Bioinformatics and Genomics News and Views

The relationship between thalassemia and atherosclerosis

Jessica P. — Tue, 09 Mar 2010 13:34:24 +0000

Sardinia is an Italian island where thalassemia incidence is really high. Giving the complications of atherosclerotic disease and the necessity of frequent blood transfusions for thalassemic patients, scientists from the University of Cagliari (Italy) were interested in the relationship between these two diseases.
They provided a genetic analysis of patients affected by thalassemia major or intermedia in comparison with age matched healthy controls, by checking genes involved in iron detoxification and in cholesterol metabolism. Indeed, cholesterol levels are a crucial factor to determine the atherosclerotic lesions as well as iron overload, especially in heart, is important to cause cardiovascular complications. They identified an increase of TNFa and ACAT mRNA levels, involved in iron metabolism and cholesterol metabolism, respectively and a reduction of Hepcidin and ILa. Serum iron levels were higher in patients than in control, while HDLs were lower. Since gene expression was altered in factor that had a key role in cholesterol metabolism rather than in iron homeostasis, scientists suggested that possible cardiovascular complications in patients affected by thalassemia intermedia were due, at least in part, to the occurrence of premature atherosclerotic lesions. By contrast, the role of iron overload was further confirmed in thalassemia major patients. This preliminary study allows clarifying how relationship between important diseases, such as thalassemia and atherosclerosis, may contribute to complicate the clinical profile.

Hela cells, a story lasting 60 years.

Jessica P. — Thu, 04 Mar 2010 15:09:13 +0000

Henrietta Lacks died in 1951 at the Johns Hopkins hospital in Baltimore because of an aggressive form of cervical cancer. She would be probably unknown now, if your cells hadn’t been extracted and cultured as HeLa cells. Scientists of every molecular biology and cellular lab know about these cells because they have used them at least one time or because they have studied their application on biology books. However, it’s very interesting the history about HeLa cells. Henrietta was 31 years old when she died and she had five children. She was the unwitting protagonist of the story, because on 1950s none informed consent was asked her. Doctor Gey and his wife had all scientific merits to make possible HeLa cell culture. They put these cells on Petri dishes; at that time they were performing a lot of experiments to try to culture human cell lines. HeLa cells were able to quickly grow in established conditions, differentially from other cells tested. Dr Gey sent his cells to many laboratories around the world and shared information about culture conditions and so on. This generosity allowed important scientific advances, especially in vaccination field because HeLa cells were firstly used to test and produce the Polio vaccine. Unfortunately, giving their ability to grow also in unfavorable conditions, HeLa cells became one of the most dangerous contaminant agents of other cell lines. The doubt that scientists were using HeLa cells in their experiments rather than breast, prostate or placental cells made necessary further analyses to figure out the true identity of cell lines used. Thus, after almost thirty years from her death, the Hopkins Hospital contacted Henrietta’s children and familiar to invite them donate some blood or tissue samples.
Genetic analyses and blood type were information required by scientists to complete the Henrietta’ profile and recognize HeLa cells from others. Even if the scientific purpose was correct, Henrietta’ family didn’t have all explanation needed to well understand physicians’ operations. This was only one of dark points from an ethical point of view present in this story. Fortunately after Henrietta’s experience, ethical question has acquired great importance in experimental medicine and now informed consent is required for every medical action. Another important issue of this story were the moral and legal questions that arose about the commercial value of something derived from human body. Who may have the copyright of HeLa cells? With these cells several billions of dollars have been gained by pharmaceutical companies, research institutes and so on, but Henrietta’s family haven’t had any benefit. But on other hand, what has been the role of Henrietta in whole story? She was just a poor mother who died too soon.

NatureEvents website

Jessica P. — Tue, 02 Mar 2010 16:26:30 +0000

Are you looking for a specific congress or for some award to fund your work? Have you already visited the NatureEvents.com website? This tool is important for both scientists and companies because is a melting point of several disciplines. Indeed, a large number of events, such as congress, workshop and seminar, are posted, now for free by companies or associations, and this is the best, cheapest and most reliable manner to find new clients or new affiliated in scientific world. Otherwise, for scientists this tool can be important because allow them finding educational events that are maybe less famous, but not for this reason less valuable from a scientific point of view. So, have a look at this website! You will find events divided in sub-categories by countries, by date or by discipline. Each citation has a link to website or contact information related to the event of interest, in order to make easy subscription and a possible attendance. Finally, also companies that work in this field can choose the best meetings which are necessary to participate at, in order to have the better marketing return. Fortunately, this kind of IT tools is now available, because allows scientists being updated and saving time.

Role of natural antioxidant elements in cardiovascular disease prevention

Jessica P. — Sat, 27 Feb 2010 15:55:01 +0000

Natural antioxidant elements consist of carotenoids, vitamins, mineral salt contained in food. These components are important to remove free oxygen derived compounds that are highly reactive and generate lipid peroxidation and DNA damage. Lipid peroxidation is one cause of lipoprotein modifications. In particular low density lipoproteins (LDLs) are intensively modified by free radicals and several forms of altered LDL have been identified.
The overall effect is an increasing likelihood to produce atherosclerotic lesions, followed by an increased risk to have cardiovascular problems. In vitro some evidences about the ability of natural antioxidants to remove free radicals have been observed, but it’s not totally clear what is the significance in human, because clinical studies still are controversial. Even if some studies demonstrated a protective role of natural antioxidants against cardiovascular diseases, it’s quite difficult to evaluate the exact concentration of these components in the serum, and few dose- response studies are available up to date. Vitamin E seems particularly involved in cardiovascular disease protection because low levels of this compound have been measured in patients who had stroke or other cardiovascular problems. Unfortunately, prospective study is a limited tool to evaluate the efficacy of vitamin supplement as a tool to prevent heart failure. Further analyses must be done to ascertain the role of antioxidants in disease prevention; at this time we can still eat a lot of fruit and vegetables for our pleasure.

Novel applications of nanobodies

Jessica P. — Thu, 25 Feb 2010 17:18:41 +0000

Camelid derived single domain peptides are a novel form of antibody which maintain the same antigen binding properties but have greater stability and smaller size than traditional antibody. These molecules can be conjugate with several chromophores, for instance with green fluorescent protein for cellular imaging applications.
A group from the University of Munich (German) applied its deepen knowledge about GFP modifications to nanobodies, this is the name of camelid peptides. The result was an improvement in GFP brightness modulation. By performing a phage display screening, they found out seven different molecules able recognize GFP and enhance or minimize its fluorescent signal. To validate the system, they produced a GFP- tagged oestrogen receptor and a nuclear binding enhancer nanobody, in presence of hormone the receptor moved into the nucleus and GFP signal increased five- fold its brightness. Several applications can be thought for this tool. For instance, nanobodies for each cellular compartment can be useful to determine how the protein of interest tagged with GFP change their position inside the cells in response to specific stimuli. Alternatively, protein- protein interaction can be studied because nanobody can bind one protein and after interaction with the second protein fluorescent signal can be modulated, as well as it should be possible to evaluate the duration of interaction self. A novel and flexible tool is now available for biologists.

CXCR1 in breast cancer

Jessica P. — Tue, 23 Feb 2010 13:26:00 +0000

Scientists from the University of Michigan and the INSERM (France) identified Cxcr1 gene as differentially expressed in cancer stem cells in comparison with other cancer cells in breast malignancies.
CXCR1 is the receptor for interleukin 8 and has been involved in tumour progression and metastasis in several kinds of cancers, such as prostate, glioma, ovarian and breast cancers. Furthermore, IL8 has been implicated in self renewal of stem cells in vitro. French researchers tested some small molecule inhibitors targeting CXCR1 or some antibody against this receptor in order to evaluate the effect on cellular behavior. These inhibitors directly acted versus cancer stem cells and at the same time indirectly induced cell death in bulk tumour. The promising result was that the whole cancer population was eliminated. A possible explanation for this larger effect could be the release of FAS ligand after inhibiting CXCR1 that determined apoptosis in all cancer cells. In animal model CXCR1 inhibitors reduced tumour mass and blocked metastasis, either alone or in combination with other drugs. Another possible approach to block cancer progression by acting on CXCR1 pathway is to interfere with IL8 production. Scientists from the University of Texas demonstrated that siRNA-IL8 reduced tumour weight in comparison to control in animal models. These studies seem really promising but further proof is necessary to validate CXCR1 pathway as a target for therapeutic intervention.

A novel antidepressant therapy

Jessica P. — Mon, 22 Feb 2010 00:35:44 +0000

Current antidepressants usually marketed compensate the low level of serotonin, the main cause of depression, anxiety and mood problems. These compounds selectively block the re-uptake of neurotransmitter into the synaptic space. Serotonin still longer available for the interaction with its receptors located onto the plasma membrane of post synaptic neurons. Unfortunately, clinical studies reported an high variability in the response and some patients acquired resistance after few months of treatment. Furthermore, clinical efficacy has a lag of two or three weeks after starting the therapy, before obtaining significant benefit for patients.
Scientists for the Columbia University demonstrated that a possible responsible of the resistance is an auto-receptor for serotonin located onto the membrane of pre synaptic neurons that regulates serotonin release with negative feedback. Mouse carrying lower level of this receptor than normal mouse showed higher tolerance to environmental stress and other stimuli and a better response to traditional inhibitors. In human, high level of auto- receptor causes low reactivity of amygdale, a brain portion crucial to overcome stress and difficult situations. Inhibitors of this serotonin auto-receptor will be a novel drug useful to treat resistant forms of depression and anxiety or to improve activity of current antidepressant compounds.

Mutational analysis of promoter region

Jessica P. — Wed, 17 Feb 2010 15:08:04 +0000

Promoter region is the regulatory portion of genes that controls transcription. Even if this portion is crucial for finely tuning protein expression, and is known that epigenetic alterations are dangerous for this control, poor knowledge are available about the role of point mutations. Indeed, several point mutations are identified in promoter region, their biological consequence is poorly understood and studied. Scientists of the University of Washington set up an array to screen the effect of mutation on promoter functionality. They analysed all possible point mutations into a core promoter: the construct presented the native sequence, followed by mutated promoter and the transcription fragment. Each construct was codified by a barcode; thus, after transcription, a quantitative measure of transcriptional activity was obtained. In this way, all mutations were screened and quantitatively characterized. A surprising result was that one mutation generated down-regulation of the expression, while two mutations didn’t alter so much the transcriptional activity. A possible explanation was that the interaction between DNA and polymerase was stabilized in presence of one mutation, reducing the capability to move onto DNA molecule. This experiment was performed in vitro with cellular extract. Scientists knew that the best way to accomplish this screening is to use transfected cell lines, and this will be the possible next step.

The value of negative results

Jessica P. — Mon, 15 Feb 2010 13:49:16 +0000

Negative results are similarly important than positive results for science advances. Indeed, a large number if hypothesis could be excluded if we considered negative results from other studies. Unfortunately, negative results are not so easily accepted and published in peer reviewed journal, thus are not available for science community.
Scientists from the German Research Centre for Environmental Health and from the University of Munich spent their time to collect negative results from protein-protein interaction studies and built a database, called “negatome”. They used data from literature search and from structural information retrieved into Protein Data Bank and identified almost two thousand of not interacting pairs. The novelty is that the not-interaction is experimentally demonstrated and published, while in previous work not- interaction was determined from not co-localization: if two proteins are differentially located, they will not interact. This sentence could be true, but is not predictive of interaction, just co-localization. The Negatome can contain some false negative pairs, but in general it can be considered a useful tool to compare and confirm results from immunoprecipitation or two hybrid system or other techniques that usually generate some false positive. We hope that this example should be followed by other databases for negative results.

Monoclonal antibodies

Jessica P. — Fri, 12 Feb 2010 17:35:26 +0000

Monoclonal antibodies are important tool in molecular biology, diagnostics and clinical studies. These protein are produced by a single cells isolated from immunized animals. Current protocol requires an immunization of an animal host, for instance rabbit or mouse; then spleen cells are selected in vitro and B cells are isolated. B cells from spleen are fused with tumoral mouse cells of mieloma in order to stabilize and make possible the B lymphocyte culture. Indeed, B cell culture is difficult to set up and maintain.
The hybridoma technology allows overcoming these difficulties because of genetic transformation of mieloma cells. Finally, hybridomas are serially diluted and the antibodies are obtained from cell hybridomas cultures derived from a single cell. Which are the advantages of monoclonal antibody in respect with polyclonal ones? Monoclonal antibodies are codified by the same gene and none point mutations are present to generate some difference into antibody population. Thus, the whole population is identical and specifically recognizes one antigen. Cross reactivity is reduced with monoclonal antibodies and the interaction between antigen and antibody is usually more stable. Furthermore, this technique is also really flexible because it’s virtually possible to create antibody versus each antigen, when it’s possible to immunize the host animal. Which are the applications for monoclonal antibody? Monoclonal antibodies are currently used in molecular biology and biochemistry laboratories for imaging, western blotting, immunoprecipitation and so on. A lot of protocols are based on antibody use. In diagnostics, monoclonal antibodies are used in ELISA dosage or in flow cytometric analyses, as well as infection detection or pregnancy diagnosis.

Clinical applications of monoclonal antibody are prevalently in oncology. In 1997, the first monoclonal antibody was approved for non- Hodgkin lymphoma treatment. Since this year, several antibodies have been optimized against breast cancer, leukaemia, colon cancer and recently lung cancer. Each antibody recognizes a tumoral antigen and specifically kills only the cells (tumoral) that present that molecule. Thus, adverse effects associated with the use of monoclonal antibodies are reduced if compared with traditional drugs. Based on their specificity, antibodies can be used to carry other useful drugs to cells. For instance, an antibody can be conjugated to radioactive compounds to be addressed to cancer cells. Furthermore, other drugs can be carried into the brain, giving the capability of monoclonal antibody to overcome the blood- brain barrier. Parkinson’s disease can be treated with this approach. Improvement of biochemical characteristics of monoclonal antibodies is one challenge for scientists for the next future. Indeed, it’s important to improve the delivery of monoclonal antibody into all districts of human body. The specificity will be a must if clinical or diagnostic applications are planned for the monoclonal antibody. Furthermore, cheaper technology must be optimized to allow large scale production. Research development in this field is really promising.