Molecular Genetics and Cancer

Trypanosoma cruzi:Host cell infection and intracellular replication

Trypanosoma cruzi is a species of parasitic euglenoid trypanosomes. This species causes the trypanosomiasis diseases in humans and animals in America. Transmission occurs when the reduviid bug deposits feces on the skin surface and subsequently bites; the human host then scratches the bite area which facilitates penetration of the infected feces.



Life cycle

Trypanosoma cruzi life cycle starts in an animal reservoir. These reservoirs are usually mammals, wild or domestic, and include humans. A reduviid bug serves as the vector. While taking a blood meal it ingests T. cruzi. In the reduviid bug, they go into the epimastigote stage. This makes it possible to reproduce. After reproducing through mitosis, the epimastigotes move onto the rectal cell wall. There, they become infectious. Infectious T. cruzi are called trypomastigotes. Then, while the reduviid bug is taking a blood meal from a human, it defecates. The trypomastigotes are in the feces.
The trypomastigotes enter the human host through the bite wound or by crossing mucous membranes. When they enter a human cell, they become amastigotes. This is another reproductive stage. After reproducing through mitosis until a large amount of amastigotes are in a cell, pseudocysts are formed in infected cells. The amastigotes then turn back into trypomastigotes, and the cell bursts. The trypomastigotes swim along to either infect other cells or get sucked up by other reduviid bugs.

Telomeres and Telomerase in Human Stem Cells and in Cancer

Telomerase, a specialized ribonucleprotein reverse transcriptase, is important for long-term eukaryotic cell proliferation and genomic stability, because it replenishes the DNA at telomeres. Thus depending on cell type telomerase partially or completely (depending on cell type) counteracts the progressive shortening of telomeres that otherwise occurs. Telomerase is highly active in many human malignancies, and a potential target for anti-cancer approaches. Furthermore, recent collaborative studies have shown the relationship between accelerated telomere shortening and life stress and that low telomerase levels are associated with six prominent risk factors for cardiovascular disease.

Perspectives on Ocean Science: Drugs from the Sea

Explore the discovery and understanding of marine symbionts that may provide novel sources of new drugs with Scripps Institutions' Margo Haygood

Building the Brain: From Simplicity to Complexity

What are the mechanisms by which neurons differentiate to achieve the spectacular complexity of the brain? Join UCSD's Nick Spitzer as he explains what we know about this process


Marine Genomes: Windows into Ocean Life

How will researchers harness the genetic potential of marine organisms? Join Dr. Terry Gaasterland as she describes how scientists at the new Scripps Genome Center are pioneering research in marine genomes.



Understanding Disease at the Level of Individual Molecules

Join three researchers from UCSD's Department of Chemistry and Biochemistry for a fascinating look at how they are working to find new ways to treat disease by understanding how disease works at the molecular level

Perspectives on Ocean Science: Marine Genomics: Discovering the Secrets of Survival in the Abyss

How do organisms survive the extreme pressures and temperatures of the ocean abyss? Join Dr. Doug Bartlett as he describes genomics research to understand how deep sea bacteria have adapted to these extremes, and how this may lay the groundwork for biotechnology using deep sea bacterial genes. 

Molecules: Breaking and Making Chemical Bonds

Dudley Herschbach, Professor of Science at Harvard and winner of the Nobel Prize for chemistry, delivers the Hitchcock Lecture at UC Berkeley. He explores the fascinating world of molecular science for a general audience as he discusses how molecular bonds are made and broken.

Repairing DNA: Put Best Defense Against Cancer

Cancer occurs when a single cell in the body stops performing its normal function and grows out of control. Damage to DNA can lead to permanent changes, called mutations, which can result in cancerous growth. Lawrence Livermore National Laboratory scientist John Hinz explores how cells repair DNA, the consequences of unrepaired DNA damage, and the fates of individuals born without DNA repair proteins.


Genome Science and Personalized Cancer Treatment

Results from the Human Genome Project are enabling scientists to understand how individual cancers form and progress. This information, when combined with newly developed drugs, can optimize the treatment of individual cancers. Joe Gray, director of Berkeley Lab's Life Sciences Division and Associate Laboratory Director for Life and Environmental Sciences, focuses on this approach, its promise, and its current roadblocks - particularly with regard to breast cancer.

Stem Cell Research Insights


Zebrafish used to visualize blood stem cell generation

Stem cell generation Video

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How to Sequence a Genome

Animated and narrated segments presenting all the essential steps in sequencing a genome. From the NHGRI's Online Education Kit: Understanding the Human Genome Project.


Building Clone Libraries


Sub Clones

E. Coli Storage



Preparing DNA for Sequencing

Sequencing Reactions


Products of Sequencing Reactions

Separating the Sequencing Products


Reading the Sequencing Products


Assembling the Results




Working Draft Sequence


Conclusion

Telomerase and the Consequences of Telomere Dysfunction(Nobel Prize 2009)

Nobel laureate Carol Greider, Ph.D., presents the seventh annual Jeffrey M. Trent Lectureship in Cancer Research

Carol Greider lab is interested in telomere function, the regulation of telomere length and the biochemistry of telomerase. Telomeres are essential for both chromosome stability and for length maintenance. Telomerase is a ribonucleoprotein reverse transcriptase that synthesizes telomere repeats onto chromosome ends. Telomerase is required for telomerase length maintenance: in the absence of telomerase, telomeres shorten progressively.




To understand the telomerase, we initially focused on the well characterized Tetrahymena enzyme. We extensively characterized the functional regions of the Tetrahymena telomerase RNA. Using a reconstitution system, we mapped the essential RNA functional region. To extend this analysis to mammalian telomerase we established the secondary structure of the vertebrate telomerase RNA. We cloned and sequenced telomerase RNA genes from 35 vertebrate species and determined the secondary structure using phylogenetic comparative analysis. We identified four highly conserved domains in the RNA structure and found that the global architecture is conserved from Tetrahymena to human. We are currently analyzing the function of these regions in human and mouse telomerase enzyme.

To understand how telomere functions to provide chromosome stability and how telomerase might play a role in cancer, we generated a telomerase null mouse. Mice that lack the gene encoding the mouse Telomerase RNA (mTR) show progressive telomere shorting during successive breeding. The mice are viable for up to six generations although in the later generations there is severe reduction in fertility due to apoptosis in the germ cells. Crosses of these telomerase null mice to other tumor prone mouse models suggest that under some circumstances tumor formation can be greatly reduced when telomerase is absent. This suggests that telomerase inhibition may be a useful approach to cancer treatment. However when both telomerase and p53 are deleted, an increase in tumor formation is seen. This suggests that the loss of telomerase contributes to genomic instability and may cooperate with loss of p53 in tumor initiation. We tested whether the absence of telomerase increases genetic instability by examining the mutation rate in the absence of telomerase in yeast. We found an increase in terminal deletions and the structure of chromosomes resembled the nonreciprical translocations that are frequently found in human tumors. Thus analysis of chromosome rearrangments in yeast will allow us to dissect the genetic requirements of chromosome stability.

We are using the mTR-/- mice to understand the cellular events that occur when telomere function is lost. Germ cell apoptosis in mTR-/- mice is triggered by short telomeres at the onset of meiosis. Evidence suggests that loss of telomere function leads to a DNA damage checkpoint and subsequent apoptosis. We have ongoing experiments designed to study how a cell recognizes a dysfunctional telomere as DNA Damage.

Text Reference:http://www.hopkinsmedicine.org/pharmacology/research/greider.html

Biological Sequence Analysis



Mining Data from Genome Browsers

Next-Generation Sequencing Technologies



Regulatory and Epigenetic Landscapes of Mammalian Genomes


ClinSeq: A Large-Scale Medical Sequencing Clinical Research Pilot Study

The purpose of ClinSeq is to pilot large-scale medical sequencing (LSMS) in a clinical research setting. By sequencing targeted regions of a person's genome and returning relevant and individual results to that person, we will begin investigating some of the technical, medical and genetic counseling issues that accompany the implementation of LSMS in the clinical setting.

Specifically, we seek to develop the technologic and procedural infrastructure to facilitate this type of research and demonstrate that it is feasible to sequence and interpret large amounts of genomic sequence data and return individual results to subjects.

Human Skin Microflora: DNA Sequence-Based Approach to Examining Hand Disease

The skin creates a barrier between the body and the environment. Using animal models, Dr. Julie Segre's laboratory focuses on the genetic pathways involved in building and repairing this skin barrier. The Segre laboratory estimates that approximately one million bacteria reside on each square centimeter of skin and many common skin conditions are associated with both impaired skin barrier function and increased microbial colonization. Dr. Segre moderated the discussion, answered questions and addressed comments. In addition, the webinar discussed details of the Human Microbiome Project. More: http://www.genome.gov/27535424

Palmitic Acid

Translation: Atomic View

Sliding Clamp


New Perspectives on Menopausal Hormones and Heart Disease

Recent Women's Health Initiative (WHI) studies demonstrated that hormone therapy carries a number of health risks in woman not considered earlier, such as the increased likelihood of blood clots and stroke. Marcia Stefanick, PhD, professor of medicine at Stanford School of Medicine, served as chair of the WHI steering committee and she continues to analyze the project's data for other ill-effects.

Three Faces of P53 Tumor-Suppressor

Nanomanufacturing Technologies

A lecture by Mark Pinto for the Stanford University Computer Systems Colloquium (EE 380). This presentation explores technology challenges in IC nanomanufacturing and reviews the most likely directions needed to sustain the pervasive growth of semiconductor content. Other applications of related nanomanufacturing technologies are also examined.

Isotopes Video

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Inner Workings of Cytochrome P450

The active site of cytochrome P450 contains a heme iron center. The iron is tethered to the P450 protein via a thiolate ligand derived from a cysteine residue. This cysteine and several flanking residues are highly conserved in known CYPs and have the formal PROSITE signature consensus pattern [FW] - [SGNH] - x - [GD] - {F} - [RKHPT] - {P} - C - [LIVMFAP] - [GAD]. Because of the vast variety of reactions catalyzed by CYPs, the activities and properties of the many CYPs differ in many aspects. In general, the P450 catalytic cycle proceeds as follows:
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1. The substrate binds to the active site of the enzyme, in close proximity to the heme group, on the side opposite to the peptide chain. The bound substrate induces a change in the conformation of the active site, often displacing a water molecule from the distal axial coordination position of the heme iron,[6] and sometimes changing the state of the heme iron from low-spin to high-spin. This gives rise to a change in the spectral properties of the enzyme, with an increase in absorbance at 390 nm and a decrease at 420 nm. This can be measured by difference spectrometry and is referred to as the "type I" difference spectrum (see inset graph in figure). Some substrates cause an opposite change in spectral properties, a "reverse type I" spectrum, by processes that are as yet unclear. Inhibitors and certain substrates that bind directly to the heme iron give rise to the type II difference spectrum, with a maximum at 430 nm and a minimum at 390 nm (see inset graph in figure). If no reducing equivalents are available, this complex may remain stable, allowing the degree of binding to be determined from absorbance measurements in vitro
2. The change in the electronic state of the active site favors the transfer of an electron from NAD(P)H via cytochrome P450 reductase or another associated reductase This takes place by way of the electron transfer chain, as described above, reducing the ferric heme iron to the ferrous state.
3. Molecular oxygen binds covalently to the distal axial coordination position of the heme iron. The cysteine ligand is a better electron donor than histidine, with the oxygen consequently being activated to a greater extent than in other heme proteins. However, this sometimes allows the bond to dissociate, the so-called "decoupling reaction", releasing a reactive superoxide radical, interrupting the catalytic cycle.
4. A second electron is transferred via the electron-transport system, either from cytochrome P450 reductase, ferredoxins, or cytochrome b5, reducing the dioxygen adduct to a negatively charged peroxo group. This is a short-lived intermediate state.
5. The peroxo group formed in step 4 is rapidly protonated twice by local transfer from water or from surrounding amino-acid side chains, releasing one water molecule, and forming a highly reactive iron(V)-oxo species.
6. Depending on the substrate and enzyme involved, P450 enzymes can catalyse any of a wide variety of reactions. A hypothetical hydroxylation is shown in this illustration. After the product has been released from the active site, the enzyme returns to its original state, with a water molecule returning to occupy the distal coordination position of the iron nucleus.

S: An alternative route for mono-oxygenation is via the "peroxide shunt": interaction with single-oxygen donors such as peroxides and hypochlorites can lead directly to the formation of the iron-oxo intermediate, allowing the catalytic cycle to be completed without going through steps 3, 4 and 5. A hypothetical peroxide "XOOH" is shown in the diagram.

C: If carbon monoxide (CO) binds to reduced P450, the catalytic cycle is interrupted. This reaction yields the classic CO difference spectrum with a maximum at 450 nm.

Because most CYPs require a protein partner to deliver one or more electrons to reduce the iron (and eventually molecular oxygen), CYPs are properly speaking part of P450-containing systems of proteins. Five general schemes are known:

* CPR/cyb5/P450 systems employed by most eukaryotic microsomal (i.e., not mitochondrial) CYPs involve the reduction of cytochrome P450 reductase (variously CPR,POR, or CYPOR) by NADPH, and the transfer of reducing power as electrons to the CYP. Cytochrome b5 (cyb5) can also contribute reducing power to this system after being reduced by cytochrome b5 reductase (CYB5R).
* FR/Fd/P450 systems which are employed by mitochondrial and some bacterial CYPs.
* CYB5R/cyb5/P450 systems in which both electrons required by the CYP come from cytochrome b5.
* FMN/Fd/P450 systems originally found in Rhodococcus sp. in which a FMN-domain-containing reductase is fused to the CYP.
* P450 only systems, which do not require external reducing power. Notably these include CYP5 (thromboxane synthase), CYP8, prostacyclin synthase, and CYP74A (allene oxide synthase).

Induced-Fit Model Video

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In 1958, Daniel Koshland suggested a modification to the lock and key model: since enzymes are rather flexible structures, the active site is continually reshaped by interactions with the substrate as the substrate interacts with the enzyme. As a result, the substrate does not simply bind to a rigid active site; the amino acid side chains which make up the active site are molded into the precise positions that enable the enzyme to perform its catalytic function. In some cases, such as glycosidases, the substrate molecule also changes shape slightly as it enters the active site. The active site continues to change until the substrate is completely bound, at which point the final shape and charge is determined.

Fatty Acids

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Diabetes Video

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DNA - acridine complex structure Video

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Cohesion Transport Video

The major mechanism for long-distance water transport is described by the cohesion-tension theory, whereby the driving force of transport is transpiration, that is, the evaporation of water from the leaf surfaces. Water molecules cohere (stick together), and are pulled up the plant by the tension, or pulling force, exerted by evaporation at the leaf surface.

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Water will always move toward a site with lower water potential, which is a measure of the chemical free energy of water. By definition, pure water has a water potential of 0 MegaPascals (MPa). In contrast, at 20 percent relative humidity, the water potential of the atmosphere is -500 MPa. This difference signifies that water will tend to evaporate into the atmosphere. The water within plants also has a negative potential, indicating water will tend to evaporate into the air from the leaf. The leaves of crop plants often function at -1 MPa, and some desert plants can tolerate leaf water potentials as low as -10 MPa. The water in plants can exist at such low water potentials due to the cohesive forces of water molecules. The chemical structure of water molecules is such that they cohere very strongly. By the cohesion-tension theory, when sunlight strikes a leaf, the resultant evaporation first causes a drop in leaf water potential. This causes water to move from stem to leaf, lowering the water potential in the stem, which in turn causes water to move from root to stem, and soil to root. This serves to pull water up through the xylem tissue of the plant.

Cdk2 Video

Cyclin-dependent kinase 2 also known as CDK2 is a human gene.The protein encoded by this gene is a member of the cyclin-dependent kinase family of Ser/Thr protein kinases. This protein kinase is highly similar to the gene products of S. cerevisiae cdc28, and S. pombe cdc2. It is a catalytic subunit of the cyclin-dependent kinase complex, whose activity is restricted to the G1-S phase of the cell cycle, and is essential for the G1/S transition. This protein associates with and is regulated by the regulatory subunits of the complex including cyclin E or A. Cyclin E binds G1 phase Cdk2, which is required for the transition from G1 to S phase while binding with Cyclin A is required to progress through the S phase. Its activity is also regulated by phosphorylation. Two alternatively spliced variants and multiple transcription initiation sites of this gene have been reported.

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Inhibitors
Known CDK inhibitors are p21Cip1 (CDKN1A) and p27Kip1 (CDKN1B). Drugs which inhibit Cdk2 and arrest the cell cycle may reduce the sensitivity of the epithelium to many cell cycle-active antitumor agents and therefore represent a strategy for prevention of chemotherapy-induced alopecia.

Cell ATP release Video

The major energy currency molecule of the cell, ATP, is evaluated in the context of creationism. This complex molecule is critical for all life from the simplest to the most complex. It is only one of millions of enormously intricate nanomachines that needs to have been designed in order for life to exist on earth. This motor is an excellent example of irreducible complexity because it is necessary in its entirety in order for even the simplest form of life to survive.
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cAMP Signaling Video

Cyclic adenosine monophosphate (cAMP, cyclic AMP or 3'-5'-cyclic adenosine monophosphate) is a second messenger important in many biological processes. cAMP is derived from adenosine triphosphate (ATP) and used for intracellular signal transduction in many different organisms, conveying the cAMP-dependent pathway.
cAMP is synthesised from ATP by adenylyl cyclase located on the inner side of the phospholipid bilayer. Adenylyl cyclase is activated by a range of signaling molecules through the activation of adenylyl cyclase stimulatory G (Gs)-coupled receptors and inhibited by agonists of adenylyl cyclase inhibitory G (Gi)-protein-coupled receptors. Liver adenylyl cyclase responds more strongly to glucagon, and muscle adenylyl cyclase responds more strongly to adrenaline.

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Mechanism

Activation

Each PKA is a holoenzyme that consists of two regulatory and two catalytic subunits. Under low levels of cAMP, the holoenzyme remains intact and is catalytically inactive. When the concentration of cAMP rises (e.g., activation of adenylate cyclases by G protein-coupled receptors coupled to Gs, inhibition of phosphodiesterases that degrade cAMP), cAMP binds to the two binding sites on the regulatory subunits, which leads to the release of the catalytic subunits.

Catalysis

The free catalytic subunits can then catalyse the transfer of ATP terminal phosphates to protein substrates at serine, or threonine residues. This phosphorylation usually results in a change in activity of the substrate. Since PKAs are present in a variety of cells and act on different substrates, PKA and cAMP regulation are involved in many different pathways.

The mechanisms of further effects may be divided into direct protein phosphorylation and protein synthesis:

* In direct protein phosphorylation PKA directly either increases or decreases the activity of a protein.
* In protein synthesis PKA first directly activates CREB, which binds the cAMP response element, altering the transcription and therefore the synthesis of the protein. This mechanism generally takes longer time (hours to days).

Inactivation
PKA is thus controlled by cAMP. Also, the catalytic subunit itself can be down-regulated by phosphorylation.

Downregulation of protein kinase A occurs by a feedback mechanism: One of the substrates that is activated by the kinase is a phosphodiesterase, which quickly converts cAMP to AMP, thus reducing the amount of cAMP that can activate protein kinase A.


Anchorage

The 2 regulatory subunits of protein kinase A are important for localizing the kinase inside the cell, with the aid of A-kinase anchoring protein (AKAP), AKAP binds both to the regulatory subunits and to either a component of cytoskeleton structure or a membrane of an organelle, anchoring the enzyme complex to a particular subcellular compartment.

The catalytic function of protein kinase A would sometimes couple with the AKAP, binding PKA together with phosphodiesterase to form a complex that functions as a signal module. For example, an AKAP locating near the nucleus of a heart muscle cell, would bind to both PKA and phosphodiesterase that hydrolyzes cAMP. As phosphodiesterase contributes to the steady low concentration of cAMP in unstimulated cells, as the cell is stimulated, PKA is then responsible for the activation of phosphodiesterase (adjacent to PKA) in order to lower the concentration of cAMP. In this condition, as PKA and phosphodiesterase have formed a complex, the proximity increases the efficiency of PKA's activity.