Category Archives: Research

Regain memory by Regenerating your brain cells

The simple flat worm may reveal a method to treat memory loss. Gardeners dislike these flat worms because they eat their valuable earthworms. However, memory scientists adore flatworms. Consider the fact that the non parasitic flatworm, Planarians planarians, has the ability to retain all memory when it regenerates a severed brain within 14 days – yes, these worms can routinely regenerate a severed brain or any other severed body part. This ability is because the worms have a very high percentage of pluripotent stem cells which can develop into any cell type, when required. But how does it retain the memory lost in the severed brain cells? Quoting CBS News :

Apparently losing your head doesn’t have to mean losing your mind. At least, not if you’re a worm.

Brain, Stem cells and Memory – a worm’s role?
You might ask what memory can a lowly worm have? For over two decades Scientists have trained flatworms to show memory traits that can be measured.  An environmental familialization protocol can be measured automatically.

The Flat worm can regenerate any lost body part

The Flat worm can regenerate any lost body part

A trained decapitated worm can exhibit memory retrieval after regenerating a new head. The time limit for memory retrieval is about 14 days. They needed a lesson but the memory returned once stimulated said Dr Levin of Tuft University. This allows scientists to study the relation of the brain and the body in memory. The worm does not automatically lose it’s memory when it loses it’s brain. Where does the worm store it’s memory if not in it’s brain? There is obviously a connection between brain, unknown body cells and memory loss since there is a 14 day window of memory retention in these flatworms.

The unlimited possibilities of severed brain research
Are you thinking what Pursue Natural is thinking? If you are suggesting that perhaps this worm offers the opportunity to study brain regeneration and memory therapy in humans, then yes. Is it possible that the aging Alzheimers Dementia person has a hope that they could regenerate memory – that is if worm research can reveal how pluripotent stem cells in worms retain memory lost in a severed brain. Where and how is memory stored in a worm – if not in the brain?

The answer might help not only aging humans but also any memory loss patients such as athletes, who lose memory during a sports concussion. Pursue Natural hopes it might assist the Autistic individual regain their lost communication skills, which are apparently controlled by an interconnection between the brain and the immune system, in an unknown manner.  Could similar research reveal how communication skills are controlled by the brain and might be “lost” from an unknown environmental trigger/s? Perhaps if these worms could be trained to communicate in a manner that can be measured, then the loss and regain issues related to brain – body may be revealed.

Pluripotent stem cells are obtained from the human donor in need of therapy, can self renew, and largely mitigates any immune reaction. Ethical questions are skipped since these stem cells are not derived from an embryo but the patient’s own cells and can produce specific specialized cells instead of an entire human being.

Quoting Dr. Levin of Tufts University,

“The implications are that learned information can be stored in tissues outside the brain, and that this information can be imprinted upon newly regenerating brains. We do not know how much of this extends to humans, although these worms are not primitive creatures — they have a true centralized brain and many similarities to the human body-plan and genome”.

Memory Regeneration
Who is working on regenerating severed brains?
Scientist around the world are working on this problem since it is a hot topic in biologial research.  Naturally, parts of the world which are uneducated about the positive implications of stem cell research are either behind or unable to participate in this growing biological field.

Tuft University researchers T. Shomrat and M. Levin shed light on the fundamental interface between body patterning and stored memories and published their results in the Journal of Experimental Biology in the summer of this year, 2013.

Many genes have been identified for brain regeneration. Click here for the detailed review of process in 2008 by which the brain is regenerated or the genes involved in brain regeneration by Kiyokazu Agata and Yoshihiko Umesono of Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan.

The worm CNS or central nervous system has been analyzed by the team including K. Agata as early as in 1998 when at  Kobe University, Nada, Kobe, Japan.

The proteins and genes involved in relevant stem cell maintenance are being researched and beginning to be identified. Click here for  the team led by Vittorio Gremigni of Università di Pisa, Pisa, Italy in 2005.

Other science sites discussing the phenomenon of worm brain regeneration.

Scientific Forefront


ZME Science

i09 we come from the future – has a photo of a decapitated worm’s progress to a new head in 7, 10, and 14 days.

CBS News – which has an illustration of the a decapitated worm’s progress to a new head in 7, 10, and 14 days along with a pictorial suggesting what memory is lost with decapitation and how this memory gradually returns.

If you appreciate such research, do encourage these researchers around teh world to continue their work.

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Role of “love hormone” and fresh infant food in autism and allergy

Adding to thirty years of research, scientists have discovered a potential role and mode of action of oxytocin, a naturally occuring brain hormone commonly called the “love hormone”. Neuropsychopharmacologists study the effect of chemicals in the brain and behavior. A team consisting of Dr. Tsien (Stanford University, CA), his graduate student Scott Owen, Dr. Gord Fischell (NYU Langone Medical Center, NY), his graduate student Sebnem Tuncdemir, and collaborators Patrick Bader, and Natasha Tirko resolved how oxytocin increases signaling to neurons and published their findings online on August 4, in the Journal Nature. This hormone can quiet background noise and enhance brain circuits. Individuals with autism lack the ability to filter desirable information processing signals. How this hormone can modulate fast spiking interneurons will continue to be researched, in addition to it’s therapeutic potential in individuals with Autism Spectrum Disorder (ASD). To read the original article in nature click here.

…Neuromodulatory control by oxytocin is essential to a wide range of social1, 2, parental3 and stress-related behaviours4. Autism spectrum disorders (ASD) are associated with deficiencies in oxytocin levels5 and with genetic alterations of the oxytocin receptor (OXTR)6. Thirty years ago, Mühlethaler et al.7 found that oxytocin increases the firing of inhibitory hippocampal neurons, but it remains unclear how elevated inhibition could account for the ability of oxytocin to improve information processing in the brain….

Research in repetitive behavior in ASD
With rising rates of autism spectrum disorder, especially among boys, there is a sense of urgency to find answers. We must not ignore the years of research effort by countless scientists working on how to reduce repetitive behaviors in individuals in the autism spectrum. For example, a 2003 article in the journal Neuropsychopharmacology was published by a team of Neuropsychopharmacologists suggested

….Repetitive behavior in autism spectrum disorders may be related to abnormalities in the oxytocin system, and may be partially ameliorated by synthetic oxytocin infusion…

which you can click here to read.  The problem lies in the fact that a cure is still elusive.  Some parents find that keeping individuals with ASD active in a repetitive sport helps ease the symptom of repetitive behavior, with a regulated repetitive movement resulting in enjoyment rather than frustration. However, it is a challenge getting an ASD individual to concentrate on such a sport.

Role of a love hormone in ASD
Why is it called the “love hormone”? Several articles explain that which you might enjoy reading in eurekalert, by Craig Andrews, by clicking here. What is the role of this hormone in conception to pregnancy and how is it involved in autism spectrum disorder? Researchers will labor on to find the answers.

Role of infant food in allergy
With the observation that certain diets reduce the risk of allergy in infants, one begins to wonder about the role of introduction of chemicals during conception and pregnancy that might interfere with hormones like the love hormone involved in development of normal brain circuits. To read the article on role of processed food and infant allergy click here by the scientist Kate Grimshaw (University of Southampton, UK).  In this article, the scientist published results of research on correlation between infant dietary pattern in first year of infancy and development of food allergy by age two.  Babies brought up on fresh food, presented lower allergy rates.

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SynapDx Corporation lands 15.4 million for Big Autism clinical Study

Geneticists and venture capitalists alike believe that a Massachusetts-based company, SynapDx, can develop the earliest and most informative blood test for autism, and Autism Spectrum Disorders (ASD) using advanced technologies. They specialize in differential expression of certain genes in blood cells that may form the basis of an ASD biomarker. The best diagnostic tests in the near future will combine the knowledge of your genomes, which you inherited from your parents and will pass on to your children, with the technology of computer skills able to handle incredibly large data. A medical technology startup, SynapDx, is currently studying large databases of children who have been clinically diagnosed with autism to discover a shared genomic blueprint. Since all children do not have autism, there might be a particular genomic blueprint among the children that are diagnosed with autism. It is also working on a RNA based blood test to differentiate between patients referred for developmental concerns.  Interested in SynapDx’s clinical study for autism? To learn more click here.

Venture Capital
A group of venture capitalists led by Google Ventures have backed SynapDx autism blood test with 15.4 million, which will help fund the large-scale effort to research 660 children at the same time using advanced computer technology.  The children will be between the ages of 18 months and five years in North America and include children from the Lurie Center of Autism in Massachusetts.  The study will be led by Stan Lapidus, the company CEO. The potential to diagnose children at a very young age, as early as 19 months, is a breakthrough technology currently in clinical trials. Today, an autism diagnosis can be confirmed when a child is 4-5 years, when a child can no longer communicate effectively in society.  This is considered disastrously late.  This infusion of funding will enable the clinical trial to be expanded to 20 sites. The hope is that Google’s expertise with handling big data will aid in pinpointing the role of genome changes in early autism diagnosis.

Autism Diagnosis and Therapy
The earlier a child is diagnosed, the faster a parent may be advised to begin therapy and the use of communication aids. The ipad from Apple company has been a boon for children with ASD helping them to communicate more effectively. More such Apps are also being funded for development to simultaneously pair with therapy of autism.

The role of the gut microbiome has also been recognized as critical since all children with autism have very restrictive eating habits. Research into probiotics and prebiotics are playing a significant role in therapy of autism and ASD. Read “Related Articles” below.

Hopefully, researchers will be able to find a clue as to why parents with multiple sclerosis have children with autism, allergy, and ASD. Is there a genomic blueprint that predisposes a family when exposed to certain unknown triggers? When exposed as a child – ASD; when exposed as an adult – multiple sclerosis. Read “Related Articles” below for discussions on autism, role of aging parents, shank gene, coffee intake of father, G-proteins that try to prevent autism, gut microbiome and good/bad germs, role of Vit-D, and more.

Is Autism observed only in Developed Countries?
Although, this company may only provide a partial answer to the mysterious rise in the number of children developing autism, especially boys, it may give researchers a clue into why children from certain ethnicities develop autism when born in developed countries. Why is autism not observed in developing countries? To read a discussion click here for “Why is Autism observed in America and not in underdeveloped countries?”.  Autism does not discriminate by ethnicity.  It has been observed in Caucasians, Asians, Hispanics and blacks. When children of Somali descent are born in underdeveloped Somalia, they do not develop autism while they do in developed countries like Sweden and USA.  This has led to research on the role of Vitamin D from sunlight in autism, since Somalia is in Africa and has mostly sunny days, while Sweden and USA have far less sunny days, and more indoor activities of an advanced civilization with computer games and television. However, since all children in Sweden and USA have mostly similar indoor activities, why do only some of them have autism? The answer may lie in their genomic blueprint differences and/or exposure to a yet unknown environmental trigger.

Today, developing countries may show more cases of dyslexia or mild autism spectrum disorder. However, as these countries become more like Sweden or USA, will there be more cases of autism diagnosed there too? The answer might be yes, since the autism trigger suspects might be in a developed country lifestyle.  The answer might lie in the way we eat, live, clean, and prevent in an effort to be healthier.  Yet, in that very effort we may unwarily be introducing the triggers like pesticides or herbicides or toxic landfills and spills, that set up local children for autism by damaging the genome of the growing delicate foetus in the womb, depleting our gut of healthy germs that protect symbiotically, or by not understanding all the complex cellular interactions of some of our vaccine components and how they interact with a damaged genome (see below Related Articles).

Related Articles
The Gut Microbiota: your good germ friends to nurture to strengthen your immune system against “Allergy”
Worm Theory: to improve the immune system to fight asthma, multiple sclerosis and more
Autistic child or severely Allergic child with Multiple Sclerosis parent
G proteins: the connector proteins that try to prevent Autism Spectrum Disorder
Know your G proteins: relevant for Allergy, Autism, Aspergers and ASD
Four facts about allergy: parents, children, patients, genes and researchers
Autism in pristine Phu Quoc island of Vietnam – is the rise in numbers simple overdiagnosis?
A single shared component has been confirmed in allergy and autoimmune diseases
World’s largest collection of frozen Autism brains ruined in freezer malfunction
Are we less healthy than our parents and grandparents – both mentally and physically?
Are there any Gays and Lesbians who are autistic?
Why and how to add Calcium in the diet of a person with Autism Spectrum Disorder

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Colitis and Arthritis share what?

New research is revealing that various types of Arthritis share a common factor with diseases that afflict the gut of younger age groups.  A ten year old, Emma, uses fecal transplants and maintenance doses of medicines to manage her ulcerative colitis.  The idea of fecal transplants, perhaps a more extreme form of probiotics, is to “borrow” the stool from a healthy person with  a healthy balance of intestinal bacteria. The theory behind this is that a healthy person without leaky gut, colitis, Crohns, and irritable bowel syndrome (IBD) may have an environment inside their bowels that supports the growth of natural “good” bacteria, while a person with IBD may lack such natural “good” germs.

What could be common between Arthritis and IBD? Although the ultimate cause of Rheumatoid Arthritis remains elusive, new research suggestions on the role of the gut microbiome is summarized here by scientists Dr. Scher and Dr. Abramson. The gut’s natural bacteria support environment, predisposing genetic factors and environmental triggers are required for disease manifestation. Other scientists have demonstrated that Atherosclerosis was accelerated in “germ-free” mice on a low cholesterol diet. These scientists concluded that identifying the “good” germs and understanding how they exert their beneficial activities, could aid in disease prevention and treatment. Click here to read this scientific study by Dr. Tlaskalova-Hoganova and team.

Colitis and Arthrtis share immunology
It is no surprise that families share arthritic pain, irritable bowel syndrome, and colitis. However, it is a surprise find that the same families share these conditions. Arthritis is an inflammation of the joints and an outside the intestine condition. While arthritis is commonly seen with aging, irritable bowel disease is commonly seen even in children. Of these, arthritis is the most common shared condition found in 25 percent of all irritable bowel disease syndrome sufferers (IBD).  Arthritis and IBD are both autoimmune diseases. They need to be looked at as “co-existing” conditions that influence and interact, while searching for the causes of the auto-immunity.

Prevention is the major goal. The incidence of arthritis in people with IBD is same in men, women and children, which indicates a genetic linkage form of inheritance. Different intestinal diseases like ulcerative colitis, Crohn’s disease, diverticulitis, and celiac disease can lead to different forms of arthritis. Read more.

Ancient Food Habits included Whole Grain. Yet, a gluten - free diet and other life style changes in modern day may keep many free of Irritable Bowel Syndrome and Arthritis. Copyright 2013 (c) Pursue Natural

Ancient Food Habits included Whole Grain. Yet, a gluten – free diet and other life style changes in modern day may keep many free of Irritable Bowel Syndrome and Arthritis. Copyright 2013 (c) Pursue Natural

Learn more about these auto immune diseases by clicking here,  from the Crohn’s and Colitis foundation of America. to read more on the relationship between ulcerative colitis and psoriatic arthritis click here, from Health Central.

Dr. Elena Koles, of the UK Medical system finds it unfortunate that western medical system separates different body systems by ignoring their intricate relationship. Quote

…They need to be looked at as “co-existing” conditions that influence and contribute to one another, rather than two separate, unrelated illnesses. Only a thorough approach that addresses the causes of auto-immunity and recognizes the interaction of IBD and arthritis can ameliorate both diseases….

Unquote. Read more.

A personalized approach is best. Pursue Natural prefers that it’s readers are comfortable with the term ‘pharmacogenomic’ which essentially means that if you know how your genes are different from other people, your treatment could in the near future be tailored to the genes that you inherited from your parents. So, assuming that with each article our readers will get quite used to the concept of their own genes being different and unique to require personalized attention to detail, we suggest the following steps:
1) Your treatment must be individualized, by a physician open to a holistic approach combining the knowledge of modern medicine with the following;
2) Physiotherapy and Yoga – individualized routine to keep you pain free and in constant motion; Yoga has helped ease IBD, perhaps by slowing down the breathing rate of anxiety, and relaxing fatigued muscles. Read more.
3) Supplementation – to make up for lack of any minerals and vitamins dictated by modern diagnostics;
4) A comprehensive dietary plan – adding or removing one food item at a time to discover which one causes an auto immune reaction;
5) A comprehensive “emotion review” plan – maintaining a diary of minor or major event each day, because IBD is triggered by an emotional reaction to excitement, fear or unknown fact of life.

Genetics and Shared Immunology of IBD and Arthritis
They share at least the following five genetic factors:

1) Genetic susceptibility to abnormal antigen presentation
2) Aberrant recognition of self, autoantibodies against specific antigens shared by the colon and other 3) extracolonic tissues,
3) Increased intestinal permeability, and
4) An infectious trigger.

The immunological alterations shared are the following:

• E-cadherin expressed highly in gut of patients with IBD and SpA;

• Th1, Th17, and Treg cells active in the intestinal mucosa of patients with IBD and synovial fluid of those with ankylosing spondylitis and SpA;

• Tumor necrosis factor (TNF) alpha is a dominant cytokine in IBD and SpA;

• Interaction of antigen-presenting cells with microorganisms;

• Toll-like receptors TLR-2 and TLR-4; and

• HLA-B27+ and IgA anti-saccharomyces cerevisiae antibodies in CD.

In addition, HLA-B27 transgenic rats develop IBD, psoriasis, enthesitis (inflammation at the sites where tendons or ligaments attach to bone), synovitis, and epididymitis.entation
Abherrant recognition of self
Autoantigens against antigens shared by the colon and other extra colonic tissues
Increased intestinal permeability
Infectious trigger

Read more in medscape.

Related Articles
Multiple Sclerosis cured by worm therapy
Worm Theory: to improve the immune system to fight asthma, multiple sclerosis and more

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Race, ethnicity and kidney disease

African Americans, Hispanics, and American Indians are at high risk for developing kidney failure. This risk is due in part to high rates of diabetes and high blood pressure in these communities. Is this risk genetically pre-determined and further assisted with inferior diet choices? Will it be inethical for your doctor to advice you based on your ethnicity, if you face a higher chance of getting kidney failure in the future, based on genetically supported scientific data?  Below (under related articles) is more information about kidney failure for each of these groups, prevention and maintenance steps.
Kidney Disease

Rising diabetes and high blood pressure are the leading causes of kidney failure. Since the year 2000, the number of Hispanics with kidney failure has increased by more than 70 percent. While African Americans account for only 13 percent of the population, they account for more than 32 percent of the population with kidney failure.

If you have diabetes or high blood pressure, and are African American, you must strongly consider getting checked for kidney disease. Read more. Diabetes is the number one cause for kidney failure among African Americans, and high blood pressure is a close second. The goal is to keep blood pressure below 130/80, suggests the National Institute of Health.

High sugar diets can lead to diabetes. The fact is that ready-made food is made more appealing by adding sweeteners. Also, several cheap alternatives to sugar may be more dangerous than sugar itself. The poorer the person, the likelier that person is to choose a cheaper food, which might be sweetened to make up for the lack of taste from fresh food. Eating such sweetened food too often can lead to higher risk of diabetes. It is not surprising that the poorer people are getting more obese – another side reaction to eating sweetened food and drinking sweetened beverages. Diabetic persons are frequently obese from such food and beverage choices.  You might want to read “For the First Time in Human History, Overweight People Outnumber the Underfed“, by blogger Mother Nature’s Diet. Scientists have known for several decades that this obesity epidemic is restricted to specific, inferior diet choices, and dictated by differences in the genes inherited from family. Certain ethnic groups will get more obese simply because they do not inherit the genes required to “digest” or “metabolize” inferior food choices. Will it be inethical of the doctor to tell them that the eight year old, 300 pound little child is obese because of her ethnicity, dictated by the genes she inherited from her family, not giving her the ability to digest her fatty and sweetened school lunch? Which country has the highest obesity? Which country has the highest percentage of obese people? You might enjoy reading that the answer to the first is Mexico and the second is Nauru, a small country in the South Pacific (their inherited genes) in “Is this a Good Thing“, which summarizes the United Nation’s Food and Agriculture report.

A refreshing, non-scientific travel observation by blogger gaelic girl on “Victoria’s view: Why are Americans so obese compared to the Irish“, discusses smaller food portions, organic groceries, walking instead of using automobiles for errands, and higher rate of smoking among the Irish. It does not discuss their inherited genetics, since it isn’t scientific, but nonetheless, brings up excellent discussion topics on how to prevent obesity perhaps with the above life style choices, based on the observation that Irish people are a lot skinnier than the Americans, and are not even on the top 25 in the list of obese countries by United Nation’s Food and Agriculture report.

Genetically, there are certain ethnic groups far more at risk for diabetes and high-blood pressure and hence, kidney disease. The genes and junk regions around the genes that you inherited from your parents do define you (Read more). You might wonder why your friend can eat the same foods as you and yet not gain any weight or be at risk for diabetes, while you could be getting obese and at risk for getting diabetes followed by kidney disease.

High Blood Pressure
High blood pressure is another indicator/ risk factor of kidney disease with significant ethnic differences.

….compared to Caucasians, Afro‐Caribbeans and people of African descent have a higher incidence of stroke and end‐stage renal failure, whereas coronary artery disease is less common. Conversely, South‐Asians (defined as people originating from the Indian subcontinent and East Africa) have a higher incidence of coronary heart disease….

Read more. Quoted above from a study of patients in the United Kingdom, such ratios are similar in other developed countries with rising rates of high blood pressure.

In a landmark study, 18 genes have been discovered to be co-related with most of the deaths from heart disease, Britain’s biggest killer. Read more. A few ethnic groups account for most of the deaths from this killer disease, because they inherit these culprit genes from their families.

Getting to know your family takes on a whole new meaning with the knowledge that your biological inheritance from your family also determines your health and longevity. However, this same knowledge allows you to take prevention steps from this moment. You may have to have more self-control than a friend who lacks the culprit genes, but it may save your life.

Related Articles
Race, Ethnicity and Kidney Disease – National Kidney Disease Education Program. to learn more about kidney disease in each specific race.
How the biological inheritance from your parents defines you
Should we risk taking calcium supplementation with risk of heart attack, bones breaking and kidney disease?
Mineral balance is critical for healthy body functions – Role of the kidneys and increasing kidney disease
Kidney care and okra
Kidney care and natural nutrition
What are the five stages of kidney disease?
What African Americans with Diabetes or High Blood Pressure need to know and steps to take forward.

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How the biological inheritance from your parents defines you

PursueNatural has a goal to encourage you to be the master of your own genome – the biological inheritance from your parents.  In a few years, it will become apparent that biological inheritance knowledge may be a life saver , and a gift  equally valuable as financial inheritance.  However, heredity is not destiny since genes alone do not define you.  Harvard School of Public Health says that environmental factors (unknown), nutrition and physical activity offset the action of inherited obesity genes; however, the presence of the obesity genes in some people necessitate actions for prevention of obesity suchas higher levels of physical activity.

Just like you know how to regulate the temperature of your own home with the simple flip of a switch, in the same way you should want to know which “switch” controls the temperature of your body.  How does your body regulate and differentiate between an infection and a very cold day? Today, we do not know the answer but the day is near when we will. At the very least, in the near future, we will be able to pinpoint a region in your genome which is different from that of your best friend, who could possibly tolerate a cold day far better than you and yet, succumb to an infection which you can fight off easily.

The ENCODE project studied 140 of the hundreds of cell types and identified many of the cell type specific  control elements in the human body. The results of the ENCODE project (see below) best describe the regulation of the human genome.

“We were surprised that disease-linked genetic variants are not in protein-coding regions,” said Mike Pazin, Ph.D., an NHGRI program director working on ENCODE. “We expect to find that many genetic changes causing a disorder are within regulatory regions, or switches, that affect how much protein is produced or when the protein is produced, rather than affecting the structure of the protein itself. The medical condition will occur because the gene is aberrantly turned on or turned off or abnormal amounts of the protein are made. Far from being junk DNA, this regulatory DNA clearly makes important contributions to human health and disease.”

The DNA-Helix
Let us begin the narration in the year 1953, when biologists, chemists and physicists became united in their excitement for the first time because James D. Watson and Francis Crick discovered the DNA-helix  and shared the Nobel Prize nine years later with Maurice Wilkins, for solving one of mankind’s great riddles. The revolution in molecular genetics had begun.

The Discovery of the First Human Disease Gene
The first human disease gene was discovered in 1989 and announced with the publication of three historic papers on the process of discovery of the Cystic Fibrosis (CF) gene in the Journal Science, by three teams led by team leaders Dr. Lap Chi Tsui, who discovered that 70 percent of cystic fibrosis patients had three mutations in the CF gene; Dr Jack Riordan, who could detect the three mutations in diseased CF patient tissue; and Dr. Francis Collins who identified the CF gene segment on chromosome 7 and cloned the CF gene with the technique of chromosome walking and jumping. The latter technique of chromosome jumping was published a few years earlier in 1984 by Dr. Francis Collins under the direction of Dr. Sherman Weissman at Yale University.  For the next nine years Dr. Francis Collins’s laboratory perfected the technique of identifying disease genes earning him the title of ‘gene hunter’.  In 1993, looking for a successor after the resignation of Dr. James Watson, the National Human Genome Research Institute (NHGRI) of the NIH  requested gene hunter, Dr. Francis Collins to lead them. For over a decade he led the institute to benefit science, medicine and humankind.  He has been a proponent of personalized medicine and emphasized the importance of legal and ethical issues in genetics and genomics, particularly those concerned with privacy of genetic information, and discrimination in employment and insurance based on genetic information.

The First Sequence of the Human Genome
The age of biology probably began in 2001, when the International Human Genome Consortium published and reported the first initial analyses of the draft sequence of the human genome. A year earlier, in 2000, a completion of a working draft of the human genome sequence was announced amid much fanfare by President Bill Clinton with Dr. Francis Collins and Dr. Craig Venter. Since then, the international collaboration has been working to convert this draft into a complete genome sequence with high accuracy and nearly complete coverage. An update was published with 99% coverage and an error rate of 1 event per 100,000 bases in build 35 which has 2.85 billion nucleotides interrupted by only 341 gaps. This update publication serves as a firm foundation for biomedical research. Notably, the human genome seems to encode only 20,000 to 25,000 protein – coding genes.  Many of the remaining gaps have duplications which will require new methods of study.

The First Supreme Court Decision on The Human Genome through a Controversial Gene patent
Dr. Francis Collins belongs to the group that believes in keeping the genome sequence free for all to access.  Dr. Craig Venter belongs to the group that is a proponent of gene patents for commercial interests. Academic and commercial interests on genetic sequences clashed with the breast cancer gene patents owned by Myriad, over the cost of diagnosis of a breast cancer gene. The patents on the breast cancer genes used in diagnosis where owned by one company and this right was challenged all the way to the Supreme Court. In a unanimous 9-0 historic ruling, the Supreme Court announced the bar of human gene patenting and indicated that the naturally occuring genes of the Human Genome must remain free for all (Read the “Case summary and information” by the ACLU; read the New York Times article by Adam Liptak, “Justices, 9-0, bar patenting of Human Genes“). Ironically, the University of Washington’s geneticist, Dr. Marie-Claire King, who discovered the breast cancer gene is elated with the Supreme Court’s landmark ruling. Exclusive rights to genetic material have hampered research and the progress of science. While Dr King discovered the genes and the location of the genes, scientists at the University of Utah cloned the genes, patented them and marketed them. Dr. King can now market a better test that her team has developed, which had been prohibited by the patent.  A 2013 film, “Decoding Annie Parker” dramatizes the story of the Breast cancer gene patent battle involving a single patient, Annie Parker, and discusses a little bit of the relevant science behind the patent.

The question remains how much exclusivity do you grant creatively to commercial entities to make it worth their while to invest in new discoveries.  Is there a creative answer to encourage industry participation in the human genome era?

The ENCODE Project challenging the traditional view of how the Human Genome functions
Recently, there has been a very controversial sequel to the Human Genome Project announcement of the Draft sequence in 2000. The traditional view is that the human genome consists of a small number of genes and a vast expanse of junk-DNA with no function.  Which means the junk-DNA is not biologically active.  The ENCODE project was established by the NHGRI to identify all functional elements of the human genome. They published a set of papers in 2007 which challenged the traditional view of our genetic blueprint having discovered that genes do not function as independent entities. Rather, through a complex network, genes interact with DNA sequences that do not encode proteins; junk-DNA is involved in biologically active processes in a yet unknown manner. Read “New Findings Challenge Existing Views on the Human Genome“.  This was the result of a pilot effort involving 35 groups in 80 world-wide organizations over 14 years to identify all functional elements in 1% of the Human Genome.

Dr. Francis Collins says this pilot project blazed the way to explore the functional landscape of the entire human genome.  Several evolutionary biologists criticized the publication of the ENCODE data, being of the view that ENCODE was a group of computer biologists who did not understand the biology of the human genome. The protein coding segment of the human genome accounts for about 2% of the functional genome and evidenve exists for important functions in the rest of the genome.  To access the human ENCODE data at UCSC click here.

On September 2012, an NHGRI funded study published a more dynamic view of how the Human Genome functions. Read “ENCODE data describes function of human genome“. Dr. Eric D. Green, the new Director of the NHGRI since 2009, is of the view that ENCODE has revealed that most of the human genome is involved in the complex choreography of converting genetic information into living cells and organisms (Read). The remarkable scale of this ENCODE project involved hundreds of researchers in USA, UK, Singapore, Japan and Spain with technologies standardized across the consortium. Some of the technologies only became available five years before this publication.

The ENCODE Consortium placed the resulting data sets as soon as they were verified for accuracy, prior to publication, in several databases that can be freely accessed by anyone on the Internet. These data sets can be accessed through the ENCODE project portal ( as well as at the University of California, Santa Cruz genome browser,, the National Center for Biotechnology Information, and the European Bioinformatics Institute,;

The coordinated publication set includes one main integrative paper and five related papers in the journal Nature; 18 papers in Genome Research; and six papers in Genome Biology. The ENCODE data are so complex that the three journals have developed a pioneering way to present the information in an integrated form that they call threads.

Since the same topics were addressed in different ways in different papers, the new website,, will allow anyone to follow a topic through all of the papers in the ENCODE publication set by clicking on the relevant thread at the Nature ENCODE explorer page. For example, thread number one compiles figures, tables, and text relevant to genetic variation and disease from several papers and displays them all on one page. ENCODE scientists believe this will illuminate many biological themes emerging from the analyses.

In addition to the threaded papers, six review articles are being published in the Journal of Biological Chemistry and two related papers in Science and one in Cell.

The ENCODE data are rapidly becoming a fundamental resource for researchers to help understand human biology and disease.

The NHGRI will invest in four more years to cover some more of the remaining part of the human genome.


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The advantages and challenges of storing your medical information on the internet

Doctors in offices can communicate with their patients located in remote destinations. New forms of access and service will spawn a new generation of portable internet technology.  Large data is changing health care delivery for the better.  In certain small rural clinics, your blood pressure can be automatically entered into the network as it is being measured and your health chart is updated in real time. It is understood that CT scans and MRIs involve acquiring and processing large amounts of data to provide surgeons real time three dimensional data about organ deformation.  Arrays of electrodes implanted around the brain create large data sets for neurologists.  Small sample numbers and nonstationery behavior specific signals complicate the ability to develop statistical models. Nanoscale cell studies have added another level of complex challenges. Diseases in many cases may be linked to rare genetic variants, with a limited number of replications. DNA copy number variations and gene expression levels are based on analysis of large data sets. Traditional challenges in genomics and medical imaging have kept the medical informaticians busy. Now there is an added challenge of analyzing the inter-genomic regions, the parts of the genome which lies inbetween the genes and only recently recognized as playing a major role in cell organization.  For the mathematicians it has become increasingly important to gather those with interdisciplinary backgrounds to join research groups with exceptional contemporary importance or interests, suchas at the Institute for Mathematics and its applications. The health care challenges of the future calls for interdisciplinary action groups.

Health Analyses of the family using the internet

Health Analyses of the family using the internet

Large Data, medical information and Innovation
The advent of affordability of powerful computing, pervasive networking, and portable communication via smart phones and devices like the ipad, is making possible nomadic computing and communications. Policy makers and leaders are emphasizing their commitment to investment in the infrastructure of internet technology towards large data in medicine, by putting patients in charge of their own health, liberating health data, and promoting medical internet innvotion.  Dr. Atul Gawande, Professor of surgery at Harvard Medical School, encourages new apps and technologies to use data while also making them more cost effective. Jonathan Bush, Co-founder of Athenahealth, wants more health data released by Health and Human Services (HHS).  Kathleen Sebelius, Secretary of HHS, believes in unlocking data, and is optimistic that the health care delivery system and the market place are at a very exciting evolutionary juncture. The first ever Health Data Liberators Award was presented to Dr. Nirav Shah, New York State Commissionar for Health, on June 04, 2013, at Health Datapalooza IV.

What will a smarter health care system look like? There has been a historic increase in electronic health records. How can every person be connected to high quality health care? Large health data is changing the economics of health care and at the cusp of transforming the nature of health care analsis and delivery. Check out the latest presentations and videos by the health data consortium in the future of health care delivery:

The Health Data Consortium is a collaboration among government, non-profit, and private sector organizations working to foster the availability and innovative use of data to create a health data ecosystem to improve health and health care. The Consortium advocates with data sources to promote best practices and information sharing, and works with businesses, entrepreneurs, and academia to help them understand how to use data to develop new products, services, apps, and research insights. We work to evangelize, connect, spark, and enable — to provide a space for all stakeholders to come together.

Brief History of the Internet
The internet is evolving to our interests with yet another generation of underlying network technologies. How will this evolution be managed? The number of stakeholders now include the government, institutional investors and the inventors. The history of the development of the internet has always included a core group of designers and developers but today, there is also a group of both economic and intellectual stakeholders who may direct any future evolution of the internet.  Investment in the internet can be successful. Large investments are needed for future growth strategies of network communication. What rationale will guide the form of the social structure of the internet of the future, especially in the role of preserving and analyzing large medical data?

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Migraine is a brain disorder according to latest research

Recent research advances strongly suggest genetic changes. People with migraines may have brains that not only look different structurally under an MRI but may function differently, allowing it to be labeled a neurological disorder.  Migraine patients could be more susceptible to pain and process stimuli differently.  These findings were published online March 26, 2013 in Migraine Radiology, and come from MRI scans of 63 adults with migraines, and 18 migraine-free men and women, entitled “Cortical Abnormalities in Patients with Migraine: A Surface-based Analysis”.

A summary of migraine research findings
An excellent article including detailed figures summarizing our current understanding of migraine as a primary brain dysfunction(s) and susceptibility to cortical spreading depression is in the scientific journal Cell, May 25, 2012 – Summary. Migraine is a common disabling brain disorder whose key manifestations are recurrent attacks of unilateral headache and interictal …

Neurologists present their opinions on this scientific discovery : WebMD presents the MRI studies that suggest changes in the brain regions associated with pain; the outer layers of the brain (cortex) is thinner and smaller than in headache-free adults, Mar 26, 2013 – That’s important because it helps “legitimize” migraine as a neurological disorder associated with “real structural changes in the brain”.

What is migraine?
Migraine is three times more common in women than in men and affects about 10 percent of the people world-wide. People with migraines tend to have recurring attacks. There is currently no treatment since the pathophysiology of this “throbbing unbearable pain in the head” condition remains to be understood. Prevention is very important from allowing this condition to become chronic.

More about migraine
1) More about what is a migraine is discussed in the National Institute of Neurological Disorders and Stroke Researchers believe that migraine is the result of fundamental neurological abnormalities caused by genetic mutations at work in the brain. New models are …

2) A New York Times article discussing Migraine causes, treatment, alternative names and as a brain disorder, Feb 11, 2012 – A migraine is caused by abnormal brain activity, which can be … are due to muscle tension, sinus problems, or a serious brain disorder.

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ADI collaborates to develop a hand-held device to use during disease outbreaks

Antigen Discovery Inc.,(ADI) is developing hand-held point-of-care (POC) diagnostics to meet a vital need. First responders during major disease outbreak need a portable device, that is easy to use, and will give a prompt answer to the question, “What is making so many people very sick?” The biotech company, ADI, is collaborating with the academic team from a Biomedical Department of the Henri Samueli School of Engineering to embark on this project with the goal of developing a device, probably compatible with our current hand-held-phones, with the necessary portability, ease-of-use, and prompt sample-to-answer times.  Towards this purpose, ADI has received a Phase I SBIR Grant, which shows confidence, recognition and support of their key technology by leaders in this field. Hopefully, this small, portable device will work in a field environment during a disease crisis and also be a financial success. Such a collabortion of the best of biotechnology academic and development & marketing capabilities, might save many lives.

A Reactive Antigen Microarray (40, 80, 160, or 400 arrays/pkg) for quick Malaria detection

A Reactive Antigen Microarray (40, 80, 160, or 400 arrays/pkg) for quick Malaria detection

The technology utilizes proteome microarrays in immune response profiling. The diagram on their website details very simply their basic technology of antigen discovery for vaccine and diagnostic development. Proteins are printed on a microarray – these proteins are from the known infectious organisms. Antibodies from the patients’ blood will bind to a few of these proteins if they are infected with any of those known infectious organisms. They have the basic infectious agent disease technology. What they do not have is the technology required to get this information quickly, at a field site, where there might be hundreds of people dying mysteriously or getting very sick after a natural disaster from a mysterious disease. For this they turned to a collaboration with an advanced engineering biomedical department.

A team led by Abraham Lee Chair, Biomedical Engineering Director, Micro/Nano Fluidics Fundamentals Focus Center The Henry Samueli School of Engineering University of California, Irvine provided them a solution.

The Henry Samueli School of Bioengineering, Irvine, CA collaborating with Antigen Discovery Inc., CA

The Henry Samueli School of Bioengineering, Irvine, CA collaborating with Antigen Discovery Inc., CA

Dr Lee’s team’s goal is to unveil biological events such as cell signaling pathways, genetic mutation processes, or the immune responses to pathogens, with a method to generate large-scale, multifunctional nano-bio interfaces with readout and control. Professor Lee’s research group is developing integrated microfluidic platforms with the goal of generating programmable synthesis of multifunctional nanotransducers. One of the research interests is micro devices for distributed surveillance in liquid-based environments.

Professor Abraham “Abe” Lee’s research interest focuses on the development of integrated micro and nano fluidic chip processors for the manipulation and self-assembly of biomolecules and other synthesized nanoparticles. These integrated chip processors will also be designed for the sample preparation of biological fluids to extract the required ingredients for on-chip transducers. Applications for these fluidic processors include programmable precision production of biological reagents for nanomedicine, biomolecular nanosystems that utilize biophysics principles, and platforms to perform controlled studies of molecule-molecule/cell-molecule interactions.

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War against the aging effects of menopause – Three activities which help

Is this worth signing up for? “Plus, receive your FREE Bonus Report, Living to 100: What’s the secret?” promises Harvard University’s free newsletter, HEALTHBeat. What are the chances that you might live until you are one hundred years old? Pretty good, if you allow every creaking, malfunctioning organ inside your body to be replaced. The combined features of personalized medicine, 3-D printing and organ tissue culture are achieving true leaps in science.

However, men and women’s aging remains a mystery. The hormone Estrogen, which provides vitality and fertility to young women works with a few other hormones and minerals like Calcium in a rather mysterious manner. It is apparently controlled by a master, age – controlled switch, which decides when a woman will begin to decline cognitively. Yes, menopause controls when a woman becomes “foggy”, in a manner which is unclear, since women in some cultures never become “foggy”.

So, here we are attempting to discuss modern scientific discoveries that prevent aging, post – menopausal women from becoming “foggy”. Chances are, if your mother or grandmother is not “foggy” you have inherited good aging genes and need read no further. However, if you are aware of declining cognitive function in your gene pool, then perhaps, you might want to be aware of latest scientifically backed products claiming to reverse this decline.

Are there any effective products in the market today to revert effects of menopause?

Scientists are specializing in different parts of the body where these hormones of health and vitality may play a role. The brain, or the Neurogenesis and gender, is a major frontier being explored. A Rockefeller scientist, Dr. Bruce S McEwen, has devoted his career to this and is of the opinion we have a long way to go. He showed as early as the year 1999 that the hormone Estrogen had an effect on the brain. Estrogen changes brain structure, learning and memory he discovered. In the year 2004, Dr McEwen’s team published scientific evidence of a specific area in the brain where Estrogen plays a role – Estrogen controls dendritic spines formations and synaptic complexes. Estrogen may be associated with enhancement of hippocampal-dependent memory.

Physical activity, social contacts, intellectual pursuits
The conclusion even today from Dr. McEwen is that physical activity, social contacts, intellectual pursuits will do far more to help your personal war against the aging effects of menopause than any current market therapy available. They have a similar effect on stimulating the dendritic spines and synaptic connections of the brain and scientists who have devoted their career to this field have no explanation for this. Psychologists studying the aging woman’s brain activity say it is a myth that woman will definitely lose their cognitive function as they age because many women have perfectly great cognition, some even better than many middle – aged people.

Three things an aging woman will definitely benefit from:
1) Physical activity – exercise daily to invigorate your brain
2) Social contacts – seek out people and have conversations and relations; laugh and cry
3) Intellectual pursuits – learn a new subject every week and “master” it
All three above activities are known to stimulate the hippocampus with no detrimental side-effects.

Estrogen unknowns
Why does Estrogen control the brain? How does Estrogen control the brain? What controls Estrogen? When will we discover this master switch that regulates Estrogen and controls a woman’s moods and cognitive functions?

The hormone Provera has been prescribed along with Estrogen to menopausal women. However, Provera has side effects. The above discussion has shown how little we understand the master menopausal hormone, Estrogen. We understand Progesterone even less. Provera is an attempt to recreate Progesterone artificially. The side effects are considerable and the risks and benefits must be considered with the long-term view in mind. In brief, Provera, the artificial form of Progesterone, counteracts the beneficial effects of Estrogen therapy, when in combination therapy. Which means you might negate any positive effect of Estrogen therapy. This process, is incompletely understood, but if you have a choice, AVOID Provera, until studies satisfy and assure you of the long-term benefits.

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