sequences: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome
GENSAT: gene expression atlas of mouse central nervous system: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gensat
GEO DataSets: experimental sets of GEO data: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gds
GEO Profiles: expression and molecular abundance profiles: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=geo
HomoloGene: eukaryotic homology groups: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene
Nucleotide: sequence database (GenBank): http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide
OMIA: online Mendelian Inheritance in Animals: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=omia
OMIM: online Mendelian Inheritance in Man: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM
PopSet: population study data sets: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PopSet
Probe: sequence-specific reagents: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=probe
Protein: sequence database: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein
PubChem BioAssay: bioactivity screens of chemical substances: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pcassay
PubChem Compound: unique small molecule chemical structures: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pccompound
PubChem Substance: deposited chemical substance records: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pcsubstance
SNP: single nucleotide polymorphism: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=snp
Structure: three-dimensional macromolecular structures: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure
Taxonomy: organisms in GenBank: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Taxonomy
UniGene: gene-oriented clusters of transcript sequences: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene
UniSTS: markers and mapping data: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unists
Another source they provide is the Human Genome. This resource contains an entirely different list of great tools and resources. I encourage you to explore the Human Genome more on your own.
Human Genome (an integrated, one-stop, genomic information infrastructure for biomedical researchers): http://www.ncbi.nlm.nih.gov/genome/guide/
Last, for today, but not least, is the Genetics Home Reference (GHR). The GHR serves as a bridge between the technical information for researchers and the consumer or general public. It includes information on the correspondence between specific genes and diseases, diagnostic signs/symptoms, an much more. Although the information is for consumers, it can still be fairly technical. It includes a handbook and glossary, which helps, and provides information at a level that can also be useful for the clinician. In addition, they include a list of resources about genetic conditions specifically for clinicians.
NLM: Genetics Home Reference: http://ghr.nlm.nih.gov/
GHR: Genetics Resources for Clinicians and Health Professionals: http://ghr.nlm.nih.gov/ghr/resource/clinicians
Among their newest topics on conditions, you'll find Dentinogenesis Imperfecta and Amelogenesis Imperfecta. Among their new pages on specific genes, you'll find amelogenin (amelogenesis imperfecta 1, X-linked), dentin sialophosphoprotein (DSPP), enamelin, and matrix metallopeptidase 20 (MMP20 or enamelysin). They have also recently added information on a number of specific genes that are associated with the Charcot Marie Tooth Disease. Here is a sampling of pages on dental-related conditions and genes.
CONDITIONS:
Condition: Achondrogenesis: http://ghr.nlm.nih.gov/condition=achondrogenesis
Condition: Amelogenesis Imperfecta: http://ghr.nlm.nih.gov/condition=amelogenesisimperfecta
Condition: Dentinogensis imperfecta: http://ghr.nlm.nih.gov/condition=dentinogenesisimperfecta
Condition: Fibrodysplasia ossificans progressiva: http://ghr.nlm.nih.gov/condition=fibrodysplasiaossificansprogressiva
Condition: Greig cephalopolysyndactyly syndrome: http://ghr.nlm.nih.gov/condition=greigcephalopolysyndactylysyndrome
Condition: Platyspondylic lethal skeletal dysplasia, Torrance type: http://ghr.nlm.nih.gov/condition=platyspondyliclethalskeletaldysplasiatorrancetype
Condition: Sotos syndrome: http://ghr.nlm.nih.gov/condition=sotossyndrome
GENES:
Gene: DNM2: dynamin 2: http://ghr.nlm.nih.gov/gene=dnm2
Gene: MMP20: matrix metallopeptidase 20 (enamelysin): http://ghr.nlm.nih.gov/gene=mmp20
Gene: SH3TC2: SH3 domain and tetratricopeptide repeats 2: http://ghr.nlm.nih.gov/gene=sh3tc2
Gene: YARS: tyrosyl-tRNA synthetase: http://ghr.nlm.nih.gov/gene=yars
Posted by pfa at 02:16 PM | Comments (0)
July 19, 2006
Omics E-Books (Omics Series, 8)
Genomics, as a discipline or research field, is more mature than either proteomics or nanotechnology. This, combined with the observation that books usually represent a later stage in the life of an idea, justifies why most of the online or free e-books are about genomics. For this reason, today's selections are not organized in the three groups we have used in the other blog entries of this series. Instead, you will find a list of selected recent electronic books on a variety of Omics topics and other matters of interest to Omics researchers. As this is a small sampling, at the end of this entry are suggested tools and techniques for discovering additional books available online.
Ensuring an Infectious Disease Workforce: Education and Training Needs for the 21st Century - Workshop Summary. 2006. http://www.nap.edu/books/0309100100/html/51.html
GeneReviews. Pagon, Roberta A., Editor-in-chief; Cassidy, Suzanne B.; Bird, Thomas C.; Dinulos, Mary Beth; Feldman, Gerald L.; Smith, Richard J.H.; Dolan, Cynthia R.; Associate editors; Baskin, Patricia K., Technical editor. Seattle (WA): University of Washington; c1993-2006. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=gene.TOC
Genes and Disease. Bethesda (MD): National Library of Medicine (US), NCBI. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=gnd.TOC&depth=2
Genetic Landscape of Diabetes. Dean, Laura; McEntyre, J.R. Bethesda (MD): National Library of Medicine (US), NCBI; 2004 Jun. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=diabetes.TOC&depth=1
Genomes 2nd ed. Brown, T.A. New York and London: Garland Science; c2002. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=genomes.TOC&depth=2
Genomic Signal Processing and Statistics. Edited by: Edward R. Dougherty, Ilya Shmulevich, Jie Chen, and Z. Jane Wang. 2005. http://books.google.com/books?vid=ISBN9775945070&id=0YGlW6Oo2kMC&printsec=frontcover
Globalization, Biosecurity, and the Future of the Life Sciences. 2006. http://www.nap.edu/openbook/0309100321/html/index.html
Human ATP-Binding Cassette (ABC) Transporter Superfamily. Dean, Michael. Bethesda (MD): National Library of Medicine (US), NCBI; 2002 Nov. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=mono_001.TOC&depth=2
Human Molecular Genetics 2, 2nd ed. Strachan, Tom and Read, Andrew P. New York and London: Garland Science; c1999. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=hmg.TOC&depth=2
Implications of Nanotechnology for Environmental Health Research. 2005. http://www.nap.edu/openbook/0309095778/html/index.html
Informing the Future: Critical Issues in Health, Third Edition. 2005. http://www.nap.edu/catalog/11469.html
Introduction to Genetic Analysis, 7th ed. Griffiths, Anthony J.F.; Miller, Jeffrey H.; Suzuki, David T.; Lewontin, Richard C.; Gelbart, William M. New York: W. H. Freeman & Co.; c1999. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=iga.TOC
KEGG: Kyoto Encyclopedia of Genes and Genomes. http://www.genome.jp/kegg/
KEGG2: Kyoto Encyclopedia of Genes and Genomes, 2nd edition. http://www.genome.jp/kegg/kegg2.html
KIR Gene Cluster. Carrington, Mary; Norman, Paul. Bethesda (MD): National Library of Medicine (US), NCBI; 2003. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=mono_003.TOC&depth=2
Making Babies: reproductive decisions and genetic technologies, 31 January 2006. http://www.hgc.gov.uk/Client/document.asp?DocId=112&CAtegoryId=8
Mapping Protein/DNA Interactions by Cross-Linking. Paris: Institut National de la Santé et de la Recherche Médicale (INSERM); c2001. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=inserm.TOC
Medical Biotechnology: Achievements, Prospects and Perceptions. By Albert Sasson. http://books.google.com/books?vid=ISBN9280811142&id=WjC_e27xgUEC&printsec=titlepage
Modern Genetic Analysis. Griffiths, Anthony J.F.; Gelbart, William M.; Miller, Jeffrey H.; Lewontin, Richard C. New York: W. H. Freeman & Co.; c1999. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=mga.TOC
Molecular Imaging and Contrast Agent Database. Bethesda (MD): National Library of Medicine (US), NCBI; 2004-2005. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=micad.TOC
Nanotechnology for the Intelligence Community. 2005. http://www.nap.edu/openbook/0309096650/html/index.html
National Academies: Keck Futures Initiative. Designing Nanostructures at the Interface between Biomedical and Physical Systems: Conference Focus Group Summaries. 2005. http://www.nap.edu/openbook/0309096685/html/index.html
National Academies: Keck Futures Initiative. The Genomic Revolution -- Implications for Treatment and Control of Infectious Disease: Working Group Summaries. 2006. http://www.nap.edu/openbook/0309101093/html/index.html
Proceedings from the Workshop on Biomedical Materials at the Edge: Challenges in the Convergence of Technologies. 2006. http://www.nap.edu/openbook/030910209X/html/index.html
Reaping the Benefits of Genomic and Proteomic Research: Intellectual Property Rights, Innovation, and Public Health. 2006. Board on Science, Technology, and Economic Policy (STEP); Science, Technology, and Law (STL). http://www.nap.edu/openbook/0309100674/html/index.html
Regenerative Medicine (Sackler NAS Colloquium). PNAS September 30, 2003; 100 (Suppl. 1). http://www.pnas.org/content/vol100/suppl_1/
Sequence - Evolution - Function: Computational Approaches in Comparative Genomics. Koonin, Eugene V; Galperin, Michael Y. Norwell (MA): Kluwer Academic Publishers; c2003. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=sef.TOC&depth=1
Small Wonders, Endless Frontiers: A Review of the National Nanotechnology Initiative. 2002. http://www.nap.edu/openbook/0309084547/html/index.html
Utilization of genomic information for tropical disease drug and vaccine discovery. Report of a WHO/TDR Scientific Working Group, Geneva, 18-20 February 1998. http://www.who.int/tdr/publications/publications/genomic.htm
* WANT MORE?
Today's selections primarily highlight resources available free to the world via the Internet. There are many other excellent electronic books that are included in the collections of our libraries. To discover these, go into Mirlyn, click on "Command Language", then copy and paste in the following search string.
( WRD=( omics OR genomics OR proteomics OR nanotechnology ) ) and WTP=( CF | CE ) and WTP=BK
To discover additional free electronic books, try first browsing the collections available via the National Academies Press and the PubMed Bookshelf. Those include only peer-reviewed materials, usually of exceptional quality. It is also possible to search Google or WikiBooks to discover fulltext books online in various topics. Example searches are included below.
National Academies Press: http://www.nap.edu/
NCBI: PubMed: Bookshelf: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books&itool=toolbar
Google Books: Genomics: http://books.google.com/books?q=genomics&btnG=Search+Books&as_brr=1
Google Books: Proteomics: http://books.google.com/books?q=proteomics&btnG=Search+Books&as_brr=1
WikiBooks: Proteomics: http://en.wikibooks.org/wiki/Proteomics
WikiBooks: Proteomics and Drug Discovery: http://en.wikibooks.org/wiki/Proteomics/Proteomics_and_Drug_Discovery
Google Books: Nanotechnology: http://books.google.com/books?q=nanotechnology&btnG=Search+Books&as_brr=1
Wikibooks: Nanotechnology: http://en.wikibooks.org/wiki/Nanotechnology
Posted by pfa at 08:23 AM | Comments (1)
July 18, 2006
Periodontitis or Biofilms as a Source of Disease?
As a break from the Omics blog series, I'd like to just mention an interesting article recently released from the CDC.
O'Connor SM, Taylor CE, Hughes JM. Emerging infectious determinants of chronic diseases. Emerg Infect Dis 2006 Jul. http://www.cdc.gov/ncidod/EID/vol12no07/06-0037.htm
To my mind, this sounded like it really ought to mention some of the recent research in dentistry linking periodontal infections and heart disease. This article doesn't do that, but it does mention biofilms as being related to this line of research. More generally, it is a very interesting overview of research in many different areas of medicine linking various infectious agents with chronic diseases, including cancer. Worth a look.
Posted by pfa at 05:55 PM | Comments (0)
Other International Omics Resources (Omics Series, 7)
The resources for today were selected to illustrate the range of resources and activities happening around the globe. These may represent initiatives at the level of a single country, or collaborative efforts involving a region. Just as with the United States governmental resources, these sites often provide a range of information including both education for the general public and indepth detailed resources for researchers. Researcher resources begin with publications and presentations continuing on to databases and datasets. The resources are usually available in English, although sometimes they are provided in multiple languages.
* GENERAL / MULTIDISCIPLINARY
Australian Research Council Centre in Bioinformatics (ACB): http://bioinformatics.org.au/
Bioinformatics Canada: http://bioinformatics.ca/
Canadian Bioinformatics Help Desk: http://gchelpdesk.ualberta.ca/servers/servers.php
European Bioinformatics Institute: http://www.ebi.ac.uk/
Hong Kong Bioinformatics Centre: http://www.hkbic.bch.cuhk.edu.hk/
Hong Kong Bioinformatics Centre: Biotechnology Dictionary: http://www.hkbic.bch.cuhk.edu.hk/BioTechDict/
National Research Council Canada: Molecular Sciences: Steacie Institute for Molecular Sciences (NRC-SIMS): http://steacie.nrc-cnrc.gc.ca/
UK: York Structural Biology Laboratory: http://www.ysbl.york.ac.uk/
* GENOMICS
Australia: Human Genetics Advisory Commission: http://www.nhmrc.gov.au/about/committees/hgac/index.htm
Australian National Genomic Information Service (ANGIS): http://www.angis.org.au/
Canada's Michael Smith Genome Sciences Center: http://www.bcgsc.ca/
Canadian Genetic Disease Network (CGDN): http://www.cgdn.ca/
Canadian Genome Education Centre: Centre d'éducation sur le génome: http://www.genomeeducation.ca/
Centre for Integrated Genomics: http://www.cigenomics.bc.ca/
Chinese Academy of Sciences: Beijing Genomics Institute: http://www.genomics.org.cn/bgi/english/index.htm
European Science Foundation Programme: Functional Genomics: http://www.functionalgenomics.org.uk/
Genome Canada: http://www.genomecanada.ca/
Karolinska Institutet: Center for Genomics & Bioinformatics (CGB): http://www.cgb.ki.se/
Kyoto University: Institute for Chemical Research: Bioinformatics Center: GenomeNet: http://www.genome.jp/
Medical Research Council (MRC): Toxicology Unit: Microarray and Bioinformatics: http://www.le.ac.uk/mrctox/microarray_lab
Netherlands Genomics Initiative: http://www.genomics.nl/
Sanger Institute: Genomics and Genetics at the Sanger Institute: http://www.sanger.ac.uk/genetics/
UK Human Genetics Advisory Commission (HGC): http://www.hgc.gov.uk/
* PROTEOMICS
Australian Proteome Analysis Facility: http://www.proteome.org.au/
Canada: Protein Engineering Network of Centres of Excellence (PENCE): http://www.pence.ca/
INCLUDES:
PENCE: Proteomics Resources: Directory of Proteomics in Canada
Canadian Proteomics Initiative: http://cpicanada.org/
Ontario Centre for Structural Proteomics: http://www.uhnres.utoronto.ca/proteomics
SPINE, Structural Proteomics in Europe: http://www.spineurope.org/
* NANOTECHNOLOGY
Canada: EthicsWeb: Ethical Issues in Nanotechnology: http://www.ethicsweb.ca/nanotechnology/
European Union: Thematic Network: Nanoforum.org (European Nanotechnology Gateway): http://www.nanoforum.org/
Institute of Nanotechnology (IoN) (UK): http://www.nano.org.uk/
Japan: National Institute of Advanced Industrial Science and Technology: Nanotechnology Research Institute (NRI): http://unit.aist.go.jp/nanotech/
National Institute for Nanotechnology / Institut national de nanotechnologie: http://nint-innt.nrc-cnrc.gc.ca/home/index_e.html
National Research Council Canada: Nanotechnology: http://www.nrc-cnrc.gc.ca/randd/areas/nanotechnology_e.html
Royal Society / Royal Academy of Engineering: Nanotechnology and Nanoscience: http://www.nanotec.org.uk/
Posted by pfa at 02:59 PM | Comments (0)
July 17, 2006
Genomics and the World Health Organization (Omics Series, 6)
The World Health Organization is a non-governmental organization that is a rich resource for information in global and public health. In this role, it has made available a number of resources on genetics and genomics, particularly with respect to birth defects and genetically modified foods. Here are the two most significant collections of resources and activities relevant to Omics from the WHO.
World Health Organization (WHO): Human Genetics Programme: http://www.who.int/genomics/
Publications: http://www.who.int/genomics/publications/en/index.html
INCLUDES:
* Genetics, genomics and the patenting of DNA: Review of potential implications for health in developing countries (2005)
* Global registry and database on craniofacial anomalies (2003)
* World Atlas of Birth Defects (2003)
* Global Strategies to Reduce the Health Care Burden of Craniofacial Anomalies (2001)
World Health Organization (WHO): Genomic Resource Centre: http://www.who.int/genomics/anomalies/cfaproject/en/
INCLUDES:
"Ask the expert"
"Send your questions about genomics to members of a judiciously selected group of health professionals in genetics and related disciplines, who are committed to the development of genomics, public health systems and public engagement in the development of science and technology."
Here is a sampling of some of the additional resources they have made available in this area of enquiry.
Biotechnology (GM Foods): http://www.who.int/foodsafety/biotech/en/
Craniofacial Anomalies Directory of Resources: http://www.who.int/genomics/anomalies/cfadirectory/en/
INCLUDES: Patient support groups; Epidemiological and Genetic databases; Organizations & institutes; Articles.
Diagnostics for the Developing World [PDF: 236KB]:
http://www.who.int/std_diagnostics/publications/Diagnostics%20for%20the%20developing%20world.pdf
Executive course on genomics and public health policy: http://www.emro.who.int/rpc/pdf/GenomicsCourse-2003.pdf
Food Standards (Codex Alimentarius): http://www.who.int/foodsafety/codex/en/
International Collaborative Research on Craniofacial Anomalies: http://www.who.int/genomics/anomalies/en/
International Database on Craniofacial Anomalies (IDCFA): http://www.who.int/genomics/anomalies/idcfa/en/
Introduction to biotechnology: http://whqlibdoc.who.int/publications/2004/9241546506_partV.pdf
Public Health: Innovation and Intellectual Property Rights ... April 2006: http://www.who.int/intellectualproperty/en/
20 questions on genetically modified foods: http://www.who.int/foodsafety/publications/biotech/20questions/en/
Workshop on Application of Proteomics and Transcriptomics in EMF Research (30 October - 1 November 2005 / Helsinki, Finland): http://www.who.int/peh-emf/meetings/proteomics_helsinki05/en/
Posted by pfa at 09:50 AM | Comments (0)
July 14, 2006
National Governmental Omics Resources (Omics Series, 5)
As in so many other ways, the United States government has taken a leading role in providing information resources in leading edge topics, such as omics. There are a number of national initiatives and research centers that provide educational support, research resources, funding opportunities, technical information, and much more. This is a small sampling, including only the major sources in these topics from the US goverment.
* CROSS-DISCIPLINARY
Oak Ridge National Laboratory: Life Sciences Division: http://lsd.ornl.gov [See: Research Tools: http://lsd.ornl.gov/tools.html]
NIH: Roadmap for Medical Research: http://nihroadmap.nih.gov/
President's Council on Bioethics: http://www.bioethics.gov/
* GENOMICS
Argonne National Laboratory (ANL): Midwest Center for Structural Genomics: http://www.mcsg.anl.gov/
Brookhaven National Laboratory (BNL): Genome Group: http://www.genome.bnl.gov/
CDC: Genomics and Disease Prevention: http://www.cdc.gov/genomics/
DOE: Human Genome Project: Genomics Primers: Genomics and Its Impact on Science and Society: The Human Genome Project and Beyond (2003): http://www.ornl.gov/sci/techresources/Human_Genome/publicat/primer/index.shtml
DOE: Joint Genome Institute: http://www.jgi.doe.gov/
Lawrence Berkeley National Laboratory: Arkin Laboratory for Dynamical Genomics: http://genomics.lbl.gov/
Lawrence Livermore National Laboratory: Biosciences Directorate: Human Genome Center: http://bbrp.llnl.gov/genome/genome.html
Library of Congress: Selected Internet Resources: Molecular Biology and Bioinformatics: http://www.loc.gov/rr/scitech/selected-internet/molecular.html
National Human Genome Research Institute: http://www.genome.gov/
National Institute of Allergy and Infectious Diseases (NIAID): Pathogen Functional Genomics Resource Center (PFGRC): http://pfgrc.tigr.org/
NIH: Computational Molecular Biology: http://molbio.info.nih.gov/
NIH: NCBI: What Is a Genome: http://www.ncbi.nih.gov/About/primer/genetics_genome.html
NIH: NCI: The Genomics and Bioinformatics Group: http://discover.nci.nih.gov/
* PROTEOMICS
Argonne National Laboratory (ANL): Proteomics: http://gelbank.anl.gov/
FDA: National Center for Toxicological Research (NCTR): Center for Proteomics: http://www.fda.gov/nctr/science/centers/proteomics/index.htm
National Center for Research Resources (NCRR): Proteomics: Proteomics Research Resource for Integrative Biology at PNNL: http://ncrr.pnl.gov/
NIH: NCI: Clinical Proteomic Technologies for Cancer: http://proteomics.cancer.gov/
* NANOTECHNOLOGY
CDC: NIOSH Safety and Health Topic: Nanotechnology: http://www.cdc.gov/niosh/topics/nanotech/
FDA: Nanotechnology: http://www.fda.gov/nanotechnology/
Library of Congress: Nanotechnology: Science Tracer Bullets - Research Finding Aids from the Library of Congress, Science Reference Services: http://www.loc.gov/rr/scitech/tracer-bullets/nanotechnologytb.html
Library of Congress: Nanotechnology: Selected Internet Resources in Nanotechnology: http://www.loc.gov/rr/scitech/selected-internet/nanotechnology.html
NASA: Center for Nanotechnology: http://www.ipt.arc.nasa.gov/
National Nanotechnology Initiative: http://www.nano.gov/
NIH: NCI: Alliance for Nanotechnology in Cancer: http://nano.cancer.gov/
NIH: NCI: Nanotechnology Characterization Lab (NCL): http://ncl.cancer.gov/
NIST: Center for Nanoscale Science and Technology: http://cnst.nist.gov/
NSF: National Nanotechnology Initiative (NNI): http://www.nsf.gov/crssprgm/nano/
Sandia National Labs: Nanotechnology: http://nano.sandia.gov/
* WANT MORE?
Google: (omics OR genomics OR proteomics OR nanotechnology) site:.gov
Science.gov: Applied Science & Technologies: Nanotechnology: http://www.science.gov/browse/w_113P.htm
Posted by pfa at 01:51 PM | Comments (0)
July 13, 2006
Omics Institutes and Research Centers (Omics Series, 4)
Research centers and institutes are excellent sources not jsut of training but also cutting edge research, recent publications, innovative techniques, custom databases and software tools, and links to core resources. If you are trying to discover more about any of the omics areas or are seeking partners for collaboration, these are great resources. There are many research centers and institutes around the world in these areas, ranging from those embedded in educational or government organizations, independent organizations, and commercial research entities. The following list highlights a few of the leaders in all these areas. At the end of this entry there is a web search if you want to discover more like these.
* GENOMICS
Institute of Genomics and Integrative Biology: http://www.igib.res.in/
North Carolina Center for Genomics and Public Health: http://www.sph.unc.edu/nccgph/
Novartis Research Foundation: Genomics Institute: http://www.gnf.org/
Pennsylvania State University: Center for Nanotechnology Education and Utilization: http://www.cneu.psu.edu/
The Genomics and Bioinformatics Group: http://discover.nci.nih.gov/
The Genomics Institute: http://www.wadsworth.org/genomics/
The Institute for Genomic Research (TIGR): http://www.tigr.org/
University of Michigan Center for Genomics and Public Health: http://www.sph.umich.edu/genomics
University of Washington Center for Genomics and Public Health: http://depts.washington.edu/cgph
* PROTEOMICS
Harvard Institute of Proteomics: http://www.hip.harvard.edu/
Johns Hopkins: NHLBI Proteomics Center: http://www.proteomics.jhu.edu/
Yale: NHLBI Proteomics Center: http://info.med.yale.edu/nhlbi-proteomics/
* NANOTECHNOLOGY
Center for Responsible Nanotechnology: http://www.crnano.org/
Foresight Institute: Nanotechnology: http://www.foresight.org/
Institute for Nanotechnology: http://www.ctn.northwestern.edu/
Institute of Nanotechnology (UK): http://www.nano.org.uk/
NanoTechnology Institute: http://www.nanotechinstitute.org/
NASA: Center for Nanotechnology: http://www.ipt.arc.nasa.gov/
University of Wisconsin: Center for NanoTechnology (CNTech): http://www.nanotech.wisc.edu/
Washington University: The Center for Nanotechnology: http://www.nano.washington.edu/
* WANT MORE?
Google: (institute OR center) (genomics OR proteomics OR nanotechnology) -site:.com
Posted by pfa at 12:20 PM | Comments (0)
July 12, 2006
Omics Tutorials and Training (Omics Series, 3)
So, where can you go to learn more about Omics? There are a variety of both online tutorials for specific tasks, as well as training programs and "boot camp" tutorials that require registration and personal attendance. We'll start with local resources, and then go on to a sampling of online resources in the specific topics.
* MICHIGAN
- Hot off the press! Just announced today, you might want to register for the upcoming short course on information resources in bioinformatics and omics.
National Center for Biotechnology Information: Short Course, September 2006 (Hosted by the Program in Bioinformatics, Department of Human Genetics & Taubman Medical Library): http://www.hg.med.umich.edu/ncbi/
- Michigan (General)
Michigan Proteome Consortium: Training: http://www.proteomeconsortium.org/training.html
- University of Michigan
Center for Computational Medicine and Biology: http://www.ccmb.med.umich.edu/
Center for Proteomics Training (requires UM login): http://sitemaker.umich.edu/gannon
Michigan Nanotechnology Institute for Medicine and Biological Sciences: http://nano.med.umich.edu/
School of Public Health: Michigan Public Health Training Center: Six Weeks to Genomic Awareness: https://www.sph.umich.edu/iscr/mphtc/courses/one-online-course.cfm?id=108
- Michigan State University
MSU Proteomics: http://proteomics.msu.edu/
MSU Genomics: Research Technology Support Facility: http://genomics.msu.edu/
Nanoscale Interdisciplinary Research Team (NIRT): http://nirt.pa.msu.edu/
* OMICS (General)
Genetic Engineering News has an Omics skills-building tutorial article in almost every issue of the journal. Here are a few example of past tutorial articles, but you may want to browse the journal for more.
Genetic Engineering News: http://www.genengnews.com/
Tutorial: Omics: Next-Generation RNA Interference: http://www.genengnews.com/current/article.aspx?cat=Tutorial&id=1321
Tutorial: Omics: Assay: Parallel Approaches to Target Identification: http://www.genengnews.com/current/article.aspx?cat=Tutorial&id=1708
Tutorial: Omics: Barcoding and Automated Electophoresis: http://www.genengnews.com/current/article.aspx?cat=Tutorial&id=1769
* GENOMICS
Genomic Awareness: http://www.genomicawareness.org/
Genome Biology: Tutorials: http://genomebiology.com/tutorials/
Keck-UNM Genomics Resource: A Primer for Using Microarrays in Biomedical Applications: http://hsc.unm.edu/som/micro/Genomics/newbies.html
M.D. Anderson: Bioinformatics: Tutorials (microarrays): http://bioinformatics.mdanderson.org/tutorial.html
United States: CDC: Genomics: Training: Six Weeks To Genomics Awareness: http://www.cdc.gov/genomics/training/sixwks.htm
* PROTEOMICS
National Center for Research Resources: Proteomics: Training and Protocols: http://ncrr.pnl.gov/training/
Proteome Software: Tutorials on Proteomics For Scientists: http://www.proteomesoftware.com/Proteome_software_link_tutorials.html
Proteomics: 2D electrophoresis for proteomics tutorial / by James R. Jeffries: http://www.aber.ac.uk/~mpgwww/Proteome/Tut_2D.html
Proteomics: Protein identification (PMF) tutorial / by James R. Jeffries: http://www.aber.ac.uk/~mpgwww/Proteome/MS_Tut.html
Spot the Difference: Analysing Gel Images for Proteomics (Roland Wilson): http://www.dcs.warwick.ac.uk/~rgw/spot/index.html
* NANOTECHNOLOGY
Nanotechnology Characterization Lab (NCL): Education & Training: http://ncl.cancer.gov/working_education-training.asp
Nanotechnology Industries: Education and Career: http://www.nanoindustries.com/edu.html
National Nanotechnology Infrastructure Network (NNIN): Education Portal: Nanotechnology: http://www.nnin.org/nnin_edu.html
Pacific Nanotechnology: Atomic Force Microscopes - Tutorial Page: http://www.pacificnanotech.com/afm-tutorial.html
* WANT MORE?
Google Search: (training OR tutorial) (genomics OR proteomics OR nanotechnology) -site:.com
Posted by pfa at 03:48 PM | Comments (0)
July 11, 2006
General Resources about Genomics, Proteomics and Nanotechnology (Omics Series, 2)
Yesterday's blog focused on introductory resources describing a few core omics concepts. Today we are providing resources that are more technical, as well as a couple of sources that list the over 300 different types of "omics" research areas. Each section includes web resources, searches for more information and collections of general articles on these topics.
* OMICS
- Books (Dentistry Library)
Bioinformatics : a practical guide to the analysis of genes and proteins / edited by Andreas D. Baxevanis, B.F. Francis Ouellette. 2005. Dentistry - Books - In the Book Stacks | QH 324.2 .B5471 2005
The dictionary of gene technology : genomics, transcriptomics, proteomics / Günter Kahl. 2001. Dentistry - Reference - Main Floor | QH 506 .K3331 2001
Redei, G. P. Encyclopedic dictionary of genetics, genomics, and proteomics / George P. Rédei. 2003. Dentistry - Reference - Main Floor | QH 430 .R432 2003
- Terms, Citations, Searches
Argus Biotech: Current topics in biotechnology: X-omes & X-omics: http://www.argosbiotech.de/700/omics/Xomics.htm
Biodirectory: Omics: http://www.biodirectory.com/directory/Top/Omics_274.html
CiteULike: Tag: Omics: http://www.citeulike.org/tag/omics
Connotea: Tag: Omics: http://www.connotea.org/tag/omics
Google Scholar: Omics
- Resources
Nature: Omics Gateway: http://www.nature.com/omics/index.html
OmicsWorld: http://www.omicsworld.com/
Omics Wiki: http://omics.org/
* GENOMICS
- Books (Dentistry Library)
Brown, Stuart M. Essentials of medical genomics / Stuart M. Brown ; with contributions by John G. Hay and Harry Ostrer. 2003. Dentistry - Books - In the Book Stacks | RB 155 .B6741 2003
Human genome epidemiology : a scientific foundation for using genetic information to improve health and prevent disease / edited by Muin J. Khoury, Julian Little, Wylie Burke. 2004. Dentistry - Books - In the Book Stacks | RB 155.5 .H861 2004
Recombinant gene expression : reviews and protocols / edited by Paulina Balbás and Argelia Lorence. 2004. Dentistry - Books - In the Book Stacks | QH 443 .R361 2004
- Terms, Citations, Searches
Google Scholar: Genomics
Wikipedia: Genomics: http://en.wikipedia.org/wiki/Genomics
- Resources
PLoS Primer: Comparative Genomics: http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0000058
Functional Genome Analysis / by Dr Jörg Hoheisel: http://www.dkfz-heidelberg.de/funct_genome/index.html
Functional Genomics / by Y.F. Leung: http://ihome.cuhk.edu.hk/~b400559/
Functional Genomics Experiment (FuGE): http://fuge.sourceforge.net/
NOTE: "Functional genomics experiments present many challenges in data archiving, sharing and querying. As the size and complexity of data generated from such experiments grows, so does the requirement for standard data formats. To address these needs, the Functional Genomics Experiment [Object Model / Markup-Language] (FuGE-OM, FuGE-ML) has been created to facilitate the development of data standards."
Human Genome Project: http://www.doegenomes.org/
The Institute for Genomic Research (TIGR): http://www.tigr.org/
Translational Genomics Research Institute: http://www.tgen.org/
International Genomics Consortium: http://www.intgen.org/
* PROTEOMICS
- Books (Dentistry Library)
Protein arrays, biochips and proteomics : the next phase of genomic discovery / edited by Joanna S. Albala, Ian Humphery-Smith. 2003. Dentistry - Books - In the Book Stacks | QP 551 .P6957 2003
Proteomics of microorganisms : fundamental aspects and application / volume editors, M. Hecker, S. Müllner. 2003. Dentistry - Books - In the Book Stacks | TP 248.3 .P76 2003
Westermeier, Reiner. Proteomics in practice : a laboratory manual of proteome analysis / Reiner Westermeier, Tom Naven. 2002. Dentistry - Books - In the Book Stacks | QP 551 .W47 2002
- Terms, Citations, Searches
Google Scholar: Proteomics
Wikipedia: Proteomics: http://en.wikipedia.org/wiki/Proteomics
- Resources
ExPASy Proteomics Server: http://www.expasy.org/
Nature: Focus on Proteomics: http://www.nature.com/reviews/focus/proteomics/index.html
Protein Society: http://www.proteinsociety.org
PROWL - a resource for protein chemistry and mass spectrometry: http://prowl.rockefeller.edu/
Science: Functional Genomics Resources: Proteomics: http://www.sciencemag.org/feature/plus/sfg/resources/res_proteomics.dtl
* NANO
- Books (Dentistry Library)
Luo, Jiazhong. Inorganic-organic nanocomposites formed using porous ceramic particles. 1998. Dentistry - Books - In the Book Stacks | RK 655 .L86 1998a
Mann AB, Dickinson ME. "Nanomechanics, chemistry and structure at the enamel surface." IN: The teeth and their environment : physical, chemical and biochemical influences / volume editor, Ralph M. Duckworth. 2006. Dentistry - Books - In the Book Stacks | RK 305 .T441 2006
- Terms, Citations, Searches
Google Scholar: Nano
Wikipedia: Nanotechnology: http://en.wikipedia.org/wiki/Nanotechnology
- Resources
NanoWerk: Introduction to Nanomaterials: http://www.nanowerk.com/n_nanomaterials_1.html
NanotechWeb.org: http://nanotechweb.org/
INCLUDES: News, events, press releases, the journal Nanotechnology, opinions / editorials, features, jobs, "nano & society" article archive, resources and links
Ralph Merkle's Nanotechnology Homepage: http://www.zyvex.com/nano/
INCLUDES: articles, awards, FAQs, groups / organizations,
National Nanotechnology Initiative: http://www.nano.gov/
Nanotechnology Now: http://www.nanotech-now.com/
Nanotechnology - Foresight Institute: http://www.foresight.org/
Scientific American Magazine (April 2004): The First Nanochips
Posted by pfa at 12:53 PM | Comments (0)
July 10, 2006
Background Information about Omics (Omics Series, 1)
To start our series off, we'd like to some definitions and background information about Omics for people who are new to the topic. The resources listed below also include a number of glossaries and terminology tools that may be useful for researchers.
Glossaries
This first resource (from ColorBasePair) is a nice, relatively simple, one-page overview of just the primary concepts -- what are genomics, proteomics, and nanotechnology. A useful starting place.
ColorBasePair: What is Bioinformatics: Bioinformatics Definitions
http://www.colorbasepair.com/what_is_bioinformatics.html
Here are two glossaries from reputable sources, both moderately sized -- bigger than a loaf of bread and smaller than a building, to describe it colloquially.
Genomics & Proteomics Magazine: Glossary:
http://www.genpromag.com/Glossary.html
National Cancer Institute: Clinical Proteomic Technologies for Cancer: Glossary:
http://proteomics.cancer.gov/resource_room/glossary.asp
This next glossary is a motherlode of technical jargon and definitions, with over 5,000+ definitions compiled & edited by Mary Chitty, the head librarian for Cambridge Healthtech Institute. Truly a masterful and comprehensive resource, frequently updated, so always current and at the cutting edge. The place to go when you aren't sure about a new term.
Genomic Glossaries (BioPharmaceutical Glossary, Taxonomies and guide to 21st century therapeutics, technologies and trends):
http://www.genomicglossaries.com/
INCLUDES:
* Molecular Diagnostics & Molecular Medicine glossary:
http://www.genomicglossaries.com/CONTENT/clinical_genomics_email.asp
* Biology: Basic genetics & genomics: Basic biopharmaceutical genetics & genomics:
http://www.genomicglossaries.com/CONTENT/Basic_Genetic_Glossaries.asp
What is Genomics?
The following resources describe what genomics is for a variety of audiences, from children and the general public (NOVA and the DoE) to resources for a more advanced audience.
Canada: BioPortal: BioBasics: Genomics: http://biobasics.gc.ca/english/View.asp?x=738
Comparative Genomics Tutorial (Phillipe Gautier): http://rsat.scmbb.ulb.ac.be/rsat/Comparative_Genomics/tutorial/
United States: Department of Energy (DoE): Joint Genomics Institute: Education: http://www.jgi.doe.gov/education/index.html
Includes: An Introduction to Genomics; How Sequencing is Done; Historical Timeline
NOVA: Sequence for Yourself: http://www.pbs.org/wgbh/nova/genome/sequencer.html
What is Proteomics?
This group of resources about what is proteomics tends to focus on resources appropriate for persons and high school and older.
Annenberg/CPB: Rediscovering Biology: Unit 2, Proteins and Proteomics: What is Proteomics?:
http://www.learner.org/channel/courses/biology/textbook/proteo/proteo_1.html
Children's Hospital Boston: Introduction to Proteomics: http://www.childrenshospital.org/cfapps/research/data_admin/Site602/mainpageS602P0.html
INCLUDES:
Guide to Sequencing and Identifying Proteins:
http://www.childrenshospital.org/cfapps/research/data_admin/Site602/mainpageS602P0.html
The Basics: http://www.childrenshospital.org/cfapps/research/data_admin/Site602/mainpageS602P1.html
United States: National Cancer Institute: Explore Proteomic Technologies and Cancer:
http://proteomics.cancer.gov/resource_room/animation.asp
What is Nanotechnology?
NanoWord: Introduction to Nanotechnology / by Steve Lenhert, Quanteq, LLC:
http://www.nanoword.net/pages/intro.htm
INCLUDES: A Brief History of Nanotechnology
MITRE: Introduction to Nanotechnology and Nanocomputers (Tutorial):
http://www.mitre.org/tech/nanotech/intronano.html
Nanotechnology Now: Nanotechnology Introduction:
http://www.nanotech-now.com/introduction.htm
Harper, Tim. What is Nanotechnology? (Institute of Physics)
2003 Nanotechnology 14: http://www.iop.org/EJ/abstract/0957-4484/14/1/001
Institute of Nanotechnology (UK): Glossary: http://www.nano.org.uk/nano/glossary.htm
Want More?
Want to know more or explore on your own? Here are some web searches to find materials similar to those above.
Google (for web pages only): (genomics proteomics (nanotech OR ~nanotechnology)) ("what is" OR definitions OR glossary OR dictionary)
a9 (finds books and more, in addition to web pages): (genomics proteomics nanotechnology) (definitions OR glossary OR dictionary)
Posted by pfa at 01:58 PM | Comments (1)
Introducing our Omics Blog Series
This time of year, new graduate students are flooding into the School and faculty are intensely working on their research projects while the teaching course load is somewhat lighter than during September through May.
While there are a variety of research areas and interests, the University of Michigan and the School of Dentistry have a committed interest in the research areas that have come to be known popularly as "Omics" (genomics, proteomics, nanotechnology, and related bioinformatics concepts).
In the interests of providing useful information for those working in these areas and those who would like to know more about what their colleagues might be doing, the Dentistry Library today begins a roughly two week series of blog entries on OMICS.
The entire collection of entries will be collected at this location, with more added periodically in the future:
http://mblog.lib.umich.edu/dentlib/archives/resources/research/omics/index.html
Posted by pfa at 01:40 PM | Comments (1)
July 06, 2006
Dentistry @ Nature
dentistry@nature.com: http://www.nature.com/dentistry/index.html
If you haven't seen this section of the Nature web site, it might interest you. Nature uses these topical sections to gather journals, articles, and resources of interest all in one place. Of course, this is only the journals / articles / resources that they make available, but it is still worth checking out every once in a while. For resources, it includes job, events, and a searchable buyer's guide. Resources and positions listed focus on those of interest to the dental life-science researcher.
Posted by pfa at 04:03 PM | Comments (0)
New Articles from UM SoD Faculty: July 06, part 1
Hsiong SX. Mooney DJ.
Regeneration of vascularized bone.
Periodontology 2000. 41:109-22, 2006.
PMID: 16686929
Lee YL. Liu J. Clarkson BH. Lin CP. Godovikova V. Ritchie HH.
Dentin-pulp complex responses to carious lesions.
Caries Research. 40(3):256-64, 2006.
PMID: 16707876
Sisk EA. Kim TB. Schumacher R. Dechert R. Driver L. Ramsey AM. Lesperance MM.
Tracheotomy in very low birth weight neonates: indications and outcomes.
Laryngoscope. 116(6):928-33, 2006 Jun.
PMID: 16735883
Thomas JE. Straffon L. Inglehart MR.
Child abuse and neglect: dental and dental hygiene students' educational experiences and knowledge.
Journal of Dental Education. 70(5):558-65, 2006 May.
PMID: 16687641
Wang L. Zhang ZG. Zhang RL. Gregg SR. Hozeska-Solgot A. LeTourneau Y. Wang Y. Chopp M.
Matrix metalloproteinase 2 (MMP2) and MMP9 secreted by erythropoietin-activated endothelial cells promote neural progenitor cell migration.
Journal of Neuroscience. 26(22):5996-6003, 2006 May 31.
PMID: 16738242
Posted by pfa at 10:54 AM | Comments (0)
July 03, 2006
What's Hot from the IADR (Our 100th Blog Entry)
As things wind down from the IADR meeting in Brisbane, what are the hot topics that were presented at IADR and receiving attention in the popular press? Cranberries and dentin. That's two ideas, not one.
* Cranberries
Cranberries are receiving renewed attention as a way to prevent caries. The mechanism is similar to the way cranberry juice is known to prevent and cure urinary tract infections -- preventing the bacteria from adhering to the cell surfaces. For dentistry, the idea is that cranberry juice helps to prevent S. mutans from adhering to the teeth, and thus prevents the build up of plaque.
IADR: Berry Good News for Tooth Decay Prevention, by Neil Osterweil:
http://www.medpagetoday.com/PrimaryCare/DietNutrition/tb/3647
Koo, Hyun et al. "Cranberry flavonoids on expression of virulence by S. mutans." IADR Abstract 179, presented June 28, 2006 (Brisbane).
* Dentin
Dentin is making news with the popular concept that people can grow new bone. In this case, not only new bone in general, but specifically new dentin. "The data demonstrated that AC-100 stimulated the formation of new dentin (the hard tissue of teeth that protects the tooth pulp and supports the outer enamel) when applied to tooth defects."
Acologix' AC-100 (Dentonin(R)) Phase II Data on Dentin Formation in Humans Presented at the Annual Meeting of the International Association for Dental Research: http://biz.yahoo.com/prnews/060629/sfth064.html?.v=56
Lazarov, Mirella et al. "AC-100, Novel Biological Approach to Promoting Dentin Formations in Humans." IADR Abstract 545, presented June 29, 2006 (Brisbane).
Lazarov, Mirella et al. "AC-100, A Novel Biological Agent for Dentin and Bone Regeneration." IADR Abstract 268, presented June 28, 2006 (Brisbane).
Posted by pfa at 02:59 PM | Comments (0)