Thursday, November 1, 2012

Stem Cell Problem: Solved?

Introduction:
An important part a scientist’s work is being aware of the ethical issues surrounding their research and the implications these have on the wider community. Some scientists dedicate their careers to resolving these ethical issues. The winners of the 2012 Nobel Prize in Physiology or Medicine, John Gurdon and Shinya Yamanaka, have pioneered a method which hopefully represents a big step towards solving the ethical issues involved in the use of Stem Cells.
 
The Stem Cell Problem:
Imagine that there was a potential cure for illnesses such as Alzheimer’s, heart disease, spinal cord injuries, or any number of others. Then assume that in order to achieve this, an unborn embryo has to be destroyed. What would you do? This dilemma is at the heart of the Stem Cell Problem.
Embryonic Stem Cell’s (ES) are used in a number of areas of research. The use of these cells is controversial since they are taken from human embryos, initially created for In Vitro Fertilisation (IVF) but not implanted, these ‘spare’ embryos are then donated to scientific research. Unfortunately, during the course of the research the embryo is destroyed; a fact which has led some organisations, such as the Catholic Church, to claim that research using ES cells is tantamount to murder.
The reason ES cells are so important to medical research is that certain properties, only possessed by these young cells, makes them ideal for therapeutic manipulations. Mature cells in the human body are highly specialised towards their function, whether this is in the blood, liver, brain or elsewhere. However, stem cells are immature cells which have yet to develop into their final specialised form. Stem cells act as the body's master cells, providing the source material for all other cells. When required, the stem cell is stimulated by certain factors in its environment and eventually develops into a specific mature cell type, for example a blood cell. This means that an embryonic stem cell has the potential to become any cell in the body, given the right environment! ES cells are also able to replicate themselves many times over, unlike specialised adult cells. Therefore these cells are invaluable to scientists investigating cell behaviour and methods for regenerating damaged tissue.They could transform medicine by regenerating tissue for diseases ranging from blindness to Parkinson's disease. The therapeutic uses for stem cells range from understanding cancer to regenerating tissue in a whole number of degenerative disorders.
Creating embryo-like stem cells without destroying embryos gets round a key controversy by avoiding the need to process embryos left over at fertility clinics - a system that has led to political objections in the United States and elsewhere.
 
The journey to the Solution:
At 15, Gurdon was ‘bottom of the bottom form’ in biology and told his dream of becoming a scientist was completely ridiculous. Not only did he obtain the lowest marks in biology of all the 250 boys in his year but his school report in 1949 described his grasp of the subject as ‘disastrous’. Today, that school report, written by a museum curator drafted in to teach after the war, hangs in a frame in his office. The young Sir John scored just 2 out of 50 for one piece of work and repeatedly got into trouble for insisting on doing things his own way, rather than listening. Despite being ‘bottom of the bottom form’ in biology, he went on to study zoology at Oxford.
Sir John, now married with two children, said: ‘When there are problems, like when an experiment doesn’t work, which often happens, it is nice to remind yourself that perhaps after all you are not so good at this job and the schoolmaster may have been right
In 2012, as he share the  Nobel Prize for Medicine, for work he began 50 years ago and Yamanaka capped with a 2006 experiment that has possibillity of transforming the field of "regenerative medicine”. His landmark discovery was initially met with scepticism, as the journey from immature to specialised cell was previously deemed irreversible. But his theory became accepted when it was confirmed by other scientists. More than four decades later, in 2006, Prof Yamanaka discovered how mature cells in mice could in fact be turned back to their youthful state. More than 40 years after Gurdon's discovery, in 2006, Yamanaka showed that a surprisingly simple recipe could turn mature cells back into primitive cells, which in turn could be prodded into different kinds of mature cells. Basically, the primitive cells were the equivalent of embryonic stem cells, which had been embroiled in controversy because to get human embryonic cells, human embryos had to be destroyed. Yamanaka's method provided a way to get such primitive cells without destroying embryos.
The duo, John Gurdon, 79, and Shinya Yamanaka, 50, discovered ways to create tissue that would act like embryonic cells, without the need to collect the cells from embryos. These two researcher have made extraordinary advances in cell reprogramming. Their pioneering work has given scientists a clearer understanding of how cells function and also provided a method of obtaining stem cells from adult tissue. Thus, potentially solving the ethical issues surrounding the use of ES cells in research.
 
The process: Cell Reprogramming:
In 1962, at University of Cambridge, Gurdon transferred a nucleus (the part of the cell which contains DNA) from an adult frog cell into a frog egg cell. The egg developed into a normal tadpole, showing that DNA from a specialized adult cell could be reprogrammed to function in a developing embryo. This was a landmark discovery since, up until this point; Scientists thought it was impossible to turn adult tissue back into stem cells as it loses certain components of their DNA so could not function as part of a developing cell. Gurdon’s work showed that this wasn’t the case proving that mature differentiated cells contain a full complement of DNA; it’s just that some of the DNA in mature cells is inactive. This has also showed that the DNA in mature cells still had its ability to drive the formation of all cells of the body. At that time, the discovery had "no obvious therapeutic benefit at all," Gurdon told reporters in London. "It was almost 50 years before the value — the potential value — of that basic scientific research comes to light," he said. In 1997, the cloning of Dolly the sheep by other scientists showed that the same process Gurdon discovered in frogs would work in mammals.
More than 40 years later, Yamanaka produced mouse stem cells from adult mouse skin cells by inserting a small number of genes. His breakthrough effectively showed that the development that takes place in adult tissue could be reversed, turning adult tissue back into cells that behave like embryos. He developed a line of cells called induced Pluripotent Stem Cells (iPSCs). He and his colleagues adjusted the expression of certain components within adult cells, enabling them to revert back to their young, stem-cell, form. These reprogrammed cells had similar characteristics to embryonic stem cells, including the ability to mature into a variety of different cell types. Yamanaka then used the same technique with human adult cells, reverting them to a state similar to an ES cell, further developing his concept to be used in the study of human cells and diseases. As they display many of the important properties found in ES cells, iPSCs could potentially be used as a replacement for ES cells, thus eliminating the controversy surrounding the use of embryonic cells in research.
Reprogrammed cells - known as induced pluripotent stem cells, oriPS cells - offer an ethically neutral alternative .Not only are these stem cells ethically sound but they are a perfect match for the person who donated the skin. This raises the prospect of people being given hearts or sperm or eggs or retina generated in a lab from a sliver of skin taken from their hand. In the short-term, tissue from such cells offers a window into brains ravaged by diseases such as Alzheimer’s and Parkinson’s and allows thousands of chemicals to be rapidly tested to see if they have potential as drugs. As patients may one day be treated with stem cells from their own tissue, their bodies might be less likely to reject them.
"The eventual aim is to provide replacement cells of all kinds," Gurdon's institute explains on its website. "We would like to be able to find a way of obtaining spare heart or brain cells from skin or blood cells. The important point is that the replacement cells need to be from the same individual, to avoid problems of rejection and hence of the need for immunosuppression."
In just six years, Yamanaka's paper has already been cited more than 4,000 times in other scientists' work.In a news conference in Japan, he thanked his team of young researchers: "My joy is very great. But I feel a grave sense of responsibility as well."
In announcing the $1.2 million award, the Nobel committee at Stockholm's Karolinska Institute said the discovery has "revolutionized our understanding of how cells and organisms develop.”The discoveries of Gurdon and Yamanaka have shown that specialized cells can turn back the developmental clock under certain circumstances," the committee said. "These discoveries have also provided new tools for scientists around the world and led to remarkable progress in many areas of medicine." Recently, Japanese scientists reported using Yamanaka's approach to turn skin cells from mice into eggs that produced baby mice.

Applications:
The potential of iPSCs doesn’t stop at replacing ES cells. They could also herald a major advance in the science behind organ transplantation. Since, ES cells can both regenerate themselves several times over and become any cell type; their use in the replacement of damaged tissue is now being studied. Meaning it may soon be possible for patients to receive transplants composed of reprogrammed cells (iPSC’s) from their own bodies. This would solve the major problem of transplant rejection from donated tissues, caused by the recipient’s body recognizing the donated organ as foreign. In theory, an iPSC-derived tissue would not be rejected as it would be made from the patient’s own cells. In future, scientists would like to build on the work by John Gurdon and Shinya Yamanaka to create replacement tissues for treating diseases like Parkinson's and diabetes, and for studying the roots of diseases in the laboratory — without the ethical dilemma posed by embryonic stem cells.
Experts agreed that the pioneering work by the two new Nobel laureates had changed the field of stem cell research. Still, many experts believe the true promise of iPS cells is as unique  research tools, rather than necessarily forming the basis of new medical therapies. They have a key advantage over embryonic stem cells in that researchers can take them from people with a known disease, offering a window into how currently incurable illnesses develop at the cellular level. Already, researchers have made iPS cells from patients with Gaucher's disease, Down Syndrome, Parkinson's and diabetes. "I see iPS cells more for use in drug discovery and in understanding the mechanism of different diseases, rather than therapy," said Dusko Ilic, a senior lecturer in stem cell science at King's College London. Traditionally, researchers have used stand-ins for human tissue such as yeast, flies or mice for their drug research. Now, they can use human cells containing a complete set of the genes that resulted in a particular disease.
"Everyone who works on developmental biology and on the understanding of disease mechanisms will applaud these excellent and clear choices for the Nobel Prizes," said John Hardy, professor of Neuroscience at University College London. "Countless labs' work builds on the breakthroughs they have pioneered." Yamanaka deserves extra credit for overcoming fierce objections to the creation of embryos for research, reviving the field, said Julian Savulescu, director of Oxford University's Uehiro Centre for Practical Ethics. "Yamanaka has taken people's ethical concerns seriously about embryo research and modified the trajectory of research into a path that is acceptable for all," Savulescu said. "He deserves not only a Nobel Prize for Medicine, but a Nobel Prize for Ethics."

Problem Solved?
The science of iPS cells is still in early stages. Among concerns is the fear that implanted cells could grow out of control and develop into tumors. Some scientists say stem cells from embryos may prove more useful against disease than iPS cells, and the ethics of working with embryos should be defended. Nevertheless, since Yamanaka published his findings the discoveries have already produced advances. The techniques are being used to grow cells in laboratories to study disease, the chairman of the awards committee, Urban Lendahl, told Reuters. "You can't take out a large part of the heart or the brain or so to study this, but now you can take a cell from, for example, the skin of the patient, reprogramme it, return it to a pluripotent state, and then grow it in a laboratory," he said.
Recently, however, different research groups have noticed problems with iPS cells, suggesting they may not be as good as embryonic ones. In one study, iPS cells died more quickly and another found multiple genetic mutations, raising concerns that they could cause tumors. Despite this, Japanese researchers hope to test iPS cells in clinical trials for a form of blindness as early as next year - catching up with recent successful eye trials using embryonic stem cells. Researchers in the West are generally more wary.
"There is a bit of a divergence between Japan and the rest of the world on this," Chris Mason, professor of regenerative medicine at University College London, told Reuters. "Scientists in Japan are trying to move very rapidly towards clinical trials of iPS cells, whereas many of us still feel there are a lot of issues to overcome, especially in terms of safety."
The future potential for reprogrammed cells is that they could be taken from sick people who could have their own "person specific cell replacement" to mend damaged organs or tissues. But key worries include the fact that iPS technology involves using genes which could also be tumor-inducing in some circumstances and that other as-yet undetected problems might crop up after the new cells have been put into patients.
Gurdon played down such worries and said regulatory authorities and governments should take a step back and let patients assess the potential benefits and risks for themselves. "If you explain to a patient what can be done, and what might be the downside - then you should let the patient choose. Don't have ethicists or ... doctors or whoever say  you may or may not have replacement cells," he told reporters.

Last Word:
Many scientists would agree that the work undertaken by Gurdon, Yamanaka and their colleagues is incredibly exciting. It represents a great leap forward in our understanding of how cells work and new ways of studying them in a controversy-free environment.
So, does this Nobel prize-winning work signal a solution to the Stem Cell Problem? Alas, no. It is unclear whether iPSCs and ES cells are equivalent on the molecular level, casting doubt on the likelihood of iPSCs being able to completely replace ES cells in research. Another problem, as with many newly discovered techniques, is that the long-term effects of these technologies are unknown. For example, there are concerns that cells derived from any form of stem cells have a tendency to become cancerous. There has also been a surprising report that iPSCs still produce an immune response when transplanted in mice, which would lead to transplant rejection. This  Nobel Prize-winning discovery offers a way to skirt around ethical problems with human embryos, but safety concerns make their future use in treating disease uncertain.
So, unfortunately we still don’t have a comprehensive solution to the Stem Cell Problem. However, this does not detract in any way from the discoveries of Gurdon, Yamanaka and their colleagues, and there is no doubt that their innovation, expertise and skills should have been rewarded by the Nobel Prize. Only time will tell just how much more useful their discoveries will be.
 

Tuesday, October 16, 2012

Diphtheria Toxin: The Magic Bullet

DT:
The lethal protein Diptheria Toxin (DT) is secreted by Diptheria causing Corynebacterium diphtheriae, in particular its pathovarieties gravis, intermedius and mitis. Intriguingly, DT is specified for by tox, a gene carried on one of a family of related corynebacteriophages integrated into the host chromosome of C. diphtheriae. That DT is encoded by the prophage gene was demonstrated when non-pathogenic strains of C. diphtheriae became lysogenically converted upon infection with a bacterial virus known as beta phage. Moreover, mutant phages gave rise to nontoxic material that cross-reacted with diphtheria antitoxins, even though being significantly shorter than full-length DT.

For complete article click on the link below:
Diptheria Toxin: The Magic Bullet

Saturday, June 16, 2012

Structure Refinement by X-ray Crystallography

Please click on the link below for Powerpoint Presentation on-Structure Refinement by X-ray Crystallography:
https://docs.google.com/presentation/d/1uWTa6aVI9ZpPaibyh0hnRPqUUmbqRfV5q2hfat5Yn5g/edit

This presentation was given by me at Graduate Program ‘Calcium Signaling and Cellular Nanodomains’ in Homburg, Germany: GK1326.

Saturday, May 19, 2012

Expanded dynamic range of fluorescent indicators for Ca+2 by circularly permuted yellow fluorescent proteins

For the powerpoint presentation on the topic please click on the link below:

https://docs.google.com/presentation/d/15QN0ZrqU9fzb1s6rKHiPzZPKYQjIpy4-mVrM4WO2OnM/edit

The presentation was given at Graduate Program ‘Calcium Signaling and Cellular Nanodomains’ in Homburg, Germany: GK1326.

Wednesday, April 25, 2012

Study of growth property of complement C2 produced by THP-1 cells using the chemical agents –Histamine, Imidazole and β- Glycyrrhetinic acid

ABSTRACT:

Despite significant research on the role of inflammation and immunosurveillance in the immunologic microenvironment of cancer, little attention has been given to the oncogenic capabilities of the complement cascade. The complement system is the major branch of the humoral immune system.  Complement components C2 and factor B are essential for the classical and alternative pathways of complement activation, respectively, because they provide catalytic subunits for the C3 and C5 convertases, both of which are key enzymes for the complement system. Monocytes and macrophages synthesize complement proteins, thus providing an essential local source of these proteins in vivo which serve as a first-line host defense mechanism. The recent findings have shown that complement factor especially Factor B and C2 facilitates cellular proliferation and regeneration. We address this hypothesis using chemical agents Histamine, Imidazole and β- Glycyrrhetinic acid who individually influence the factor C2 production in THP-1 cells (human monocytic leukemia cell line). We investigated the growth property of complement C2 by studying the effect of these three chemical agents on the growth of THP-1 cells in time and concentration dependent manner. In this study, to our knowledge we have shown that the Complement C2 has a proliferating effect on monocytic leukemia cells. Additionally, the results show that these three chemical agents do have an influence on each other’s growth properties. Given that the traditionally held functions for the complement system include innate immunity and cancer defense, our study suggests a new way of thinking about the role of complement proteins in monocytes especially human monocytic leukemia. These results may give us leads for the treatment of monocytic leukaemias like AML-M5 which are difficult to treat.

Key words: Cancer, Complement C2, Factor B, Histamine, Imidazole and β- Glycyrrhetinic acid, THP-1, AML-M5.

For the whole article click on the link below:

https://docs.google.com/open?id=0BzdHWb7McaBDRG0tNmNFTGg2Tzg 

Tuesday, April 3, 2012

Differentiation Therapy and AML

Abstract:

Acute myelocytic leukaemia (AML) is a clonal disorder that is the consequence of acquired somatic mutations in hematopoietic progenitor cells that block normal differentiation and cell death and confer a proliferative growth advantage (Wang R. et. al., 2006). AML is basically a group of malignant bone marrow neoplasms of myeloid precursors of white blood cells.

The symptoms can be aspecific: asthenia, pallor, fever, dizziness and respiratory symptoms. Diagnostic methods include blood analysis, bone marrow aspirate for cytochemical, immunological and cytogenetical analysis, and cerebrospinal fliud (CSF) investigations. Treatment includes intensive multidrug chemotherapy and in selected cases allogenic bone marrow transplantation. Nevertheless, outcome of AML remains poor with overall survival of 35-60%. New therapeutics are required to increase the probability of cure in this serious disorder (Verschuur A. C. et. al., 2004).

Differentiation therapy has been successful as a novel treatment for APL. Several compounds including dimethyl sulfoxide, retinoic acid, phorbol ester and 1, 25-dihydroxy vitamin D3 induce AML cells to differentiate toward mature cells. Among them, retinoic acid induces AML cells to differentiate toward granulocytes, whereas 1, 25-dihydroxy vitamin D3 induces AML cells to differentiate toward monocytes (Hyun-Ock Pae a,b et. al., 2001). The following is the overview of advancement in Differentiation therapy against AML specifically AML-M5.

Key words:
AML, Hematopoietic, Symptoms, Daignostic, Therapeutics, Differentiation Therapy.

For full review click on the link below:
https://docs.google.com/open?id=0BzdHWb7McaBDM3VZMEdMS3pSdm1TSEJJbzc5UVNCUQ

Sunday, March 18, 2012

Study of growth property of complement C2 produced by THP-1 cells using the chemical agents –Histamine, Imidazole and β- Glycyrrhetinic acid

Complement System:

The complement system is the major branch of the humoral immune system. It offers a powerful defense against infection and is tightly regulated to prevent damage to self by functionally equivalent soluble and membrane regulators (Kindt T. J., 2007).

The complement system consists of a series of plasma proteins that plays an important role in host defence. There are three pathways to complement activation. The classical pathway initiates with the formation of an antibody C1q complex on the surface of a pathogen or pathogen infected cell. This complex, in turn, activates C2 via serine proteases and is itself also a serine protease. The protein C2a combines with newly cleaved protein C4a to generate a C3 convertase, C2aC4b. C3b forms the central protein complex of the complement system either by binding to complement receptors or by complexing with C2aC4b to form C5 convertase, C2aC4bC3b. This complex can bind and stabilize C5a that forms the central effector function of the complement system around which proteins C5-C9 will bind and cooperatively lyse the cell (Kindt T. J., 2007). The mannose binding pathway has a similar cascade as the classical pathway but functions independently of antibody formation. Instead, MASP1 (Mannan-binding lectin serine protease 1) and MASP2 (Mannan-binding lectin serine protease 2) binds to the mannose structures commonly found on pathogens. The Mannan-binding lectin complex is closely homologous to C1q and can activate C2 and C4. In the absence of sialic acid sugars present on normal somatic cells and which are rare on pathogens, C1q begins a lytic cascade. There is a third pathway for complement activation that begins with spontaneous activation of complement proteins. In this pathway the thioester bonds in C3 undergo hydrolysis which allows the binding of Factor B and its subsequent cleavage by plasma protease Factor D. C3b from C3 and Factor Bb from Factor B combine to form a C5 convertase (Nielsen D. G., 2009).

C3a, C4a and C5a produced acts as anaphylatoxin and regulate vasodilatation, increase permeability of blood vessels, and trigger degranulation and oxidative burst from neutrophils, eosinophiles, and basophiles. They mainly act on specific receptors to produce local inflammatory responses and when secreted in concentrations high enough to invoke a general systemic response, they cause circulatory collapse similar to an IgE mediated allergic response. They modulate the secretion of IL-6, and TNFα from B cells and serve as potent chemoattractants. C5a also works directly on neutrophils and monocytes to increase adhesion molecules, migration, and phagocytosis (Nielsen D. G., 2009).

For the whole artical click on the link below:

https://docs.google.com/open?id=0BzdHWb7McaBDSldlNUkzajBTa200Zkl0bzdKbWo2UQ


Saturday, January 28, 2012

Genomic techniques used to find new diagnostic markers for testicular cancer

Numerous recent studies have demonstrated the use of genomic data, particularly gene expression signatures, as clinical prognostic and diagnostic factors in cancer. This review highlights the usage of genomic analysis to detect diagnostic markers for testicular cancer. The carcinoma in situ (CIS) cell is the common precursor of nearly all testicular germ cell tumours (TGCT). So, there is a particular need of novel markers specific to CIS and various molecular techniques are been used for the same. In particular, the focus is on recent studies showing successful usage of microarray technology, tools used for its analysis and finally a glimpse of role of Comparative Genomic Hybridisation (CGH) in discovery of new markers for CIS diagnosis.


Saturday, January 21, 2012

A Study of Idiotypic Vaccine for Follicular Lymphoma Treatment



Lymphomas are a heterogeneous group of malignancies arising in the lymphoid tissue. Lymphomas are usually treated by a combination of the various therapies for eg : Chemotherapy, Radiotherapy, Bone Marrow Transplant, Stem cells procedure etc (Freedman J. ,2005). But there are lots of complications and side effects related to all the above mentioned methods (Scheinberg D. A. and Jurcic J. W., 2004).

A number of conventional therapeutic options can induce reasonably durable and sequential clinical complete responses in majority of patients (2). However, second and subsequent responses tend to be progressively shorter than those achieved earlier. In particular, most second complete responses obtained through standard chemotherapy last far less than 2 years, and the median duration is 13 months (Illidge T. and Johnson P. W. M., 2005). Follicular lymphomas (FL) are basically indolent diseases. While highly responsive to chemotherapy, the majority of lymphomas in patients remain incurable even by using various combinations of standard chemotherapy drugs. There is a need for novel therapies with less toxicity and more specific targeting of tumor cells (1).

For more on this click on link below:
A Study of Idiotypic Vaccine for Follicular Lymphoma Treatment

Monday, January 16, 2012

Diuretics- Treatment of Congestive Heart Failure


In Cardiovascular disease, the heart of the patient cannot pump enough oxygen and nutrients to meet the body's needs. The chambers of the heart respond by stretching to hold more blood to pump through the body or by becoming stiff and thickened. This helps to keep the blood moving for a short while but, in time, the heart muscle walls weaken and are unable to pump as strongly (2). As a result, the kidneys often respond by causing the body to retain fluid and sodium. If fluid builds up in the organs, the body becomes congested, and congestive heart failure (CHF) is the term used to describe the condition (1). CHF is the cause of significant morbimortality all over the world and its incidence and prevalence are rising. There are a variety of therapy options for CHF, but diuretics play an important role (Acuña C. et. al., 2010).

For futher information click on the link below: