Proteopedia - User contributions [en]

User:Jing Guo

2010-04-30T21:21:58Z

Jing Guo:

umass amherst chemistry department CBI (chemistry biology interface) chalk talk

<applet size='[450,338]' frame='true' align='right'
caption='YYY' />

<scene name='User:Jing_Guo/Gluconase/2'>Glucanase</scene>

Glucans are important structural compounds in the cell walls of plants and fungi. Chemically, glucans are a type of carbohydrate. They consist of the same basic building blocks (monosaccharides) as starches, but the units are arranged differently.

Many microorganisms produce glucanases, which enable them to digest glucans and use them as a source of nutrients. Industrially, bacteria are used to produce glucanases on a large scale for use in applications such as beer brewing. Glucanase supplements help beer yeasts break down glucans in barley, which can often block filters. (In Germany, glucanase additives are not permitted because they do not conform to the German Beer Purity Act.)

Genes for certain glucanases (usually b-1,3-glucanases) have been transferred to plants to enable them to degrade the glucans in disease-causing fungi. Researchers are developing grapes, wheat, and barley with glucanase-conferred fungus resistance.

Genetically modified barley with a novel gene for glucanase can help improve the quality of animal feed. Some animals lack the glucanases needed to break down long chain glucanes present in barley cell walls. Therefore, poultry raised with barley without added glucanase remain small.

User:Jing Guo

2010-04-30T21:19:09Z

Jing Guo:

umass amherst chemistry department CBI (chemistry biology interface) chalk talk

<applet size='[450,338]' frame='true' align='right'
caption='YYY' />

<scene name='User:Jing_Guo/Glucanase/2'>Glucanase</scene>

Glucans are important structural compounds in the cell walls of plants and fungi. Chemically, glucans are a type of carbohydrate. They consist of the same basic building blocks (monosaccharides) as starches, but the units are arranged differently.

Many microorganisms produce glucanases, which enable them to digest glucans and use them as a source of nutrients. Industrially, bacteria are used to produce glucanases on a large scale for use in applications such as beer brewing. Glucanase supplements help beer yeasts break down glucans in barley, which can often block filters. (In Germany, glucanase additives are not permitted because they do not conform to the German Beer Purity Act.)

Genes for certain glucanases (usually b-1,3-glucanases) have been transferred to plants to enable them to degrade the glucans in disease-causing fungi. Researchers are developing grapes, wheat, and barley with glucanase-conferred fungus resistance.

Genetically modified barley with a novel gene for glucanase can help improve the quality of animal feed. Some animals lack the glucanases needed to break down long chain glucanes present in barley cell walls. Therefore, poultry raised with barley without added glucanase remain small.

User:Jing Guo

2010-04-30T21:18:25Z

Jing Guo:

umass amherst chemistry department CBI (chemistry biology interface) chalk talk

<applet size='[450,338]' frame='true' align='right'
caption='YYY' />

<scene name='User:Jing_Guo/Glucanase/2'>Gluconase</scene>

Glucans are important structural compounds in the cell walls of plants and fungi. Chemically, glucans are a type of carbohydrate. They consist of the same basic building blocks (monosaccharides) as starches, but the units are arranged differently.

Many microorganisms produce glucanases, which enable them to digest glucans and use them as a source of nutrients. Industrially, bacteria are used to produce glucanases on a large scale for use in applications such as beer brewing. Glucanase supplements help beer yeasts break down glucans in barley, which can often block filters. (In Germany, glucanase additives are not permitted because they do not conform to the German Beer Purity Act.)

Genes for certain glucanases (usually b-1,3-glucanases) have been transferred to plants to enable them to degrade the glucans in disease-causing fungi. Researchers are developing grapes, wheat, and barley with glucanase-conferred fungus resistance.

Genetically modified barley with a novel gene for glucanase can help improve the quality of animal feed. Some animals lack the glucanases needed to break down long chain glucanes present in barley cell walls. Therefore, poultry raised with barley without added glucanase remain small.

User:Jing Guo

2010-04-30T21:17:26Z

Jing Guo:

umass amherst chemistry department CBI (chemistry biology interface) chalk talk

<applet size='[450,338]' frame='true' align='right'
caption='YYY' />

<scene name='User:Jing_Guo/Gluconase/2'>Gluconase</scene>

Glucans are important structural compounds in the cell walls of plants and fungi. Chemically, glucans are a type of carbohydrate. They consist of the same basic building blocks (monosaccharides) as starches, but the units are arranged differently.

Many microorganisms produce glucanases, which enable them to digest glucans and use them as a source of nutrients. Industrially, bacteria are used to produce glucanases on a large scale for use in applications such as beer brewing. Glucanase supplements help beer yeasts break down glucans in barley, which can often block filters. (In Germany, glucanase additives are not permitted because they do not conform to the German Beer Purity Act.)

Genes for certain glucanases (usually b-1,3-glucanases) have been transferred to plants to enable them to degrade the glucans in disease-causing fungi. Researchers are developing grapes, wheat, and barley with glucanase-conferred fungus resistance.

Genetically modified barley with a novel gene for glucanase can help improve the quality of animal feed. Some animals lack the glucanases needed to break down long chain glucanes present in barley cell walls. Therefore, poultry raised with barley without added glucanase remain small.

CBI Molecules

2010-04-30T21:13:51Z

Jing Guo:

These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].
Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground]. Follow the links below to read nontechnical descriptions in Proteopedia.

UMass CBI Members, add your molecules to the list; follow the instructions below the list.

'''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', [http://people.chem.umass.edu/thompson/index.html Thompson] & [http://www.chem.umass.edu/~rmweis/weislab/ Weis] laboratories

'''[[6-deoxyerythronolide B synthase (DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Schnarr lab (Tsung-Yi Lin)

'''[[Molecular Playground/Lysozime ]]''', Daniella Gonzalez, Thayumanavan Research Group

'''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura, Thayumanavan Research group

'''[[Molecular Playground/TRAIL]]''', Charley Swofford

'''[[Molecular Playground/Taxol]]''', [http://robertsgroup.ecs.umass.edu/ Roberts Research Group] (Rohan Patil)

'''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon, [http://www.biochem.umass.edu/garman/index.html Garman Research Group]

'''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]

'''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Rotello lab (Daniel Moyano-Marino)

'''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Thai lab (Krishna Reddy Raghupathi)

'''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Thai lab (Rami Rajasekar Reddy)

'''[[Molecular_Playground/ERMan1]]''', Johan Sunryd

'''[[Molecular Playground/Insulin]]''', [http://robertsgroup.ecs.umass.edu/ Roberts Research Group] (Whitney Stoppel)

'''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia ([http://www.chem.umass.edu/~cmartin/ Martin] lab)

'''[[Molecular Playground/Human PPCA]]''', Nilima Kolli

'''[[Molecular Playground/Alginate]]''', David Griffin

'''[[Molecular Playground/Glutamate Receptor]]''', [http://chamberslab.com/wp/ Chambers Lab] (Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano)

'''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado

'''[[Molecular Playground/FIH]]''', Knapp Lab, (Cornelius Taabazuing, Breanne Holmes, John Hangasky)

'''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Thai lab (Jiaming Zhuang)

'''[[Molecular Playground/Pancreatic Lipase]]''', [http://www.umass.edu/rotellogroup/ Rotello lab] (Rui Tang)

'''[[Molecular Playground/Trypsin]]''', Thai-Vachet lab (Murage, Gladys)

'''[[Molecular playground/beta 2 microglobulin]]''', Vachet lab (Nick)

''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Thai lab (Jing Guo)

Instructions:

'''We plan to award a prize for the best CBI Molecules page and/or scene!'''

Choose a molecule that is part of your research project.

1. If you don't already have one, request a Proteopedia account and log in. If you are new to Proteopedia, click Help in the navigation box on the left to get started.

2. Make yourself a sandbox page in which you will develop your CBI Molecule scene and description (Enter "User:your name/sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. See example [[User:Lynmarie K Thompson/Sandbox 1]]).

3. Follow the format of the sample CBI molecule page [[Molecular Playground/Bacterial Chemotaxis Receptors]]. Easiest way to do this is to copy this page (in editing mode), paste it into your sandbox page, keep the first paragraph about CBI molecules, and then edit to describe and display your molecule. Your goal is to make this an interesting, nontechnical description of the molecule. If multiple people in one group work on the same molecule, you can each make different scenes for the same CBI molecule and each describe them on the same proteopedia page. Talk with each other about your plans so you are not duplicating efforts.

4. Create an attractive scene for your molecule: use the scene authoring tools in the edit mode to create the view you like, then copy the wiki text into your window.

5. Follow instructions at [[Molecular Playground/Procedures]] as well. But don't "capture the state script for your scene"; that will be done for you (see #7). With your chosen Jmol scene for the Molecular Playground, specify a "banner", which will be projected with the molecule on the Molecular Playground. This should be a short, one-line headline for your scene that includes the name of the molecule and what is important about the scene or the molecule. Remember to design this for the general public, including non-scientists. My example is: "Molecular Playground banner: A bacterial chemotaxis receptor protein used by bacteria to "smell" their environment."

6. When you are happy with your sandbox page, make yourself a permanent Proteopedia page, which will be editable by others. Enter "Molecular Playground/your molecule" (omit quotes) in the search box, then follow the instructions to create a new page with this title. Copy the content of your sandbox to this new page.

7. When you have finished the final version of your page and scene, edit this CBI Molecules page to add a listing and link for your molecule, following the "Bacterial chemotaxis receptors" example above. Please list your lab group, with your name in parentheses. That way more than one name can be associated with a Molecular Playground page (if there are several students on the Molecular Playground page, please indicate your scene with your initials). It would be great to link the lab names to web pages too. Once this link is there, your scene is considered done, and someone will capture the state script for display on the Molecular Playground.

User:Jing Guo

2010-04-30T21:05:48Z

Jing Guo:

User:Jing Guo

2010-04-30T21:05:15Z

Jing Guo:

Molecular Playground/1,3-1,4-beta-D-glucanase

2010-04-30T19:39:02Z

Jing Guo:

==1,3-1,4-beta-D-glucanase==
Endo-1,4-beta-D-glucanases (EGases) form a large family of hydrolytic enzymes in prokaryotes and eukaryotes. In higher plants, potential substrates in vivo are xyloglucan and non-crystalline cellulose in the cell wall. Gene expression patterns suggest a role for EGases in various developmental processes such as leaf abscission, fruit ripening and cell expansion.

<applet size='[450,338]' frame='true' align='right'
caption='YYY' />

{{STRUCTURE_3H0O | PDB=3H0O | SCENE= }}

<scene name='Molecular_Playground/1,3-1,4-beta-D-glucanase/Glucanase/2'>Glucanase</scene>

Molecular Playground/1,3-1,4-beta-D-glucanase

2010-04-30T19:38:09Z

Jing Guo:

Molecular Playground/1,3-1,4-beta-D-glucanase

2010-04-30T19:30:43Z

Jing Guo:

Molecular Playground/1,3-1,4-beta-D-glucanase

2010-04-30T19:17:58Z

Jing Guo:

==1,3-1,4-beta-D-glucanase==
Endo-1,4-beta-D-glucanases (EGases) form a large family of hydrolytic enzymes in prokaryotes and eukaryotes. In higher plants, potential substrates in vivo are xyloglucan and non-crystalline cellulose in the cell wall. Gene expression patterns suggest a role for EGases in various developmental processes such as leaf abscission, fruit ripening and cell expansion.

{{STRUCTURE_3H0O | PDB=3H0O | SCENE= }}

<scene name='Molecular_Playground/1,3-1,4-beta-D-glucanase/Glucanase/1'>TextToBeDisplayed</scene>

Molecular Playground/1,3-1,4-beta-D-glucanase

2010-04-30T19:15:07Z

Jing Guo: New page: ==1,3-1,4-beta-D-glucanase== Endo-1,4-beta-D-glucanases (EGases) form a large family of hydrolytic enzymes in prokaryotes and eukaryotes. In higher plants, potential substrates in vivo are...