Category Archives: Biochemistry

Researchers have developed a more efficient platform for studying proteins that play a key role in regulating gene expression. The approach uses engineered yeast cells to produce enzyme and histone proteins, conduct biochemical assays internally, and then display the results.

Biomedical and biotech researchers are interested in the mechanisms that allow histones to regulate gene activity, says Alison Waldman, first author of a paper on the work and a Ph.D. student at North Carolina State University. But the conventional tools for histone research are unwieldy and slow. We wanted to develop something faster and less expensive and we did.

In complex organisms, chromosomes are largely made up of DNA and a group of proteins called histones. These histones are important for packing the DNA into chromosomes properly, but also play a role in regulating gene expression. In other words, they help determine when and how specific genes are turned on or off.

One of the features that makes histones challenging to study is that they often have chemical modifications that, alone or in combination, alter the role the histone plays in gene expression.

Histones essentially serve as docking sites for other proteins that influence gene expression, and the chemical modifications we see on histones play a role in determining which proteins have access to a given gene, says Balaji Rao, co-corresponding author of the paper and a professor of chemical and biomolecular engineering at NCState.

And to make matters more complicated, this is a dynamic process. A histone may have no modifications, it may retain a modification for the entire life of the cell, or modifications may be added and removed repeatedly. There is, in short, a lot going on. And enzymes are the catalysts responsible for all of those changes. Basically, enzymes are the mechanism for attaching or removing histone modifications.

So if you really want to understand whats going on with histones, you have to understand the chemical modifications. But if you want to understand the chemical modifications, you need to understand which enzymes are present and what they are doing.

Conventional methods for understanding how enzymes modify a histone involve using one of two techniques. First, you could use chemical synthesis to create enzymes and histone proteins, then conduct an assay in a test tube to see what happens. Second, you could genetically engineer one bacteria to produce an enzyme and engineer other bacteria to produce histone proteins, then harvest the relevant proteins, purify them, then conduct an assay to see what happens.

Our technique uses a genetically modified yeast cell to produce both the enzyme and the histone, Waldman says. The chemical modification takes place within the cell, and the resulting modified histone is sent to and displayed on the surface of the cell.

In other words, the yeast cell makes the relevant proteins, does the assay for you, and then displays the result on top, says Albert Keung, co-corresponding author of the work and an assistant professor of chemical and biomolecular engineering at NCState.

The modified yeast platform is significantly faster than conventional techniques. For example, examining a single enzyme/histone pairing would take a couple days, instead of a week.

But its easier to scale up than existing techniques, so you would save substantially more time if you were looking at a lot of proteins, Keung says.

In addition, there are some proteins that cant be made using chemical synthesis, or that cant be purified, Rao says. Our technique doesnt require chemical synthesis or purification, which means we can look at proteins that were difficult or impossible to assay in the past.

The researchers demonstrated the utility of the technique by having engineered yeast cells produce two types of histones and a well-studied enzyme called p300, which adds a specific acetyl group modification to histones.

Weve shown that our technique works, Waldman says. The next step is to begin expanding the modifications were looking at and scaling up the process.

The paper, Mapping the Residue Specificities of Epigenome Enzymes by Yeast Surface Display, is published in the journal Cell Chemical Biology. The work was done with support from the National Science Foundation, under grant 1830910; and the National Institutes of Health, under grant R21EB023377.

-shipman-

Note to Editors: The study abstract follows.

Mapping the Residue Specificities of Epigenome Enzymes by Yeast Surface Display

Authors: Alison C. Waldman, Balaji M. Rao and Albert J. Keung, North Carolina State University

Published: June 28, Cell Chemical Biology

DOI: 10.1016/j.chembiol.2021.05.022

Abstract: Histone proteins are decorated with a combinatorially and numerically diverse set of biochemical modifications. Here we describe a versatile and scalable platform which enables efficient characterization of histone modifications without the need for recombinant protein production. As proof-of-concept, we first used this platform to rapidly profile the histone H3 and H4 residue writing specificities of the human histone acetyltransferase, p300. Subsequently, a large panel of commercially available antiacetylation antibodies for their specificities, identifying many suitable and unsuitable reagents. Further, enabled efficient mapping of the large binary crosstalk space between acetylated residues on histones H3 and H4 and uncovered previously unreported residue interdependencies affecting p300 activity. These results show that using yeast surface display to study histone modifications is a useful tool that can advance our understanding of chromatin biology by enabling efficient interrogation of the complexity of epigenome modifications.

More here:
Turning Yeast Cells Into Labs For Studying Drivers of Gene Regulation - NC State News

Biochemistry is the branch of science that explores the chemical processes within and related to living organisms. It is a laboratory based science that brings together biology and chemistry. By using chemical knowledge and techniques, biochemists can understand and solve biological problems.

Biochemistry focuses on processes happening at a molecular level. It focuses on whats happening inside our cells, studying components like proteins, lipids and organelles. It also looks at how cells communicate with each other, for example during growth or fighting illness. Biochemists need to understand how the structure of a molecule relates to its function, allowing them to predict how molecules will interact.

Biochemistry covers a range of scientific disciplines, including genetics, microbiology, forensics, plant science and medicine. Because of its breadth, biochemistry is very important and advances in this field of science over the past 100 years have been staggering. Its a very exciting time to be part of this fascinating area of study.

To find out more about careers in biochemistry read our bookletsBiochemistry: the careers guideandNext Steps.

The life science community is a fast-paced, interactive network with global career opportunities at all levels. The Government recognizes the potential that developments in biochemistry and the life sciences have for contributing to national prosperity and for improving the quality of life of the population. Funding for research in these areas has been increasing dramatically in most countries, and the biotechnology industry is expanding rapidly.

The Biochemical Societyaims to inspire and engage people in the molecular biosciences. We offer study and careers advice toschool students,higher education studentsandteachersas well as carrying outpublic engagementevents.

The rest is here:
What is biochemistry? - Biochemistry

Reviewed by Jeffry Nichols, Associate Professor, Worcester State University on 6/1/21

Comprehensivenessrating:3see less

The material covered is fairly similar to other biochemistry textbooks, but does lack some of the details of a more comprehensive biochemistry text (i.e. Lehninger's text). This isn't a negative, just an observation. The order in which the concepts are presented is different, but again still fairly complete.

Content Accuracyrating:4

From what I could tell, the information is accurate. Examples appear to be unbiased and give good everyday correlations to biochemistry ideas.

Relevance/Longevityrating:3

The material for the basics and background for biochemistry are unlikely to change, so in that sense they are relevant. The way in which the material is presented, i.e. the formatting, does make it difficult to follow at times. The tables and figures are not always near the relevant text and often there are figures/tables that appear before the section in the text. Again, this could be a formatting issue.

Clarityrating:4

The text is easy to follow, avoids jargon for the most part (until it needs defining). As mentioned above, references to tables/figures are hard to follow and some tables/figures seem "stuck in" at random points. This hurts the clarity of the text while reading.

Consistencyrating:4

Each chapter sticks to a familiar layout and walks the student through the various topics in a coherent manner.

Modularityrating:3

Overall the text could be broken up, but again, possibly due to formatting, many of the links do not work, interrupting the flow, On all the end of chapter sections, I couldn't get any of the links to work, with a message about "to be developed" or "coming soon". This is unfortunate as these links could be great for further exploration and follow up assignments.

Organization/Structure/Flowrating:3

Yes, the organization is pretty good, although I think the introduction of electron transport and electrochemistry should come after an understanding of WHERE these molecules are coming from, i.e. metabolism, breakdown of sugars, fats, amino acids, etc. This doesn't make it "bad", just no my personal preference. And as mentioned previously, the plethora of tables/figures can be overwhelming when they don't always line up with the discussion of them in the text.

Interfacerating:2

Couldn't get the links to work--although it appears many of the links are "printed" after the end of entire book. So the material might be there, but as it is currently put together, it would be difficult for instructors or students to use these links effectively.

Grammatical Errorsrating:4

From what I can tell, the grammar is fine throughout the text.

Cultural Relevancerating:4

Again, from what I read, I didn't notice any insensitive or offensive parts. Examples were clear and highlighted the biochemical aspects without a need address social or other issues. (which could actually be good depending on the nature of the class and student's interest in how science touch many aspects of our lives)

I have hope for this book, but I couldn't readily tell if this book is being maintained or updated on a regular basis, or if it is just a framework for others to build upon. The organization isn't ideal, and there are problems with links and such, but the overall material and coverage looks pretty good.

Read more from the original source:
Biochemistry: Free For All - Open Textbook Library

Irritable bowel syndrome (IBS) is known as one of the most common irritating gastrointestinal disorders. The mechanism behind IBS is still under investigation and it is thought that it may arose from multi factors among which free radicals have been previously mentioned. Studies have found an association between oxidative stress and IBS; however, little is known about the mechanisms and oxidative stress components status during IBS. One of the key factors playing a central role in oxidative stress network is glutathione reductase (GR). Here we report the GR activity in colon tissue samples during IBS to explore a part of contributing components in IBS pathogenesis.The GR enzyme activity was measured in 15active IBS colon biopsy samples and was compared to our best available age and sex matched colorectal tissue samples from normal marginal tissue of resected colon cancers (n=15). The enzyme activity in the two groups was determined and compared using a commercial GR Assay Kit (Cayman chemical).A significant decrease in GR activity among IBS tissue samples was observed compared to anatomically normal marginal colon tissue samples (p=0.007).Lower GR activity may increase oxidized glutathione there by in turn could contribute as a main component in oxidative stress network. The lower GR activity results in hampered defense mechanism against produced free radical species. This finding may clarify a part of IBS pathogenesis. 2021 Walter de Gruyter GmbH, Berlin/Boston.References

PubMed

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Evaluation of glutathione reductase activity in colon tissue of patients with irritable bowel syndrome. - Physician's Weekly

Dr. Aruna Kilaru, associate professor of biological sciences at East Tennessee State University, and her research team have been working on a new way to combat cardiovascular disease as Americans leading cause of death by studying how to produce more good, monounsaturated fats found in plant oils, often used in cooking, and how to make them more abundant for future generations by using plants that are otherwise genetically deficient.

Saturated fats, or animals fats, increase bad cholesterol, leading to clogging of arteries. Replacing that diet with monounsaturated oils will decrease the risk of heart diseases, said Dr. Kilaru. As such, among various oils, monounsaturated oils such as those in olive and avocado fruits are considered to be heart-healthy.

Saturation refers to the lack of any double bonds in the fatty acid chain while unsaturation refers to the number of double bonds present; a single double bond is referred to monounsaturated and many as polyunsaturated.

Dr. Kilaru noted humans and other mammals lack some of the enzymes necessary to add initial double bonds to fatty acids, making plant oils a critical source of healthy oils. When consumed, these can be converted into other polyunsaturated fatty acids necessary to regulate health and development.

Vegetable oil accounts for 25 percent of human dietary calories and its demand is expected to double by 2030. Increasing production of nutritionally rich oils has become a necessity, added Kilaru.

Having already identified a regulator they believe to be responsible for high amounts of oil in avocado, Dr. Kilaru said ETSU research has made quite a bit of progress in understanding this oil biosynthesis. Now, thanks in part to funds from a recent $200,000 grant from the U.S. Department of Agriculture, the work will continue.

We have already identified one regulator that is likely responsible for high amounts of oil in avocado, said Kilaru. This funding will support continued research on the project by one of our Ph.D. students, Jyoti Behera, for two years and also the research expenses associated with further characterization of the mechanisms by which this novel regulator functions.

Plant oils, mostly stored in plant tissues as triacylglycerols, are not only an important source for human and animal nutrition, but also play important roles in the oil industry and renewable energy sources.

Added Kilaru, There is great diversity in plants tissues with regard to how much and what kind of oil they can synthesize and store. Although biochemists understand how storage oils are made, we do not fully understand what genes are responsible for dictating the content and composition in oil in plants.

Kilaru said her interest in this area of lipid biochemistry research was formed during her postdoctoral work.

I was fascinated by the diverse amounts and types of oils various plant tissues can make. For example, oil palm fruit stores its sugars from photosynthesis in the form of about 90 percent oil in the fleshy part of the fruit while its sister plant, date palm, reserves its energy as 90 percent sugar. I found these distinct abilities of plants both puzzling and fascinating. This work initiated at Michigan State University led to my further interest in using avocado as a system to understand its ability to make high amounts of monounsaturated oleic acid.

She points not only to avocados but also olives. Both synthesize and store heart-healthy, nutritionally rich monounsaturated oils, the good fats, at approximately 60-70 percent in their fleshy fruit but with negligible amounts in their seeds. Palm oil, on the other hand, contains 80 percent saturated fat in its seeds while the fleshy fruit contains only approximately 50 percent saturated oil.

In our lab, we are using avocado as a model system to identify the key regulators of oil content and composition, said Kilaru. Once we identify these key regulators and fully understand their mechanisms, we expect to utilize them to enhance production of nutritionally rich oil in other plants, as well, for human consumption.

The end result of the research could mean a healthier global population.

For more information on the research project, contact Dr. Kilaru at kilaru@etsu.edu or 423-439-5601. More information on the ETSU Department of Biological Sciences can be found at etsu.edu/cas/biology.

Contributed to the Press

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ETSU research leads the way in study to increase diversity of heart-healthy plant oils - Johnson City Press (subscription)

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biochemical diagnostic reagent Market Report Examines Business Opportunity and Worldwide Scope by Forecast 2021 to 2026 The Courier - The Courier