Molecular Biology (X107A)

Internet resources

This page was originally developed to provide supplementary materials for an upper division college level course in molecular biology, mainly for the first semester. Links to the home page for that course, to the home page for this site, and contact information are in the navigation bar at the top of this page; they are also at bottom of page.

Much of this page is organized by chapter from the textbook, by Weaver, listed in full in the Syllabus information, below.

The contents of this page overlap with some of my other pages, so I encourage you to also look at:
* BITN. BITN = Biotechnology in the News, a course for the general public, so many of the resources listed there are introductory. Also look around other BITN pages.
* Internet resources: Organic and Biochemistry, especially the Metabolism section.
* Internet resources: Biology - Miscellaneous, especially the Microbiology sections.
* Internet resources: Chemistry - Miscellaneous, especially the Biochemistry and Lab tools sections.

All my pages of Internet resources are available from the List of pages of Internet resources.

Please let me know of items listed here which are no longer appropriate, or of new items you think are particularly good.
 
Items organized by original course handouts:
Syllabus
Chapter 1
Genetics, Cells
(German, Italian, Spanish)
Chapter 2
DNA
Chapter 3
Protein structure
Chapters 4-5
Methods
(Chinese, Danish, French, Icelandic, Italian, Portuguese, Spanish)
Chapter 6
Transcription
Chapters 10-13
Transcription - eukaryotes
Chapters 14-16
Post-transcriptional events
Chapters 17-19
Protein synthesis
(Many languages)
Chapters 20-21
DNA replication
Chapter 22
Recombination

Topic-oriented sections: (Sites that are not listed in handouts, above.)
RNA: folding, technologies.
Bioinformatics, genome analysis: software and help using it, tutorials
Sites that focus on specific organisms (or groups)
Molecular biology gateway sites. (Japanese)
Gene chips (microarrays)
Genomes
Miscellaneous (including methods)

Bottom of page; return links and contact information

Links to external sites will open in a new window.
I do appreciate receiving comments if anyone finds an improper link, and I will try to fix it. See contact information at the bottom of the page.

Disclaimer. Links to commercial sites are for information only. Neither the instructor nor the school endorses any particular company or product. Molecular biology suppliers have long been great sources of technical information, in their printed materials. This now extends to web sites.


Syllabus

Textbook: R F Weaver, Molecular Biology, 2/e, 2002, WCB/McGraw-Hill. ISBN 0072345179. Course materials posted here are for this edition. Newer editions: 3/e, 2005, is ISBN 0072846119. 4/e, 2008, is ISBN 9780073319940. 5/e, 2012, is ISBN 9780073525327.

There is a web site for this book. with web links and various other materials (which vary with the edition). The web sites listed here for the earlier editions are still available and may still be useful. Starting with the 3rd edition, the link below is to the "Information Center" for the book; you will most likely want to try the "Student Center" or such (top or left menus).

5/e: http://highered.mheducation.com/sites/0073525324/information_center_view0/index.html.
4/e: http://highered.mheducation.com/sites/0072995246/information_center_view0/index.html.
3/e: http://highered.mheducation.com/sites/0072846119/information_center_view0/index.html
2/e: http://www.mhhe.com/biosci/cellmicro/weaver2/
1/e: http://www.mhhe.com/biosci/cellmicro/weavermolbio/

"Recommended": D P Clark & L D Russell, Molecular Biology made simple and fun, 2/e. Cache River Press, 2000. ISBN 1889899046. This book is intended for both a general audience and a wide range of science students. It presents the basics of molecular biology in a way that is readable and fun, yet scientifically quite sound. It may be helpful as an introduction for some students. Others will just find it fun. (Caution: You cannot use it to replace Weaver.) This book is also listed on my page of Books: Suggestions for general science reading -- Clark & Russell, 2000. 3rd edition, 2005: ISBN 1-889899-07-0. 4th edition, 2010: ISBN 978-1889899091.


Supplementary books

G M Cooper & R E Hausman, The Cell - A Molecular Approach. 7/e, 2016. ISBN 978-1-60535-290-9 (and others, depending on options). Web site, with links keyed to the chapters: http://sites.sinauer.com/cooper7e/. Some web site features require registration. New edition, February 18, 2016.

PubMed Bookshelf. http://www.ncbi.nlm.nih.gov/sites/entrez?db=Books. Searchable full text versions of some textbooks in the biomedical sciences. Books include the Alberts et al and Lodish et al textbooks in molecular and cell biology, and the Cooper cell biology book. Other books of possible relevance there include the Stryer (Berg et al) biochemistry book and the Griffiths et al genetics book. This is from the National Center for Biotechnology, and is part of the PubMed (Medline) system. More books are being added. Editions may not be the most current, but are good. (If you are already at the PubMed site, choose Books.)

J E Krebs et al, Lewin's Genes XI. Jones & Bartlett, 2014. ISBN 9781449659851. A web site for Genes IX remains, with supplemental materials, including animations: http://biology.jbpub.com/book/genes/index.cfm.

F C Neidhardt et al (ed.), Escherichia coli and Salmonella -- Cellular and Molecular Biology. 2/e, 1996. ISBN 1-55581-084-5. CD-ROM version, 1999; ISBN 1-55581-164-7C. This is now maintained as a web resource, called EcoSal Plus: http://www.asmscience.org/content/journal/ecosalplus. UC Berkeley provides subscription access.

The list here is for Internet resources. A more complete list of supplementary books is in the Syllabus.


Chapter handouts

PubMed and Entrez are available, without charge, on the Internet. See the Library Matters page.

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Chapter 1 (Genetics, Cells)

All links listed in class handouts are available as live links at my web site. This page. In addition to the links that are listed by handout, the bottom of the page contains links to sites that focus on a specific organism or specific topic, plus several "miscellaneous" sites.

For information about using the UC Libraries, including the electronic resources, see the Library Matters page at the web site. That page also includes information about doing searches of the scientific literature (using, for example, PubMed), to find articles on a topic that interests you. Major topic areas there include: UC Berkeley library; electronic journals; journal articles; PubMed searches; citation searches.

Dr Jeff Bell at Chico State has posted many materials for his Genetics class. You may find some of these helpful. http://www.csuchico.edu/~jbell/Biol207/. From that page, look at the Lecture syllabus, for topics such as Mendelian Genetics, and at some of the Shockwave animations, such as Independent Assortment. (If you explore his site further, note that some parts require registration, or may be off-limits. For example, you will not be able to get to the Virtual Fly lab experiments. But start with the parts I mention above, then proceed further at your own risk.)

Classic papers in genetics [350 BC (Aristotle) to 1965]: http://www.esp.org/. Scroll down to "Classical genetics". There are also some books, including complete copies of some of Darwin's books (among others). (This site is also listed under Internet - Miscellaneous - Books as a source of free books, and on my Classic papers page.)

MendelWeb focuses on Mendel's original paper (German and English versions available), with extensive related resources. Includes a glossary, homework problems, and a place for your comments. http://www.mendelweb.org/. (This site is also listed on my Classic papers page.)

The Complete Work of Charles Darwin Online. http://darwin-online.org.uk/. From Cambridge Univ.

"Charles Darwin's Library is a digital edition and virtual reconstruction of the surviving books owned by Charles Darwin. ... It also provides full transcriptions of his annotations and marks. In this first release (2011) we provide 330 of the 1480 titles in his library, concentrating on the most heavily annotated books." http://www.biodiversitylibrary.org/collection/darwinlibrary. From the Biodiversity Heritage Library.

Both of the Darwin sites listed here are also listed on my Classic papers page.

Cells Alive! is a collection of beautiful pictures -- micrographs and models -- about diverse aspects of cells. Brief useful explanations accompany the pictures. Of immediate relevance: the section on Cell Models (from menu bar, at left), which discusses prokaryotic vs eukaryotic cells; the section on How Big? (from main Table of Contents, in center), which gives a sense of scale. http://www.cellsalive.com.

Inside the Cell is an introductory presentation about cells, from NIGMS. The level is rather low, but it is well written and interesting. It includes good pictures, and a good historical overview. Although the depth is weak, the breadth is extensive. It starts with some basics about cell structure, but goes on to introduce a very wide range of cell and molecular biology issues. Worth a browse, especially if you want something "light" -- and might be a good site to recommend to a young student. http://publications.nigms.nih.gov/insidethecell/.

The following site is fairly new, but promises to be a quite comprehensive site on the cell nucleus. Already it includes some good animations of cell division processes, and the goal is to develop a complete course in cell nucleus issues. From M Hendzel, Univ of Alberta. http://www.cellnucleus.com.

N R Pace, The molecular tree of life changes how we see, teach microbial diversity. Microbe 3:15, 1/08. For several decades, biologists have been presenting prokaryotic vs eukaryotic cells as one of the most fundamental distinctions in biology. Pace argues that this is out of date, based on our best current understanding of the tree of life. The key distinction is between the three domains: Bacteria, Archaea, and Eukarya. That the first two of these typically lack a membrane around the nucleus is less important -- and is actually misleading. A stimulating and provocative article! Microbe, the news magazine of the American Society for Microbiology, is free online; this item is at: http://microbemagazine.org/index.php?option=com_content&view=article&id=1761:the-molecular-tree-of-life-changes-how-we-see-teach-microbial-diversity&catid=436&Itemid=574.

Kimball's Biology Pages. An excellent biology glossary, plus lots of information. It is maintained by Dr John Kimball, the biology textbook author recently retired from Harvard. In fact, the site is almost an online textbook in biology. http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/. This site, and other such resources, are listed on my page of Internet resources: Biology - Miscellaneous under Biology: books and glossaries.


Homework question #7.

I will provide occasional questions that ask you to use a resource on the Internet. The sites I suggest will usually contain many resources; I encourage you to browse. The idea is to introduce you to some of the resources. (I do not plan to discuss these in class. Feel free to ask me about them privately.)

The Biology Project at the University of Arizona maintains a web site that covers a broad range of biological topics. For each topic, practice questions, with good feedback, and tutorials are available. As a start, go to
http://www.biology.arizona.edu/
and choose Mendelian Genetics, for some Ch 1 practice. But also look through the list of topics, for future reference. This site is also available in Italian, Spanish.

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Chapter 2 (DNA)

RasMol is a program for viewing 3-dimensional molecular structures on your own computer. It was originally written for viewing protein structures, but now thousands of files for RasMol are available -- of proteins, nucleic acids, and small organic chemicals. You can even make your own files for RasMol.

I have a page at my web site, "RasMol - An Introductory Guide". This page will help you get RasMol and get started using it, with both small molecules and proteins. It includes some good sources of files to view. And it includes a section on how to make your own files for RasMol -- using free software (only practical for small molecules, but it is fun to do).

Also, my page Writing, drawing and viewing chemical formulas has links to related programs ands sources of files to view.

I encourage you to get RasMol, and get started with it, as we do Ch 2-3. You will find it useful from time to time throughout the course. Please let me know of any problems. Also, please let me know of structures that you find are helpful; I will share your suggestions with the class.


Profiles in Science, at the National Library of Medicine, featuring the papers of great 20th century scientists. https://profiles.nlm.nih.gov/. The first scientist who was featured here is relevant to this Ch, Oswald Avery. The second is Joshua Lederberg, who made pioneering discoveries in bacterial genetics. Others include Francis Crick; a link to a Crick paper at this site is given below, with Chapter 3. This site is also listed on my Classic papers page; there I show a complete list of the scientists featured at the Profiles site. (More are added from time to time, and existing Profiles are updated.)

The Left Handed DNA Hall of Fame http://users.fred.net/tds/leftdna/. This site discusses misprintings of the normal DNA structure that make it seem left-handed. It shows some examples. This is from Tom Schneider, (formerly) of the National Cancer Institute.

Schneider's home page is http://alum.mit.edu/www/toms/. Among many interesting things there, you will also find information on the 'logo' presentation of DNA consensus sites that we will show later (for ribosome binding sites and promoters).


Homework, answers

13. The web site for the company that did this is http://www.pharmaseq.com. There is technical information about the project. Reminder... Mention of company sites is not an endorsement. I include this site because it is interesting and "cute."

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Chapter 3 (Protein structure)

Further reading

F Crick, Central dogma of molecular biology. Nature 227:561, 8/8/70. Available online at https://profiles.nlm.nih.gov/ps/access/SCBCCH.pdf. (The source given here is the Profiles in Science site, listed above with Chapter 2.) This is the article in which Crick addresses attacks on the central dogma that were stimulated by the discovery of reverse transcriptase (RNA --> DNA). He clarifies what he really meant, and how reverse transcription fits right in. I had occasion to re-read this classic recently; I heartily recommend it! The Crick article that Weaver lists for Ch 3 is the original presentation of the Central Dogma. (This article is also listed on my Old articles page.)

A post in my Musings newsletter on the history of the Central Dogma: Central Dogma of Molecular Biology (August 16, 2011).

How do you find a copy of an article, such as the one above? One good way is to use Google Scholar. http://scholar.google.com Go to Advanced Search. Put a part of the title in the "with the exact phrase" box, set "where the words occur" to "in the title of the article". Optionally, you can add an author or date; however, title alone is often sufficient. Using Google Scholar for this Crick article yields several sources.

If you have not already done so, I strongly encourage you to get and install RasMol, for viewing molecular structures. This was introduced in the Computer resources section of the Ch 2 handout, and details are at the web site.

You can use RasMol to see good examples of secondary structure; see my RasMol page: "RasMol - An Introductory Guide".


I have posted a page at my site on the general properties of Amides. It was written for my introductory organic chemistry class, but you may find it useful. Remember that the peptide bond is an amide linkage. The resonance structures of an amide lead to it not behaving as you might expect.

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Chapters 4-5 (Methods)

The Biology Animations Library, Dolan DNA Learning Center, Cold Spring Harbor Laboratory: https://www.dnalc.org/resources/animations/. Among the topics listed there: How Embryonic Stem Cells Lines are Made, DNA Restriction, Gel Electrophoresis, DNA Transformation, Polymerase Chain Reaction, Sanger Sequencing, Cycle Sequencing, DNA Arrays, Model Organisms. Each topic contains a tutorial, with animations.

This is part of the Dolan DNA Learning Center. Other sections of interest there include DNA from the Beginning , DNA Interactive and Inside Cancer -- and more. To reach these, choose "Websites" from the menu across the top, or go directly to: https://www.dnalc.org/websites/. Then choose from the "websites" menu at the left. DNA from the Beginning is also available in Chinese, Danish, French, Icelandic, Italian, Portuguese (with German, Spanish promised soon). This site is also listed for BITN Resources: DNA and the genome. The Inside Cancer site is also listed for BITN Resources: Miscellaneous -- Cancer.

Genetic Science Learning Center, Univ of Utah: http://learn.genetics.utah.edu. Tutorial, on a range of molecular genetics topics. Includes some basics on DNA, but much is about technologies, including stem cells and microarrays. Also available in Spanish.

Other methods-related sites are listed in the various topic-oriented sections at the end of this page. See list of sections at the top.

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Chapter 6 (Transcription)

See the section on Gene chips.

Homework

12. Internet question. Much of the work on elongation was done by E Nudler's group (e.g., Fig 6.37 and Nudler, 1999). A reasonable question would be to ask whether he has published more recent work. To check this, you want to do a literature search. Go to the PubMed site, and enter Nudler as the author search term. See what you get, and perhaps browse the most recent item. (See my Library Matters page for how to search PubMed.)

In the answer section [of the handout], I briefly note the expected output.

Those who are experienced searchers can skip this; you are not responsible for the output. The point is to get those who are not familiar with PubMed to get started. Searching on an author, with an uncommon name, is a simple search.

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Chapters 10-13 (Transcription - eukaryotes)

The following item is a UC Berkeley news release about a new article in Science, reporting more data on the structure of TFIID. The "Scientific American" figure shown is probably one I show in class, to illustrate the complexity of the eukaryotic transcription apparatus. For more, choose the link "Transcription Factor TFIID website" near the bottom of this news release. You will get some good Figs of TFIID structure (caution -- they are rather large downloads).
http://www.berkeley.edu/news/features/1999/12/09_nogales.html

Roger Kornberg, of Stanford, was awarded the 2006 Nobel prize for chemistry "for his studies of the molecular basis of eukaryotic transcription". http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2006/

The 2004 Nobel Prize in Chemistry was awarded to three scientists for their key roles in understanding how proteins are degraded. Specifically, they discovered the role of ubiquitin, a special protein that is attached to proteins to tag them for degradation. The bigger story is the increasing recognition of the importance of protein degradation. Many proteins are made defective, and must be degraded rapidly. Some proteins are supposed to act for only a brief time, and must be promptly degraded. And some mutations lead to proteins that are unstable, and get marked for rapid degradation. See the Nobel site: http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2004/. This site is also listed for Internet resources for Organic/Biochem: Amino acids, proteins, genes.

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Chapters 14-16 (Post-transcriptional events)

RNA editing. There are numerous processes in which the base sequence of RNA is changed between its synthesis and use. Collectively, these are called RNA editing. Larry Simpson's site at UCLA is a good entry point to these fascinating processes. http://dna.kdna.ucla.edu/rna/index.aspx. The following listing, for A-to-I RNA editing, is one example; indeed, that site is listed here by Simpson.

InBase, the Intein Database. History and general information on protein splicing, Sect H. The site is maintained by New England BioLabs. http://tools.neb.com/inbase/

For more about RNA, see the section RNA: folding, technologies.

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Chapters 17-19 (Protein synthesis)

Some of the sites listed in the Ch 3 handout are appropriate for the current chapters on protein synthesis.

Codon Usage Database. Data on preferred codons in a variety of organisms: http://www.kazusa.or.jp/codon/

Protein synthesis movies from Joachim Frank: http://www.molecularmovies.com/movies/viewanimatorstudio/A.H.%20Whiting,%20J.%20Frank,%20R.%20Agarwal/...
* Elongation Cycle of Protein Biosynthesis. "An animated display of the E. coli ribosome and its interactions with the tRNA and the elongation factors during the elongation cycle, in the course of which the polypeptide chain is elongated by the addition of one amino acid."
* The Ribosome: A Molecular Ratchet. "The movie juxtaposes two cryo-EM density maps, one obtained from the ribosome bound with elongation factor EF-G in the presence of a nonhydrolyzable GTP analog, the other from the ribosome bound with P-site tRNA as a control. It is evident that the small subunit rotates with respect to the large subunit, and both undergo a major structural reorganization. The motion accompanies translocation, the process by which the tRNAs are moved from the A- and P- to the P- and E-sites, respectively, and mRNA is moved to the next codon."
- This is now part of a larger collection, "A Portal to Cell & Molecular Animation".

The 2009 Nobel Prize for Chemistry was awarded to three scientists "for studies of the structure and function of the ribosome". http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2009/.

Calculations of protein folding predictions are extremely computer-intensive. Two groups have set up distributed systems to allow home computer users to let their computers help. You may find these sites interesting about protein folding, even if you don't want to participate.
* http://folding.stanford.edu. Folding@home, from Vijay Pande, Stanford. (If you want to read about this, there are brief items in Nature 407:667, 10/12/00, and Science 290:1903, 12/8/00. The latter discusses some of the computing issues involved and how these differ among various of these distributed processes.) This site is also available in Arabic, Chinese, Danish, Dutch, French, German, Greek, Italian, Japanese, Lithuanian, Portuguese, Russian, Spanish, Swedish, Vietnamese. (The pages for non-English languages are provided by volunteers; languages are added and deleted from time to time.)
* http://boinc.bakerlab.org/rosetta/. Rosetta@home, from David Baker, Univ Washington. (For an article on this, see D Baker, Proteins by design. The Scientist 7/06, p 26. http://www.the-scientist.com/?articles.view/articleNo/24136/title/Proteins-by-Design/.) The Rosetta site is also available in Chinese, French, German, Italian, Japanese, Polish, Portuguese, Russian, Spanish. The list of languages is available under "Community", at left, near bottom. (The pages for non-English languages are provided by volunteers; languages are added and deleted from time to time.)

Ribosomal frameshifting. J D Dinman, Programmed ribosomal frameshifting goes beyond viruses. Microbe 1:521, 11/06. Discusses examples and types of frameshifting in all three kingdoms -- as well as in viruses. Good update and overview. Available through PMC: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1885200/.

Membrane proteins. A complex issue, which has lagged behind the study of soluble proteins, for obvious experimental reasons. Yet, membrane proteins are important; they provide about half of the mass of the membrane, and important functions, including transport and signaling. This site focuses on the structure and stability of membrane proteins. It deals with membrane structure and the interaction of proteins with membranes. http://blanco.biomol.uci.edu/. From the lab of S White, Univ Calif Irvine.

For more related to this chapter, see my page of Organic/Biochem Internet resources, especially the section on Amino acids, proteins, genes. The level of that page is generally more introductory than this page, but there is considerable overlap.

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Chapters 20-21 (DNA replication)

The Protein Data Bank features one protein (or other biological structure) each month, with pictures and extensive discussion. This feature, called Molecule of the Month, is maintained by Dr David Goodsell of The Scripps Research Institute. Some relevant to the current topic, DNA and its replication, include: DNA polymerase, nucleosomes, restriction enzymes, DNA, reverse transcriptase, DNA ligase, topoisomerases. Many of the others are relevant to other aspects of course material, including RNA synthesis and protein synthesis. For the complete list of featured Molecules of the Month: http://pdb101.rcsb.org/motm/

Animation showing how telomerase works:
http://faculty.plattsburgh.edu/donald.slish/Telomerase.html. From Dr Donald F. Slish at SUNY, Plattsburgh.

The 2009 Nobel Prize for Physiology or Medicine was awarded to three scientists "for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase". http://www.nobelprize.org/nobel_prizes/medicine/laureates/2009/index.html. Key parts of this work were done in the Molecular Biology Department at UC Berkeley, by Greider and Blackburn.

PDB files for sliding clamps are available, from the Protein Data Bank. This will let you visualize and manipulate these as 3D structures. See my RasMol web page for getting and working with protein files. File 2pol shows the structure of the E coli Pol III β (beta) subunit, and file 1axc shows the structure of PCNA. [Small problem: Two of the three chains of the PCNA structure display in colors that are either identical or very similar, depending on your system.]

http://www.arclab.org. The Aging Research Centre (ARC). That site is developed by a former X107 student -- who also suggests:
https://web.archive.org/web/20140122102200/http://www.pbs.org/newshour/forum/october98/glenn.html (archived copy).


Homework

16. Computer question. Load a file for a sliding clamp into RasMol. I encourage you to do these parts with both the E coli Pol III β subunit and the eukaryotic PCNA -- but at least try one. Source files for these proteins are described under Computer Resources, above.

a. Measure the inner diameter of the clamp -- the hole through which the DNA goes. (If you are not quite sure where to measure, take a few measurements.) The procedure for measuring distances between atoms is described in the RasMol web page, both for regular RasMol and for Berkeley RasMol. Note that you may need to switch to ball-and-stick display before taking these measurements.

b. Look at the structure of the clamp. Is the part that interacts with DNA mainly α-helix or β-sheet? What about the rest of the protein?

Note that Fig 21.18 shows you the answer to this. However, you should be able to produce a better view to focus on this particular question. See answer section for a hint. But before you do, experiment with various settings for Display and Colours.

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Chapter 22 (Recombination)

Structure of the Recombination Protein RuvA and a model for its Binding to Holliday Junction. It has animations showing how DNA is threaded through the Ruv protein complex during the process of branch migration. These can be thought of as animations of Weaver's Figs 22.25 and 27. Branch migrations are similar to the action of a DNA helicase. From University of Sheffield. http://www.shef.ac.uk/mbb/ruva

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RNA: folding, technologies

For more about RNA, see the section Chapters 14-16 (Post-transcriptional events). In particular, that section includes information on RNA editing. There is also a section on my BITN pages for RNAi (RNA interference or silencing).

RNA Modification database. Extensive information about modified bases in RNA. http://mods.rna.albany.edu/. From Paul Agris (SUNY - Albany), and others around the world.

RNAstructure. "RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities. It also can be used to predict bimolecular structures and can predict the equilibrium binding affinity of an oligonucleotide to a structured RNA target. This is useful for siRNA design. It can also predict secondary structures common to two, unaligned sequences, which is much more accurate than single sequence secondary structure prediction. Finally, RNAstructure can take a number of different types of experiment mapping data to constrain or restrain structure prediction. These include chemical mapping, enzymatic mapping, NMR, and SHAPE data." The program is from D Mathews and colleagues, University of Rochester; it was recommended by an X107 student. http://rna.urmc.rochester.edu/RNAstructure.html.

RNA Studio. A collection of software to deal with RNA, including structure prediction. http://bibiserv.techfak.uni-bielefeld.de/bibi/Tools_RNA_Studio.html. From the Bielefeld University Bioinformatics Server.

RNA "Basics". Among the technical docs provided by Ambion, a company that specializes in RNA, is a nice series of introductory articles on RNA methodology. Topics include RNA isolation, in vitro transcription (and translation), Northerns, RT-PCR, gene arrays (also listed under Gene chips). http://www.thermofisher.com/us/en/home/references/ambion-tech-support.html. ) Ambion is now part of Thermo Fisher; the new page link given here lists a range of Ambion materials, including "Basics".

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Bioinformatics, genome analysis: software and help using it, tutorials

Biozon, from Golan Yona, now at Stanford University. A database of databases. Biozon helps you link information from numerous databases of information on proteins and genes. Data types include nucleic acid sequences, protein sequences, protein structures, and interactions. http://www.biozon.org/.

ApE -- A plasmid Editor, by M Wayne Davis, Univ Utah. A program for dealing with plasmids. Simple but versatile. Windows & Mac. Features include (excerpted from home page): shows translation, Tm, %GC, ORF of selected DNA in real-time; reads DNA Strider, Fasta, Genbank and EMBL files; highlights and draws graphic maps using feature annotations from genbank and embl files; directly BLASTs selected sequence at NCBI or wormbase; creates graphic restriction maps - linear or circular with features indicated; draws pre-defined and user-defined DNA ladders; and much more. http://biologylabs.utah.edu/jorgensen/wayned/ape/.

Structural Biology Software Database. "This database contains programs which are thought to be of interest to researchers in the fields of structural biology, quantum chemistry, and bioinformatics." http://www.ks.uiuc.edu/Development/biosoftdb/. From University of Illinois.

SimGene: "A Portal to Free Molecular Biology and Bioinformatics Tools". http://SimGene.com. Programs currently available, for online use, include: CGView (plasmid drawing); Primer3 (primer design tool); ClustalW2 and TCoffee (sequence alignment); OligoCalc (sequence analysis); Readseq (sequence format conversion). More to come.

The Molecular Toolkit is a group of programs for analysis and manipulation of nucleic acid and protein sequence data. Programs can be used online, platform independent (they are in Java). The basics, but good. From R A Bowen at Colorado State. http://www.vivo.colostate.edu/molkit/index.html

Primo --- Your Ultimate PCR Primer Design Tools. Primo 3.4 Online. A variety of PCR-related software, to be used online. The page also includes a PCR Glossary and a Molecular Biology Glossary, both focusing on technologies. From Chang Bioscience; some of the free online software is related to their commercial products. http://www.changbioscience.com/primo/

Online Analysis Tools. Fairly basic, perhaps a good place to start. Sections include: Bioinformatics tutorials, Carbohydrates, DNA sequence analysis, Genomics, Protein sequence analysis, RNA sequence analysis, transcription analysis, Miscellaneous (which itself includes: Buffers, Centrifugation calculations, General molecular biology calculations, Meta sites for DNA & protein analysis, Sequence cleanup & conversion, Online graphics, Windows- & Java Or Perl-based programs - free molecular biology programs, Recovering sequences from Genbank). From Andrew Koprinski, Queen's University, Kingston, Ontario. http://molbiol-tools.ca/

The HSLS Online Bioinformatics Resources Collection "contains annotations and links for 2818 bioinformatics databases and software tools". From the Health Sciences Library System, University of Pittsburgh. http://www.hsls.pitt.edu/obrc/

European Bioinformatics Institute (EBI). http://www.ebi.ac.uk/. Lots of bioinformatics resources.

The Molecular Level: Tools for Structural Biology Education and Training, a student-oriented tutorial on tools for bioinformatics and structural biology. From G. Rhodes, now retired from the University of Southern Maine. http://spdbv.vital-it.ch/TheMolecularLevel/index.html

A major resource on bioinformatics, including career information. http://www.bioinformatics.org/

http://www.justbio.com/hosted-tools.html. Extensive molecular biology resources, with a strong emphasize on software. Try ignoring the registration, if you want; it is probably ok.

"BEDROCK (Bioinformatics Education Dissemination: Reaching Out, Connecting, and Knitting-together) is an NSF-funded project aimed at integrating bioinformatics throughout the undergraduate biology curriculum, using an inquiry-based approach in which students explore and analyze actual data in a way that recreates the experience of conducting research." http://www.bioquest.org/bedrock/index.php. After looking around a bit, I suggest you choose "Problem spaces".

http://www.restrictionmapper.org. Although the focus here is on programs for restriction mapping, there are links to a range of molecular biology software.

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Sites that focus on specific organisms (or groups)

Model Organisms for Biomedical Research. http://modelorganisms.nih.gov/. This is a gateway to genome and other database sites for several "model organisms". Such gateway collections can be good places to start, but they may be incomplete. As of May 2009, the list of model organisms here includes: mouse, rat, budding yeast (Saccharomyces cerevisiae), fission yeast (Schizosaccharomyces pombe), filamentous fungus (Neurospora crassa), social amoeba (Dictyostelium discoideum), round worm (Caenorhabditis elegans), water flea (Daphnia), fruit fly (Drosophila melanogaster), zebrafish (Danio rerio), frog (Xenopus laevis; X. tropicalis), chicken (Gallus gallus), and a plant (Arabidopsis).

Online Mendelian Inheritance in Man (OMIM). http://www.ncbi.nlm.nih.gov/sites/entrez?db=OMIM. "This database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information."

Online Mendelian Inheritance in Animals (OMIA). http://omia.angis.org.au/. Database of genetic diseases in animals (excluding mice). From F Nicholas, Univ Sydney.


The following sites in this section are in order alphabetically by the term shown at the start of each item. But a caution: The term used may be a narrow term or a broad one, a scientific name or a common name. In general, I chose a term that seemed appropriate for the specific site. Therefore, sites on a topic might reasonably be listed in more than one way; I encourage browsing!

For more sites focusing on specific organisms or groups of organisms, see various sections of the Internet resources: Biology - Miscellaneous page.

Algae. http://www.bigelow.org/hab/index.html. Toxic and harmful algal blooms. US toxic algae.

Annelids. http://www.annelida.net/. Annelid Resources. Earthworms, leeches, etc. Includes bibliography, back to 1705. From Geoff Read, in New Zealand.

Ants
* http://antbase.org/. Antbase. From the American Museum of Natural History (Donat Agosti) and the Ohio State University (Norman F. Johnson).
* http://www.antweb.org/index.jsp. AntWeb. From the California Academy of Sciences. You can search to find the ants for your local area.

Arabidopsis, a model plant. https://www.arabidopsis.org/. TAIR - The Arabidopsis Information Resource.

Arachnids (spiders). http://www.arachnology.be/Arachnology.html. The Arachnology Home Page. Much of the page is for students or the lay public.

Armadillos. http://armadillo-online.org/. Armadillo Online! "Welcome to the wonderful world of armadillos." From Joshua P Nixon, originally started while at Michigan State University.

Bean Beetles. http://beanbeetles.org/. "This site is dedicated to providing information to faculty and staff on using bean beetles (seed beetles), Callosobruchus maculatus (Coleoptera: Bruchidae), in undergraduate laboratory courses. This site contains a downloadable laboratory methods handbook, a searchable bibliography, links to researchers who study C. maculatus, classroom-tested undergraduate laboratory activities, and information on inquiry-based undergraduate laboratories."

Caenorhabditis elegans. C elegans is a nematode whose development has been followed in meticulous detail. In 1998 it became the first animal to have its genome "completely" sequenced.
* http://www.wormbook.org. "The online review of C. elegans biology. WormBook is a comprehensive, open-access collection of original, peer-reviewed chapters covering topics related to the biology of Caenorhabditis elegans (C. elegans). WormBook also includes WormMethods, an up-to-date collection of methods and protocols for C. elegans researchers." WormBook starts with basics, and therefore is suitable for beginners.
* http://www.wormbase.org. Wormbase, a genomics site for C. elegans.

Cephalopods. http://www.thecephalopodpage.org/. The Cephalopod Page. Cephalopods? Squid, octopus, etc. From James B Wood, Bermuda Biological Station for Research.

Chlamydomonas. Chlamydomonas is a unicellular green alga. However, photosynthesis is "optional", since it can also be grown on organic carbon. http://www.chlamy.org. The Chlamy Connection. "A Gateway to Resources for Chlamydomonas Research. This site provides access to genomic, genetic and bibliographic information on Chlamydomonas and related algae, the Chlamydomonas Resource Center (which now has its own web site), and other resources for the Chlamydomonas community."

Coelacanths, probably the closest living relatives of the first vertebrates. http://www.dinofish.com.

Conifers. http://conifers.org/. The Gymnosperm Database, from Christopher J. Earle.

Cyanobacteria. http://www-cyanosite.bio.purdue.edu/index.html. Cyanosite: A Webserver for Cyanobacterial Research.

Dinosaurs. http://dinobase.gly.bris.ac.uk/. Dinobase, from the Earth Sciences Department, University of Bristol.

Dipterans. http://www.diptera.org. The Diptera Site - Information about the World's flies. (Includes flies, midges, gnats, mosquitoes.) From F Christian Thompson, US Dept of Agriculture.

Drosophila.
* http://flybase.org/. Flybase, A Database of the Drosophila Genome.
* http://www.sdbonline.org/fly/aimain/1aahome.htm. The Interactive Fly. "A cyberspace guide to Drosophila development and metazoan evolution." From the Society for Developmental Biology, with resources for beginners through experts. Newcomers should click on "If you are new to developmental biology".

Escherichia coli. http://cgsc.biology.yale.edu. The Coli Genetics Stock Center, Yale. A repository of E coli strains, and information. (The site also includes a list of links to stock centers for other organisms.)

Flatworms. http://www.rzuser.uni-heidelberg.de/~bu6/flatintr.htm. Marine Flatworms of the World, from Wolfgang Seifarth. Platyhelminthes. Great Gallery.

Fungi. http://www.fgsc.net. The Fungal Genetics Stock Center, Univ Missouri, Kansas City. A repository of fungal strains, and information. Much is for Aspergillus and Neurospora. Includes links to genome resources for fungi.

For more about fungi see... Microbiology: fungi on my page Internet resources: Biology - Miscellaneous.

Insects
* http://www.ent.iastate.edu/list/. Entomology Index of Internet Resources.
* http://bugguide.net/. Bug Guide. Identification, Images, & Information for Insects, Spiders & Their Kin, for the United States & Canada. An online community of naturalists, hosted by Iowa State University Entomology.

Myxomycetes. http://myxobacteria.ahc.umn.edu/index.html. MyxoWeb, A Virtual Field Guide to Myxomycetes. Slime molds.

Protists. http://megasun.bch.umontreal.ca/protists/. Protist Image Data. Pictures and information on selected genera of algae and protozoa. Includes resources in protistology and related fields: microbiology, mycology, phycology, protozoology. From Charles J O'Kelly and Tim Littlejohn, University of Montreal.

Rhubarb. http://www.rhubarbinfo.com. The Rhubarb Compendium. Not very molecular, but...

Schizosaccharomyces pombe (fission yeast). http://www-bcf.usc.edu/~forsburg/. PombeNet, from Susan Forsburg's lab at Univ Southern California. Scroll down for a wide range of information; you might want to go to the pombe FAQ, listed under "Working with fission yeast".

Scorpions. http://www.ntnu.no/ub/scorpion-files/. The Scorpion Files, from J O Rein, Norwegian University of Science & Technology, Trondheim.

Seaweeds. http://www.seaweed.ie. The Seaweed Site, from Michael Guiry, National University of Ireland, Galway.

Tardigrades. http://tardigrades.bio.unc.edu. A page about water bears, from Bob Goldstein, University of North Carolina.

Xenopus, the African clawed frog. http://www.xenbase.org. "Xenbase: Xenopus laevis and Xenopus tropicalis biology and genomics resource"

Zebrafish. http://zfin.org. The Zebrafish Information Network (ZFIN), at the University of Oregon. The zebrafish has become a major model organism, as a relatively simple vertebrate. For more about ZFIN and about the developmental genetics of zebrafish, see Trends in Genetics, 15:248, 6/99.

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Molecular biology gateway sites

Typically, these have many links to a wide range of useful mol biol sites: databases, protocols, software, journals, suppliers.

Each year, the journal Nucleic Acids Research publishes two special issues of molecular biology resources. A January issue, the Database Issue, is a compilation and review of over 100 molecular biology databases available online. A July issue, the Web Server Issue, is a compilation and review of molecular biology software available online. These issues are available online, free: http://nar.oxfordjournals.org. Click on the link to the Database Issue or the Web Server Issue. Also available there is NAR Methods online; each of the collections there is a category-specific archive of Methods published in NAR from 1999 to the present. (Currently, the link buttons are along the right side.) The journal Nucleic Acids Research is now an open access journal, entirely available online for free.

National Center for Biotechnology Information. Includes the GenBank database (DNA sequences), PubMed (access to database of medical literature), and many other resources in biotechnology, including bioinformatics tools. https://www.ncbi.nlm.nih.gov/.

http://www0.nih.go.jp/~jun/research/. From Jun Ishikawa. Also in Japanese.

https://www.neb.com/. From New England BioLabs. Click on Technical Reference. They list many things there, including some of their own databases. But in particular, scroll down to "Molecular biology databases" for an extensive list. The list is in their catalog, and online at their web site.

http://shigen.nig.ac.jp/shigen/index.jsp. SHIGEN = Shared information of genetic resources. Links for information on cloning vectors as well as for many model organisms. From the Center for Genetic Resource Information, National Institute of Genetics, Japan. Also in Japanese.

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Gene chips (microarrays)

The Basics: What is a Gene Array? From Ambion. http://www.thermofisher.com/us/en/home/references/ambion-tech-support/rna-gene-expression/general-articles/the-basics-what-is-a-gene-array.html

Other sites with information on this method are in various places on this page. A text search on "array" will give them.

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Genomes

There is more about genome issues on my page Biotechnology in the News (BITN): DNA and the genome.

Genome sizes. Modern DNA sequencing yields a rather precise measure of the genome size. However, the idea of genome size predates sequencing. The general idea is that the genome size is the amount of DNA in the haploid genome; with luck, that is the amount of DNA in a gamete. For prokaryotes, it is the size of "the chromosome" -- a simple idea that begins to fail when it is realized that some have more than one chromosome. Genome size has been measured by chemical analysis of the DNA, and by size measurement of chromosomal DNA by gel electrophoresis. All these genome sizes are subject to some uncertainty, both because of the methodology and the assumptions. Genome size is commonly stated as picograms (pg) of DNA, or as base pairs (bp). 1 pg of DNA is about 109 (one billion) bp. For example, the human genome contains about 3.5 billion bp, and weighs about 3.5 pg.

The following sites are databases of genome sizes. The first one, from Ryan Gregory, also has extensive information about genome sizes, how it is measured, etc. I encourage you to look over the sections on Statistics and FAQ at Gregory's site.

Animals -- 4000 of them. http://www.genomesize.com. The Animal Genome Size Database, from T Ryan Gregory, Univ Guelph. This site is also referred to on my Unusual microbes page, under Microbes with too much DNA, and in the Musings post Who is #1: the most DNA? (March 7, 2011).

Plants -- 7000 of them. http://data.kew.org/cvalues/. The Plant DNA C-values Database, from M D Bennett & I J Leitch, Royal Botanical Gardens (Kew). Includes angiosperms, gymnosperms, pteridophytes, bryophytes, algae.

Fungi. http://www.zbi.ee/fungal-genomesize/. Fungal Genome Size Database, from B Kullman et al, Estonian University of Life Sciences.


Genome sequencing

The following site, at Oak Ridge National Laboratory (Department of Energy), contains a broad array of technical and general information on the human genome project. A brief review in Science (281:1247, 8/28/98) indicates that the first priority of the site "is making human genome science accessible" to the public. The site includes "a student primer on molecular genetics and a library of articles covering ethical, legal and social issues." http://web.ornl.gov/sci/techresources/Human_Genome/index.shtml. At this point, this site is an archive of the original "Human Genome Project", 1990-2003.

The following sites include lists of genome sequencing projects, generally listing both completed and in-progress projects. All link to the projects -- and also include more information on sequencing.
* The Comprehensive Microbial Resource (CMR), from the J Craig Venter Institute (JCVI). It is "... a free website used to display information on all of the publicly available, complete prokaryotic genomes. In addition to the convenience of having all of the organisms on a single website, common data types across all genomes in the CMR make searches more meaningful, and cross genome analysis highlight differences and similarities between the genomes." http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi.
* Genomes OnLine Database (GOLD), maintained by N Kyrpides of the Joint Genome Institute (Walnut Creek, CA): https://gold.jgi.doe.gov/.
* Quick Guide to Sequenced Genomes, maintained by Genome News Network, an online publication of the J. Craig Venter Institute: http://www.genomenewsnetwork.org/resources/sequenced_genomes/genome_guide_p1.shtml.
* Genomic biology, from NIH. https://www.ncbi.nlm.nih.gov/genome. Among other things, see Genome Resources at right, which leads to various lists of genomes under "Genome Projects Database". Lists can be sorted by various columns, including genome size.

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Miscellaneous (including methods)

    (in no particular order!)

Good resources for methods in molecular and cell biology:
* Cell Biology Lab Manual. From William H Heidcamp, Gustavus Adolphus College (Minnesota). http://homepages.gac.edu/~cellab/.
* Mama Ji's Molecular Kitchen. From Guruatma "Ji" Khalsa, Arizona State Univ. Many basic procedures -- not just protocols, but explanations. The author writes: "I've written in simple terms about a number of commonly used molecular techniques, explaining what they are and how they work." http://askabiologist.asu.edu/mama-jis-molecular-kitchen.
* Protocols for recombinant DNA isolation, cloning, and sequencing. Edited by Bruce A Roe, Judy S Crabtree and Akbar S Khan, University of Oklahoma. An older collection (1995) -- and really good with the basics. http://www.genome.ou.edu/protocol_book/protocol_index.html.
* Protocols, from Thermo Fisher (formerly Invitrogen). Sections include: Nucleic Acid Purification & Analysis; Nucleic Acid Amplification & Expression Profiling; Cloning; Proteins, Expression, Isolation & Analysis; RNAi, Epigenetics & Gene Regulation; Molecular Biology; Cell Culture; Cell & Tissue Analysis; Drug Discovery & Development; Immunology. http://www.thermofisher.com/us/en/home/references/protocols.html.
* Protocols and Applications Guide, from Promega. Topic areas include: PCR, RNA interference, apoptosis, expression, in vitro translation, cell viability. http://www.promega.com/resources/product-guides-and-selectors/protocols-and-applications-guide/.

(Company web sites are often very good sources of technical information. I offer the two above, and others scattered on this page, as examples. No endorsement of any company's products is intended.)

Biophysics educational resources. Topic areas: molecular structures, biophysical techniques, and biological mechanisms. From the Biophysical Society. http://www.biophysics.org/AboutUs/Committees/Education/EducationalResources/tabid/471/Default.aspx.

Green fluorescent protein (GFP). A site devoted to information about a protein, originally isolated from jellyfish, that has become of the most widely used tools in molecular and cell biology. It has also captured the attention of the public, through pictures such as little green mice. This site contains a wide range of information, suited for both the casual visitor and the researcher. http://www.conncoll.edu/ccacad/zimmer/GFP-ww/GFP-1.htm. From Marc Zimmer, Connecticut College.

Green fluorescent protein -- the Nobel prize. The 2008 Nobel prize in chemistry was awarded to three scientists associated with the discovery of GFP and its development into an amazing lab tool, as noted in the previous item. The scientists are Osamu Shimomura, Martin Chalfie, and Roger Y. Tsien. Tsien is a professor at the University of California -- San Diego. The Nobel site for this: http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2008/.

This Nobel is also noted in the Musings post Nobel prizes (October 8, 2008).

Reactome database. Includes both biochemical and cellular processes. Focuses on humans, but includes a range of organisms. http://www.reactome.org

The Restriction Enzyme Database, "Rebase", maintained by New England BioLabs, includes "all known" restriction enzymes. (Weaver discusses restriction enzymes, and their use in cloning, in the opening pages of Ch 4. We do not formally discuss this.) http://rebase.neb.com/rebase/

Cell and Molecular Biology Online. A collection of links (publications, methods, career resources -- and more): http://www.cellbio.com

Web Tool Box, from Sigma-Aldrich. A collection of "calculators, explorers and other helpful resources" for "Life science and biochemicals, Chromatography & analytical materials science, Chemical synthesis and lab equipment". Examples include calculators for buffers, PCR, peptide properties -- and more. Although some sections promote products from the company, much is just "general use" tools. http://www.sigmaaldrich.com/technical-service-home/web-tool-box.html.


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Last update: December 15, 2016