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MOLECULAR GENETICS OF DEVELOPMENT AND CELL DIFFERENTIATION IN MOUSE AND MAN

 

The development of complex organs and tissues, such as brain and the hematopoietic system, requires the ordered expression of key transcription factors controlling cell type- and tissue-specific gene expression. Stem cells represent the self renewing compartment of rapidly replicating cell types, as in the hematopoietic system, but are present, in small numbers, also in adult brain, heart and other organs which do not show active cell replication in adults.

The group uses a common set of approaches (conditional and standard targeted mutagenesis in mouse, cell culture and gene transduction, chromatin studies, etc.) to investigate the role of key transcription factors in the development, maintenance and differentiation of a variety of stem cells.

Molecular Computing

Molecular computation is an emerging area of study as a borderline between computational science, chemistry and biology. The objective of this study is to create an information processing mechanism using chemical reactions of biomolecules such as DNA. Other objectives include designing biomolecules and controlling their chemical reactions using information technology. Application of computational science to chemistry and biology will be discussed in this course through explanation of molecular computation and its related fields. 

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Basic extraordinary cell biology

During a recent visit with my 12-year old daughter’s science teacher, I mentioned that I had read a few books on cell biology over the past couple of years and that I was interested in sitting in on one of the upcoming sixth grade science classes–my daughter had mentioned that they were beginning to study cell biology. I mentioned a few of the things that I had found interesting about cells to the science teacher. After noticing my enthusiasm, she retracted her invitation to watch the class and, instead, invited me to teach part of the class. A few days later I made my science teaching debut.

I advised the sixth-graders that although I work as a lawyer during the day, I often read science books, and I often write about science on my website. I told them that I had no serious science education at the Catholic grade school I attended. I didn’t have any biology class at all until I was a sophomore in high school. That was mostly a nuts and bolts class taught by a Catholic nun who failed show the excitement the subject deserved. She also forgot to teach by Theodosius Dobzhansky’s maxim that “nothing in biology makes sense except in the light of evolution.”

I told “my” class that anyone who studies cells with any care will be greatly rewarded. Studying cells is actually autobiographical because “you are made of 60 trillion of cells.” These cells are so small that people cannot even see them.

One of the students then confused trillions for millions. “Keep in mind,” I cautioned, “that a trillion is a million million.” With regard to their size, there is only one human cell–the human ovum–that you can see with the naked eye—it is much bigger than the other cells in your body. Despite its tiny size, the human ovum is so incredibly small that it’s smaller than the period at the end of this sentence. See this wonderful illustration of the size of human cells, and many other small objects.

The volume of a eukaryotic cell is typically 1000 times larger than that of a prokaryotic one.
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I told the students that the study of cells is autobiographical “because each of you is a community of cells. You are a self-organized community.” Even the brain is made of cells. It thinks, even though individual cells don’t think. Individual cells can’t think, but you can think. “How is that for amazing?” One girl raised her hand.

“I don’t understand how this can be. I don’t understand how the body can be made of trillions of cells. How can it possibly work? I have a lot of questions.”

I told her that her questions prove that she “gets it.” Truly, how can something as complex as a human body, or even as complex as a single cell possibly work? It’s amazing that these things work, yet most people more often focus on the times that they break down through disease or aging.

A bacterial cell consists of more than 300 million molecules (not counting water), several thousand different kinds of molecules, and requires some 2000 genes for specification. There is nothing random about this assemblage, which reproduces itself with constant composition and form generation after generation.
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I didn’t claim to have many answers, but I told the students that I was there to share information I learned from my readings. I assured them that studying cells, including human cells, is more amazing than any fictitious story that they had ever read. Part of the reason the study of cells is so amazing is due to the complex anatomy of cells, especially eukaryotic cells. Appreciating much of the magic requires statistics. Some of it comes from the exquisite complexity of individual cells, however, and much of the magic derives from the appreciation that the scientific facts relating to cell biology are somehow true.

I then noticed a few of the students were looking puzzled. I reminded them that the scientific study of cells is not about trust. I was not asking them to trust me or their teacher. In upcoming classes, they will be invited to look into microscopes and see cells, including their own cheek cells or skin cells.  With powerful microscopes we can even see chromosomes. I urged them to investigate more about cells on their own, because there is a wealth of information on the Internet. Go out there and check the evidence; investigate as skeptics. Believe only what you see. That’s what I did, and that’s why I’m excited to learn about cells. And remember that only 400 years ago, no one had any idea that humans were communities of cells. They are privileged to be living in an age where we have such detailed knowledge available to us.

I told the students that the information I would tell them came from a variety of sources, including a book called The Way of the Cell: Molecules, Organisms and the Order of Life, by Franklin M Harold (2001). I’ve inserted several passages from Franklin’s excellent book within this post.  In case it isn’t apparent, this post is a summary of the sorts of things I taught my students. I found myself bouncing around the classroom fielding comments and questions and having a great time. My hope was that a few of the kids might see the subject of cell biology in a more compelling way after seeing me so revved about it. That was my main aim, to share my excitement.

Algorithms in Structural Molecular Biology and Proteomics

Some of the most challenging and influential opportunities for Physical Geometric Algorithms (PGA) arise in developing and applying information technology to understand the molecular machinery of the cell. Our recent work (e.g., [1-20]) shows that many PGA techniques may be fruitfully applied to the challenges of computational molecular biology. PGA research may lead to computer systems and algorithms that are useful in structural molecular biology, proteomics, and rational drug design.

Computational Structure-Based Redesign of Enzyme Activity. PNAS (2009).

Concomitantly, a wealth of interesting computational problems arise in proposed methods for discovering new pharmaceuticals. I'll briefly discuss some recent results from my lab, including new algorithms for interpreting X-ray crystallography [14, 17, 16] and NMR (nuclear magnetic resonance) data [3,9,6,19,10,5,7,18,4], disease classification using mass spectrometry of human serum [12], and protein redesign [13]. Our algorithms have recently been used, respectively, to reveal the enzymatic architecture of organisms high on the CDC bioterrorism watch-list [17,16], for probabilistic cancer classification from human peripheral blood [12], and to redesign an antibiotic-producing enzyme to adenylate a novel substrate [13]. I'll overview these projects, and highlight some of the algorithmic and computational challenges.

Toxicogenomics and Molecular Biology

 

Toxic tort claims, health risk assessments, biomonitoring, crime-scene investigations, and intellectual property cases are increasingly relying on techniques that fall under the realm of molecular biology-based science or "Toxicogenomics." Staying abreast of the rapidly evolving, cutting-edge science in this field is essential to understanding and interpreting health claims and in assessing health risks when molecular biology techniques are being used. Exponent scientists have experience in evaluating and conducting studies in the field of molecular biology, including genomics approaches such as DNA array (gene chip),  real-time Q-PCR, cloning, transgenics, stem-cell therapeutics, RNA anti-sense, knock-outs, and knock-downs; and proteomics approaches such as, recombinant protein expression, cytokine assays, ELISA, radioisotope and immuno-labeling, and protein purification and identification through 1 and 2-D electrophoresis, and column chromatography.

Increasingly, "Gene Array" or DNA profiling and Cytokine arrays are being applied in an effort to understand disease mechanisms at the molecular level. In toxic tort claims, this technology is also being exploited in an to attempt to assign genetic profiles, "footprints," or "molecular signatures” to various chemical exposure scenarios, such as benzene and asbestos in order to validate an injury claim. In many cases there are considerable limitations to the design and interpretation of the scientific studies being used to support these claims. Our strong understanding of biochemistry, molecular interactions, and fate of chemicals in the body ensures a thorough scientific evaluation of molecular biology based approaches used to identify and quantify exposure and potential health effects. As part of an overall review of the science supporting a claim, Exponent scientists can critically evaluate the relevance of molecular mechanisms and techniques that are being invoked in a selected scenario.

As understanding of the molecular mechanisms behind toxicity evolves, government agencies are re-evaluating previously derived regulatory limits, and considering molecular biology-based data in deriving regulatory limits for new chemical compounds. Understanding the new molecular biology–based technology used to evaluate and assess risk of exposure to these chemicals is essential for conducting a weight-of-evidence review to determine new regulatory standards. As biotechnology patent applications increase, the need for third-party expert review is important for maintaining protection of intellectual property and "Freedom to Operate" in commercial research and development programs. Exponent scientists with experience both in the new molecular biology techniques and in regulatory toxicology can evaluate the science that will be used by regulatory agencies to derive these new limits and standards for patent protection.

Regulatory agencies and expert panels of scientists are recommending research and development of tools in the emerging field of "Toxicogenomics" for use in exposure assessment. A National Research Council committee on biomonitoring for environmental chemicals recently recommended the use of molecular biology-based biomonitoring approaches, in order "… to move beyond the traditional approaches of exposure assessment-based on one exposure to one chemical in one environmental medium" to assess multiple exposures and multiple biologic-response pathways using genetic markers of exposure and response.

Exponent has Ph.D.-level scientists who are widely published in the fields of genomics, proteomics, molecular biology, and biochemistry, with experience in designing, executing, and evaluating molecular biology-based studies. Let our scientists assist you in this rapidly evolving and complex field.