Biochemistry Hot Sheet: hotlinks

[trouble]

I'll start a list of great web sites that you can visit to learn a little more on the biochemistry I mention in my posts here.

Cellular Energetics 101: the full nelson

See: this site (http://employees.csbsju.edu/hjakubowski/classes/ch331/oxphos/olcouplingoxphos.html) for information on ATP and coupled phospphorylation (to aerobic and anerobic respiration) plus the good shit on mito electron transport chain (ETC) - cool graphics!


Biochemical Pathways Database Sites:

http://www.expasy.org/sitemap.htm (follow the biochemical pathways box, lower right)

Another pathways website:

http://www.genome.ad.jp/kegg/pathway.html

And still another:

Reactome, of course: http://www.reactome.org

Steroid Hormone Pathways:

http://web.indstate.edu/thcme/mwking/steroid-hormones.html

Cholesterol Lipids and Lipoproteins:

http://adam.about.com/reports/000023_3.htm

http://www.med.unibs.it/~marchesi/cholest.html


Periodic Chart of the Elements: http://www.dayah.com/periodic/

[trouble]

A great read, a 3-part introduction (http://www.greensfirst.com/PhysiologicalFunctionsofPhytonutrients.pdf) to phyto-nutrient supplements.

Yet another database that is quickly searchable that lists all effects and side effects of Phytochemical and Ethnobotanical herbs and supplements...

http://www.ars-grin.gov/duke/

[trouble]

See this website (http://lpi.oregonstate.edu/infocenter/glossary.html) for an excellent alphabetical list of technical terms and their meaning.

Biomedical dictionary: http://treasuresoftheinternet.org/dictionary/intro/dictionary_frame.shtml


A list of science terminology glossaries (2 pages):
http://www.glossarist.com/glossaries/science/


A real hand-dandy biomedical term hypertext glossary:
http://www.vivo.colostate.edu/hbooks/glossary.html

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(I will find and add others to this list)

[trouble]

First, you make yourself an idiot list - a "to learn" list.

What are the primary organ and physiological systems of concern?

Make and keep a keyword list as you browse the threads here.

Get thee to a library and look for intro texts.

The next step is, yes, to use search engines and the internet to find more advanced material on these topics. In your search, you need to think about the search terms to be employed.

For instance, I used "muscle" and "how it works" to recover a variety of pages, from FASEB (Fed Am Soc for Experimental Biol):

http://www.faseb.org/opa/mh/muscle.html

Of course, Wikipedia came up, and a more in-depth presentation within the first dozen listings:

www.holycross.edu/departments/biology/kprestwi/exphys/lecture/ExPhysEx1Lect_pdf/ExPhys_03_L04_SkMusAnat.pdf

What you discover is that one page opens the doors to understand one aspect and leads you to seek more doors (sites) for others.

Muscles must interface with the nervous system. which leads to other searchs, or if you're lucky, links are supplied that lead you to concise explanations (with graphics, hopefully).

I've used both, a text (perhaps a critical review article leads me into topical waters that require more fundamental knowledge...particularly for terms and abbreviation...so I go looking for recommendations for texts on the web, then do an interlibrary loadn request for the book if they don't have it (thru public or university libraries)...and as I'm reading thru that book, other subjects come up for which I look for spot filler info - again, I resort to a web search, sometimes for yet another review article (I can't stress the importance of these current critical review articles enough, virtually every major and most minor subject areas have them, and larger regional libraries will have digital access rights that they provide to the public on a limited basis).

Which brings me to the fundamental layer of searching...that of OTHER databases beyond Pub Med which should be part and parcel of your standard search repretoire for print sources.

This is where you will probably have to resort to using the regional U library system to access the print form of many journals, as these journals often require a paid subscription for online access to the full text - that is, if the U doesn't own an limited access download right. You may have to pay a minimal cost for access, or it may be free - depends on the Regional U system and how its hardwired to grant funds to pay for subscirpt access to journals they don't carry in paper, or if they have jettisoned paper and gone totally electronic, the payment system employed to allow library patrons access to these electronic text formats.

I stress here that an abstract is a thumbnail sketch, at best, of the salient points within a paper. Its not meant to provide stand alone comprehension of the points made, its just an abbreviated statement of findings. Whether working online or at a library, you will want to chug thru the full paper when possible.

So I typed in "online science publication databases" to bring up examples of various science databases available here and in Europe:

and came back with a plethora of hits.

A good one:

http://library.ust.hk/info/databases/Science/

is a complendium of online databases.

A few that you will want to take a look at:

First Search

Science Citation Index

JSTOR

Journal Citation Reports

NIST gateway (govt pubs)

ProQuest

Scopus

There are similar gateway listing to be found here in the US - this just happened to be a nice one to make my point. This is the start of indepth search technqiues for specific journal articles on a topic.

There is a science behind database searches. The database search engine usually has a short article on methods to use to perform open and advanced searches - read it.

PubMed (ttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi) is just one version of many science citation databases out there. Pub Pub Central is the repository of free online full-text articles; some journals offer them separately at their website (free of charge), the pubmed abstract page usually indicates that these articles are available via the journal link at the top left corner of the publication abstract page.

Stanford U also has free on line full text publications in a searchable database:

http://highwire.stanford.edu/lists/freeart.dtl

See also:

http://www.sciencekomm.at/advice/full-text.html

and http://www.scirus.com/

http://www.mala.bc.ca/~mcneil/freeresearch.htm --> Free Research Resources

InfoMine. "INFOMINE is a virtual library of Internet resources relevant to faculty, students, and research staff at the university level. It contains useful Internet resources such as databases, electronic journals, electronic books, bulletin boards, mailing lists, online library card catalogs, articles, directories of researchers, and many other types of information.

INFOMINE is librarian built. Librarians from the University of California, Wake Forest University, California State University, the University of Detroit - Mercy, and other universities and colleges have contributed to building INFOMINE.

http://infomine.ucr.edu



That should get your started in online searching.

[trouble]

Assuming that your ultimate goal is to simply gain a foundational understanding of the brain and body, find and read this book. Its called:

"Job's Body" - its a 'Handbook for Bodyworkers' meaning an anatomy book for massage therapists and the like. Its tailor made for people without the depth and detail of say dr's and nurses or kinesiologists/physical therapists. Introduces some jargon and has detailed illustrations.


Another excellent little primer, this one on TCA (Krebs) Cycle and its intermediate steps, which produce our very necessary fatty acids for energy in muscle and other tissues. See this article (http://www.vitamin-resource.com/health/detail.cfm?id=341) for an easy to understand description and clues as to which supplements you may need to add to your diet if energy is flagging during the day, or during periods of exertion.

[trouble]

The hiarchy of publications goes like this:

Annual review articles (creme de la creme authors review recent papers on hot topics)

Top general journal articles (Nature, Science, Cell, and others)

Top Tier Specialty journal articles (Journal Biological Chemistry, J Molecular Biology, Biochemical Journal, etc.)

Second Tier Specialty journal articles

Rapid communications journals (BBA, BBRC, etc) - quick turnround on publications - 2-3 months, versus as long as 2 yrs wait list at the top tier publications.

Newer journals and shit journals (laughting) - not exactly low reputation, just a place to park papers that aren't top notch

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I'll quote Par Deus on an excellent observation he made on Pubmed, review articles and learning science, years ago:

"Review articles are best for giving a broad understanding of things, as far as papers go. But, you need more basic information before you start reading technical papers.

I would skim texbooks of subject matter you want to learn and read the stuff that you are particularly interested in. Then read it again and highlight important things. Then read through your highlighted material a few times.

Pubmed has lots of free e-textbooks.

After that, I would add reading fairly scientific articles (but still for a lay audience) with my new understanding, then go back through your textbooks and brush up on the stuff that you still didn't get.

At that point, you have a basic understanding, and you can start to read abstracts and full paper reviews on topics you read in articles or see on the boards.

At that point, you should be able to understand almost all articles and posts here, and you can go through pubmed on the subjects of interest and you should be able to have a pretty good idea from an abstract if an article might be a good one to read for further understanding. And, that would be when you would want to introduce non-review full papers."



PD is self taught; I worked in labs before I ever had opportunity to take higher level courses. At that time, the internet was in its infancy (back in the 70s), and there was no on-line searching for topical literature - literature searching was all conducted by hand, in vast bound compendiums, published monthly in a softback form and half yearly in hardcover, in tiny type, by alphabetical list for the biomedical lit. Chemical and physics lit had to be covered as well.

Bottom line is that most of my knowledge was acquired out of classroom, through reading textbooks and reference material, on my own dime and time.

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If you only have access to abstracts (ie, PubMed), here's another tip for finding full-length papers online.

Take the following, for example:

Thompson, J.L., Butterfield, G.E., Gylfadottir, U.K., Yesavage, J., Marcus, R., Hintz, R.L., Pearman, A., & Hoffman, A.R. (1998). Effects of human growth hormone, insulin-like growth factor I, and diet and exercise on body composition of obese postmenopausal women. Journal of Clinical Endocrinology and Metabolism, 83(5), 1477-84.

Go straight to Yahoo or Google and search for a part of the exact title. In this case, search for something like "diet and exercise on body composition of obese postmenopausal women". You'll end up finding either the full-text, or someone else's article referencing it. Either way, you're a step further than you'd be with just an abstract.

Sometimes, its the only way you can get access to a publication you really need to review, and can't access it through pubmed.

[trouble]

Another friend of mine at another forum forum wrote (on the subject of searching for technical informaton on line):

I second the idea for textbooks, at least basic ones, E textbooks on pubmed would be a good place after you get at least somewhat of a foundation. I agree with trouble's advice on how to search the net. I think that your foundation is most likely going to come from online, as there's lot of good basic info that can be found if you're willing to sort through the shit that's out there. I know it can be frustrating as I would guess that ratio of legit:shit has to be at best 1:10.

For example when I started out on my journey, my list included stuff as simple as

hypertrophy
creatine
actin + myosin
anatomy of a muscle
physiology of muscle contraction
ATP
etc.

A pretty simple list, all things considered, although I had taken intro to bio at this point so I had the background to already know some things at a very remedial level. THis is IMHO by far the most effective way to continue learning throughout your whole life, updating and going through and reupdating this list as necessary as we always have a stupid list, whether or not we want to admit it.

With that said, I personally belive that the ability of some people to understand textbooks is highly undrestated. I feel that if you really want to get it, you probably will, you just have to want it enough. So I feel that if you go through textbooks, you will take away from it what you want to. I think you should combine basic web searching with textbook reading. Searching to help you with whatever issues come up and textbooks to help give you direction as to where you want your search for knowledge to take you. In short, dont necessarily be afraid of textbooks cause you dont think you have knowledge for them."

Burton is no dummy; he's made plenty of insightful, seat-of-the-pants / anecdotal observations on phenomenom common to strength training that has been dead on target. Whats nice, is that its become common for textbook publishers to include whiz bang graphics to help visually reinforce explanatory language.

For me, that's heavenly. I think in terms of cartoons, and I when I taught, I drew figures, graphs, diagrams and schematics of concepts constantly, because it was often the easiest way to clarify material when jargon got in the way of understanding.
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[trouble]

1. Died and gone to seach heaven:

http://biobar.mozdev.org/

Biobar - A Mozilla toolbar for browsing biological data and databases.

The biobar project is a bioinformatics power-browsing toolbar for Mozilla-based browsers including Firefox and Netscape 7+. This toolbar provides access to all major biological data resources. The primary advantage of this tool is that it allows a biologist to browse and retrieve data from Genomic, Proteomic, Functional, Literature, Taxonomic, Structural, Plant and Animal-specific databases. In addition to the browsing features, biobar also provides links to important bioinformatics sites and services including services at the European Bioinformatics Institute (EBI), National Center for Biotechnology Information (NCBI) and DNA Data Bank of Japan (DDBJ). The tool also provides links to major data deposition sites for nucleotide, protein and 3D-structure data. Finally, the menu also contains links to many Sequence, Structure alignment and analysis tools.

The latest release (Version 1.4) of biobar provides browsing access to over 46 different databases (http://biobar.mozdev.org/Databases.html) (including Google Scholar, HubMed, SCIRUS etc).

2. The Hardcore Stuff.

The American Chemical society Molecular / Chemical / Pharmaceutical journals: http://pubs.acs.org/hotartcl/index.html


3. The Medical Hotstuff.

The premier medical journals are JAMA and NEJM (J Am Medical Assoc and New England Journal of Medicien, respectively).

The New England Journal of Medicine also allows free access to the full-text of their articles that are 6 months or older. http://content.nejm.org/

JAMA articles can't be accessed without registration; certain sections of the journal are available free after 6 months, via HireWire Press (http://highwire.stanford.edu/lists/freeart.dtl).

You can also use http://www.freemedicaljournals.com/#fmj as an alternative source for online full text article access.

From Emory University: MedWeb

http://www.medweb.emory.edu/MedWeb/history.htm -- info about medweb

http://www.medweb.emory.edu/MedWeb/ --- medical research web
resource

The creme de la creme of medical information: Martindale Center Health Science Guide: here (http://www.martindalecenter.com/HSGuide.html)

Humanum website. "HUMANUM is a research oriented web site maintained by the Research Centre for Humanities Computing of the Research Institute for the Humanities (RIH), Faculty of Arts, The Chinese University of Hong Kong. Our task is twofold: namely, 1) meta-indicing humanities resources worldwide, and 2) develop texts, tools and pages covering various interests in the humanistic scholarship." http://www.arts.cuhk.edu.hk/MedH.html --> Medical and Health



4. Sports / Training Educational citations:

Http://www.sportsci.org has some decent stuff on nutrtion and some really good stuff on training.

ajpendo.physiology.org

www.sciencedirect.com

www.ajcn.org

ajp.psychiatryonline.org

ajpcell.physiology.org

www.ajrcmb.org

journal.ajsm.org

ajpheart.physiology.org

www.nursingworld.org/ajn/

ajprenal.physiology.org

ajpgi.physiology.org/

ajpregu.physiology.org/

ajplung.physiology.org/

www.amjmed.org

ajpcon.physiology.org

www.jphysiol.org

www.jgp.org
jap.physiology.org

link.springer-ny.com/link/service/journals/00359/

journal.ajsm.org/


Now, it pays to visit and get to know your local University library. Many offer free on line searching via subscription search services. You need to know their internet addy and to become familiar with the library search engines. Once you mastered it, you can log in from home and conduct fairly in depth searches via these public University library access gateways.

[trouble]

A good idiot guide to the endocrine system, which I talk about quite a bit here.

http://www.vivo.colostate.edu/hbooks/pathphys/endocrine/index.html

[trouble]

Biology (see also links on same page for chemistry, physics and math):

http://www.rusd.k12.ca.us/4teachers/science/biology.html

(no, this is not a nightmare, you really do have use for this information)

[~David~]

DAMN! this thread is a Diamond mine!

I know it looks silly bumping a sticky but this is a great resource for those interested in teaching themselves anything!

[RollinsClone]

Wow. just wow. She has laid out an easy to follow plan to go from whatever level of understanding you have now about the human body and how the pathways work, to a very in depth appreciation of it all. Seriously just wow, i can't believe the time and effort that went into making this.

[mikethedon]

I think you need to pay my divorce payments.....because of the neglect my wife is going to get lol jk

Thanks for the info

[mikethedon]

So im pretty much way to stupid to read anything from any of those sites.....good for the self esteem

[RollinsClone]

^^ read all of her posts, and then go back and start looking at the sites, she breaks down how you CAN understand all of the sites. It will take alot of time, but once your done, god damn will you be glad you did, for you will understand things on a whole different level

[KIDD]

Harper's Boiochemistry is a staple in my library.