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A 17-gene expression signature to distinguish patients who are likely to achieve long-term remissions following front-line FCR chemoimmunotherapy from…
Posted: November 21, 2019 at 5:46 pm
In this paper, Carmen D Herling, Department I of Internal Medicine, Center for Integrated Oncology, Aachen-Bonn-Cologne-Duesseldorf, Cologne, Germany, and colleagues hypothesized that the duration of response to FCR chemoimmunotherapy depends on differences in the expression of protein-coding genes. Therefore, they developed and validated a 17-gene expression signature to identify patients that might achieve durable remissions following front-line FCR chemoimmunotherapy.
Study design and patients1
Results1
After the gene expression data analysis for the MDACC cohort, the authors identified 1,136 probes associated with time to progression. Using these probes, patients with similar gene expression patterns were divided into favorable, intermediate, and unfavorable prognosis subsets. The intermediate prognosis and unfavorable prognosis subset had a shorter time to progression compared with patients in the favorable subset.
Genes highly expressed in unfavorable cases (n= 424) were associated with metabolic pathways, including oxidative phosphorylation and ribonucleoside metabolism. Genes highly expressed in favorable or intermediate cases (n= 401) encoded products involved in ATP binding, purine ribonucleoside triphosphate binding, nucleic acid binding, and DNA-template transcription.
The authors developed a prognostic model with 17 genes to distinguish IGHV-unmutated patients that had an intermediate outcome from those with an unfavorable outcome after front-line FCR therapy. The development process included:
These 17 genes were validated in 109 patients with an IGHV-unmutated status from the CLL8 cohort. In this cohort, patients classified as high risk (unfavorable prognosis; median time to progression of 39 months [IQR 2269]) had a hazard ratio of 1.90 (95% CI 1.183.06; P = 0.008) compared with low-risk (intermediate prognosis; median time to progression of 59 months [IQR 2884]) patients. Of the 17 genes, 13 came from the cluster of genes highly expressed in unfavorable cases with shorter time to progression, and increased expression corresponds to increased risk of progression. Three of the 17 genes came from the cluster of genes highly expressed in favorable or intermediate cases with longer time to progression and increased expression corresponds to decreased risk.
Conclusions
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UC Davis leads in innovative gene editing research with NIH grants – The Aggie
Posted: at 5:46 pm
Researchers strive to address societal health issues through gene editing
In October, three researchers at UC Davis were awarded a $1.5 million grant to fund their project which attempts to demonstrate the effectiveness of gene editing through use of CRISPR, a powerful technology that allows alteration of DNA sequences to change gene function.
This kind of design can help enhance personalized medicine, said R. Holland Cheng, a professor of molecular and cellular biology in the College of Biological Sciences. Specific patients with specific illnesses can be treated in specific ways.
Cheng, along with Kit Lam, a distinguished professor and chair of the Department of Biochemistry and Molecular Medicine in the School of Medicine, and David Segal, a professor in the Department of Biochemistry and Molecular Medicine, were awarded this highly competitive and sought-after grant from the National Institute of Health (NIH).
UC Davis is part of the NIHs Somatic Cell Genome Editing (SCGE) consortium which has awarded grants to 45 other research institutes across the nation so they can begin groundbreaking work on gene editing. Through this consortium, the NIH hopes to find an efficient and safe way to conduct gene editing. Research programs are investigating the best delivery mechanism as well as the most dynamic gene editing tool.
The major problem with gene editing currently is the inability of cells to be edited within a living organism. It has become fairly easy and efficient to edit genes in a cell culture outside of the body but extremely difficult to do the same processes inside the body. Cheng, Lam and Segal are focused on changing this.
The question is how to do it inside of an animal and eventually a human, Lam said.
They are answering this question by utilizing Chengs work in engineering a non-toxic nanoparticle that they hope can transport the gene editing tool CRISPR into the cells of a living organism. Cheng has been able to create a Hepatitis E viral nanoparticle (HEVNP) that when manipulated could be a delivery system for CRISPR. They plan to take this nanoparticle and encase CRISPR inside of it, producing a mechanism for delivery of CRISPR.
The Hepatitis E nanoparticle has the capacity to be a highly efficient way to deliver gene editing to cells in the body due to its unique nature. HEVNP is resistant to the gastric acid environment of the intestines and stomach, enabling it to survive once its entered the body. Given its resistant abilities, HEVNP can be taken orally, making it a useful form of medicine. If able to successfully get HEVNP to the target cells in the body and deploy CRISPR, gene editing abilities could drastically change.
The addition of a cell-type specific targeting ligand to the HEVNP would code the nanoparticle to deliver CRISPR to a specific cell. The abilities of this method to be precise and safe will determine its success.
With five years of funding from the NIH, these three researchers are eager to begin work on this project and see the strides that can be made in gene editing. They have impressive goals for this research, as it has the capacity to reshape medicine.
This will redefine precision medicine as currently there is broad medicine that can cause side effects to people and not be effective, yet by making it specialized it is becoming more precise and effective, Cheng said.
As more effective and safe tools to cure illnesses are being tested and created, the benefits to society could be expansive. With so much potential to help improve the health of society, the NIH is dedicated to coming to new solutions at a quick rate. All programs that received grants will be required to share and utilize the research occurring at other funded programs. The NIH is hoping to eliminate the private nature of research through enforcing the sharing of ideas, as scientists are often constrained by the institutions they work for. It is their hope that by having communication between the programs, positive results will arise faster.
I think this is great because scientists inherently want to work with each other but have real world concerns especially with money, Segal said.
The research results, when groundbreaking, can provide incredible monetary gains and credibility to the institutions that made the discovery. Ultimately, scientists collaborating with one another will serve society as people are able to benefit earlier from this innovative research.
We want the public to know that we are working in their best interest, Segal said.
The NIH grant is competitive and still the third research program to join the consortium at UC Davis. Innovation has never been more prevalent than in this field at UC Davis. With three different programs researching gene editing, UC Davis stands out as a hotspot for this field of research.
Written by: Alma Meckler-Pacheco science@theaggie.org
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New research casts doubt on near reality of ‘designer babies’ – PRNewswire
Posted: at 5:46 pm
During the process ofin vitrofertilization (IVF), it is not unusual for embryos to undergo preimplantation genetic diagnosis (PGD) identify specific inherited disease-causing mutations for single-gene disorders, like cystic fibrosis. Recently, new developments in genetics have given the ability to assign individuals "polygenic scores," which can somewhat explain the variability seen in complex human traits. This concept, applied to IVF embryos, has raised the prospect of "designer babies." However, there has been no research published to indicate the potential success of polygenic embryo selection.
"The notion that you could accurately choose your child's height or select for a higher IQ, like in the movie 'Gattaca,' has never been tested," said Dr. Lencz, professor in the Institute of Behavioral Science at the Feinstein Institutes and co-corresponding author of the Cell paper. "Through our research, we can confidently say that trait predictions for embryos based on polygenic scores are not very accurate."
Dr. Lencz and the team analyzed embryo selection for height and IQ in the context of a hypothetical IVF cycle. Investigators used three sources of data to evaluate the efficacy of trait selection, including a mathematically-derived genetic model, simulated embryo genomes, and a real dataset of nuclear families with large numbers of offspring (10 on average) who are now fully-grown adults with available genetic and trait (height) data.
The results concluded that screening for such traits using polygenic scores would leave a large margin for error. For example, children with the highest polygenic score for height were only the tallest in a quarter of families analyzed.
"Dr. Lencz's study adds important data highlighting the unreliability of trait selection by current methods of embryo genetic screening," saidKevin J. Tracey, MD,president and CEO of the Feinstein Institutes.
The ethical and legal debate surrounding polygenic embryo selection is already underway, but, until now, without a solid scientific foundation. The research team hopes that this work will promote an open and evidence-based discussion of these aspects among the public and policymakers.
Previously, an overview of this research was presented at the American Society for Human Genetics Annual Meeting in October by Dr. Lencz's co-lead, Dr. Shai Carmi of the Hebrew University of Jerusalem.
About the Feinstein Institutes The Feinstein Institutes for Medical Researchis the research arm of Northwell Health, the largest health care provider and private employer in New York. Home to 50 research labs, 2,500 clinical research studies and 4,000 researchers and staff, the Feinstein Institutes is raising the standard of medical innovation through its five institutes of behavioral science, bioelectronic medicine, cancer, health innovations and outcomes, and molecular medicine. We're making breakthroughs in genetics, oncology, brain research, mental health, autoimmunity, and bioelectronic medicine a new field of science that has the potential to revolutionize medicine. For more information about how we're producing knowledge to cure disease, visit feinstein.northwell.edu.
SOURCE The Feinstein Institutes for Medical Research
http://www.feinstein.northwell.edu
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Researchers Working to Understand Why Some Patients with Autoimmune Diseases Develop Diabetes Instead of Arthritis – BioSpace
Posted: at 5:46 pm
Autoimmune diseases are immune system disorders where the bodys immune system attacks its own tissues. Examples of common autoimmune diseases include rheumatoid arthritis, systemic lupus erythematosus, inflammatory bowel disease, type 1 diabetes, multiple sclerosis (MS) and others.
A peculiarity of autoimmune diseases is that they have many genes in common, but they develop differently. For example, why does a patient with an autoimmune disease become a type 1 diabetic rather than have rheumatoid arthritis?
Decio L. Eizirik, a researcher at Universit Libre de Bruxelles Centre for Diabetes Research in Belgium, who is also a senior research fellow at the Indiana Biosciences Research Institute, recently published research in the journal Nature Genetics that found significant insight into this question. Eizirik took time to speak with BioSpace about the research and how a researcher in Belgium came to collaborate with researchers in Indiana, Spain, the UK and the U.S. National Institutes of Health.
Several autoimmune diseases, such as type 1 diabetes, rheumatoid arthritis, multiple sclerosis, etc., have as much as 30 to 50% of their candidates genes in common, said Eizirik, raising the question on why in some individuals the immune system attacks, for instance, the insulin-producing beta cells, causing type 1 diabetes, while in others it targets joint tissues, leading to rheumatoid arthritis. Most of the research in the field has focused on the role for these candidate genes on the immune system, but our work indicated that many of these candidates genes affect the function and survival of pancreatic beta cells, leading to a misguided dialogue between them and the immune system that culminates in diabetes.
The early stages of type 1 diabetes, for example, show local autoimmune inflammation and progressive loss of the pancreatic beta cells that produce insulin. How these genetic transcription factors, or cytokines, interact with the beta-cell regulatory environment, and the changes that occur, suggest a key role in how the immune system gets triggered to attack the beta cells.
The research was conducted by Eizirik, Lorenzo Pasquali from the Institucio Catalana de Recerca I Estudis Avancats (ICREA) in Barcelona, Spain, and colleagues from Oxford, UK; Pisa, Italy, and the NIH. For about 20 years, Eizirik has run a diabetes-focused laboratory in Brussels. In August 2019, he launched a new laboratory at the IBRI, where, he said, three top scientists and assistants, Donalyn Scheuner, senior staff scientist at IBRI, Bill Carter, research analyst at IBRI, and Annie Rocio Pineros Alvarez, postdoctoral fellow in medicine at Indiana University, are already working. These two laboratories are working closely togetherfor instance, we have weekly meetings by videoconference, and besides my regular visits to the IBRI, scientists are moving between our European and USA labs on a temporary or permanent basis.
The IBIR was created by the State of Indiana and the states leading life science companies, academic research universities and medical school, as well as philanthropic organizations. The focus is on metabolic disease, including diabetes, cardiovascular disease obesity and poor nutrition. Its laboratories and offices are housed in about 20,000 square feet of space in Indian University School of Medicines Biotechnology Research and Training Center in Indianapolis. It expects to move into a new 68,000-square-feet site in mid-2020.
Eizirik said, The IBRI offers a unique opportunity to translate our basic research findings to the clinic, and we are working closely together with colleagues at Indiana University, particularly Carmella Evans-Molina, director of the Indiana Diabetes Research Center (IDRC) and the IDRC Islet and Physiology Core, to confirm our basic research findings in patients samples, and to eventually bring them to the clinic.
The specific research study looked at the binding of tissue-specific transcription factors. Transcription factors are basically proteins whose job it is to turn genes on or off by binding to DNA. So, for example, there are specific transcription factors whose job it is to regulate insulin production in pancreatic beta cells. In the case of this research, Eizirik and his team studied tissue-specific transcription factors that open the chromatin. Chromatin is a complex of DNA and protein found in the nucleus of the cell. It allows long DNA molecules to be packaged, typically in the form of chromosomes.
For gene transcription to occur, Eizirik said, chromatin must open and provide access to transcription factors. This allows binding of pro-inflammatory transcription factors induced in the beta cells by local inflammation.
For certain people who are genetically predisposed to type 1 diabetes, this leads to the generation of signals by the beta cells, Eizirik said, that contribute to attract and activate immune cells, rendering beta cells a potential target to the immune system.
Eizirik said, These observations have clarified the role for pancreatic beta cells in type 1 diabetes and provided an explanation for the reasons behind the immune system targeting beta cells.
The amplifying loop mechanism observed potentially explains other autoimmune diseases. Eizirik notes, Binding of tissue-specific transcription factors, within an inflammatory context and in genetically predisposed individuals, could generate signals that would attract and activate immune cells against specific target tissues.
Testing the theory in other autoimmune diseases will be required to verify it, but potentially could open up new therapies or preventive treatments for type 1 diabetes and other autoimmune diseases.
Type 1 diabetes has a strong genetic component, Eizirik said. At least 50% of the disease risk is due to genetic causesand understanding the role for candidate genes in the disease may point to novel therapies. For instance, up to now, nearly all therapeutic approaches to prevent type 1 diabetes have targeted the immune system, with little success. Our findings suggest that we must also take steps to directly boost beta cell survival.
He compared targeting the immune system only in type 1 diabetes to trying to fly a plane with only one wing. Our present and previous data suggest that we need two wings: first, to re-educate the immune system to stop its attack on the beta cells, and second, to increase the beta cell resistance to the immune attack, and to find means to restore the lost beta cell mass. Unfortunately, to achieve these goals in both type 1 diabetes and other autoimmune diseases is not easy, and we must redouble our efforts.
The next stages of the research will be to study the function of two novel candidate genes for type 1 diabetes that were discovered in the research. They both act at the beta cell level. He expects to conduct that research with Pasquali. The second stage is to evaluate the impact of other immune mediators that act earlier in the disease course at the beta cell level. And the third stage is to test their hypothesis regarding the role for the target tissue in other autoimmune diseases.
In addition to that ambitious agenda, Eizirik and his group are establishing an Inducible Pluripotential Cell Core at the IBRI.
Eizirik said, This will allow us to de-differentiate, for instance, skin cells from patients into pluripotential cells, and then to differentiate them into pancreatic beta cells. This will allow us to study the impact of the novel candidate genes we are discovering on beta cell function and survival, again in collaboration with Lorenzo Pasquali and Carmella Evans-Molina. This will also provide an excellent model to test new drugs to protect the beta cells in early type 1 diabetes.
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Global Cancer Biomarkers Market, Forecast to 2026 – Emerging Economies & Personalized Medicine to Provide Ample Industry Opportunities -…
Posted: at 5:46 pm
DUBLIN--(BUSINESS WIRE)--The "Global Cancer Biomarkers Market Analysis 2019" report has been added to ResearchAndMarkets.com's offering.
The Global Cancer Biomarkers market is expected to reach $37.99 billion by 2026 growing at a CAGR of 14.2% from 2018 to 2026.
Factors such as rise in technological advancements and increase in Incidence of Cancer diseases are driving the market growth. Though, high capital investment and technical issues related to sample collection and storage are projected to inhibit the growth of the market. Moreover, emerging economies and personalized medicine may provide ample opportunities for the market growth.
By biomarker type, protein biomarkers segment acquired significant growth in the market is mainly attributed to the tremendous capability of protein biomarkers in cancer detection, diagnostics, prognostics, and clinical & therapeutic applications; and minimal cost of the protein biomarker tests as contrasted with genetic biomarker tests. The rising focus of pharmaceutical organizations towards the discovery of protein biomarkers is additionally expected to fuel the development of this market during the forecast period.
The key vendors mentioned are Qiagen N.V., Thermo Fisher Scientific, GE Healthcare, Roche Diagnostics, Abbott Laboratories, Illumina, Danaher Corporation, Agilent Technologies, Sysmex Corporation, Merck & Co., Quest Diagnostics, Becton, Dickinson and Company, Hologic, Myriad Genetics, Bio-Rad Laboratories and Biomrieux S.A.
Key Questions Answered in this Report
Key Topics Covered
1 Market Synopsis
2 Research Outline
2.1 Research Snapshot
2.2 Research Methodology
2.3 Research Sources
2.3.1 Primary Research Sources
2.3.2 Secondary Research Sources
3 Market Dynamics
3.1 Drivers
3.2 Restraints
4 Market Environment
4.1 Bargaining power of suppliers
4.2 Bargaining power of buyers
4.3 Threat of substitutes
4.4 Threat of new entrants
4.5 Competitive rivalry
5 Global Cancer Biomarkers Market, By Category
5.1 Introduction
5.2 Cancer Biomakers of Disease
5.3 Cancer Biomakers of Exposure
6 Global Cancer Biomarkers Market, By Method
6.1 Introduction
6.2 Assay Development
6.3 Biomarkers and Testing
6.4 Sample Preparation
7 Global Cancer Biomarkers Market, By Biomarker Type
7.1 Introduction
7.2 Cancer Antigen 15-3 (CA 15-3)
7.3 Cancer Antigen 27-29 (CA27-29)
7.4 Carbohydrate Antigen 19-9 (CA 19-9)
7.5 Carcinoembryonic antigen (CEA)
7.6 Epigenetic Biomarkers
7.7 Genetic Biomarkers
7.8 Glass Transition Temperature (Tg)
7.9 Glyco-biomarkers
7.10 Glycomic Biomakers
7.11 Glycoprotein Biomarkers
7.12 Human Chorionic Gonadotropin (Hcg)
7.13 Human Epidermal Growth Factor Receptor 2 (HER2)
7.14 Human Epididymis Protein 4 (HE4)
7.15 Metabolic Biomakers
7.16 Microsatellite Instability (MSI) / Measles, Mumps and Rubella (MMR)
7.17 Protein Biomarkers
7.18 Proteomic Biomarkers
7.19 Risk of Ovarian Malignancy Algorithm (ROMA)
7.20 Tumor Mutational Burden (TMB)
7.21 Tumor-Infiltrating Lymphocytes (TILs)
8 Global Cancer Biomarkers Market, By Cancer Type
8.1 Introduction
8.2 Bladder Cancer
8.3 Blood Cancer
8.4 Breast Cancer
8.5 Cervical Cancer
8.6 Colorectal Cancer (CRC)
8.7 Kidney Cancer
8.8 Leukemia
8.9 Liver Cancer
8.10 Lung Cancer
8.11 Melanoma
8.12 Non-Hodgkin's Lymphoma
8.13 Ovarian Cancer
8.14 Prostate Cancer
8.15 Stomach Cancer
8.16 Thyroid Cancer
9 Global Cancer Biomarkers Market, By Technology
9.1 Introduction
9.2 Bioinformatics
9.3 Cytogenetics-based Tests
9.4 Imaging Technologies
9.5 Immunoassays
9.6 IVD Multivariate Index Assays
9.7 Omic technologies
10 Global Cancer Biomarkers Market, By Test Type
10.1 Introduction
10.2 Alpha-Fetoprotein (AFP) Tests
10.3 Anaplastic Lymphoma Receptor Tyrosine Kinase Gene (ALK) Tests
10.4 BReast CAncer gene (BRCA) Tests
10.5 Cancer Antigen (CA) Tests
10.6 Carcinoembryonic Antigen (CEA) Tests
10.7 Circulating Tumor Cell (CTC) Tests
10.8 Companion Diagnostic Tests (CDx)
10.9 Estimated Glomerular Filtration Rate (EGFR) Mutation Tests
10.10 Human Epidermal Growth Factor Receptor 2 (HER2) Tests
10.11 Kirsten Rat Sarcoma Viral Oncogene Homolog (KRAS) Mutation Tests
10.12 Laboratory Developed Tests (LDTs)
10.13 Prostate-specific Antigen (PSA) Tests
11 Global Cancer Biomarkers Market, By Analytical Technique
11.1 Introduction
11.2 Immunohistochemistry (IHC)
11.3 Next Generation Sequencing (NGS)
11.4 Polymerase Chain Reaction (PCR)
12 Global Cancer Biomarkers Market, By Product
12.1 Introduction
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This miracle drug was designed and manufactured for just one person a 9-year-old Boulder girl – The Colorado Sun
Posted: at 5:46 pm
Mila Makovec has high pigtails in her dark hair and a cloth doll tucked under her arm as she wakes up in a hospital bed, where shes just been injected with a one-of-a-kind drug intended to save her life.
The drug works for only one person in the world this 9-year-old girl from Boulder.
In a spectacular example of what the future might hold for precision medicine, the drug was made only for her in a quest to save Mila from a neurological disease that is destroying her brain. Her DNA is in the formula. The 22-letter genome sequence in the drugs recipe matches the one in Milas cells that is broken.
It is the first time the FDA has approved a drug for a single person.
The drug appropriately called milasen might not have come soon enough to save Mila, as it can only slow the process of degeneration, not replace the brain cells that have already died.
But this story is no longer just about Mila; it never actually was.
This is not just for my daughter anymore, said Julia Vitarello, who took to social media to fundraise and find a researcher and drug manufacturer who would help her. This is for something much bigger.
Milas case catapulted specialized drug development at least a decade into the future, her doctors say, opening a new path for other children with rare genetic diseases that have no cure.
Childrens Hospital Colorado, where Mila was diagnosed three years ago and now receives her treatment, and Boston Childrens, where her drug was designed, are leading the way in creating a model in which academic researchers could help perhaps a handful of children each year by crafting one-of-a-kind medicines. Next year, Childrens Colorado will begin whole-genome sequencing with a new machine called a Novaseq, a major step in the process of finding mutations in DNA.
The whole concept raises ethical questions for sure: How safe is it to initiate a clinical trial for a single child? Who makes sure the children who could benefit most not just those whose families have money or the ability to raise money get the specialized treatment?
Vitarello, who created Milas Miracle Foundation and raised $3 million while trying to save her daughter, wants to establish funding for children who need drugs tailored to their own cellular biology. She suggests an admissions process where the researchers deciding whether to help a child do not know that childs name, face or ability to pay.
There are going to be parents who are going to do anything for their kid, Vitarello said. They are going to come with money. Thats totally fine, no judgment. I would do the same thing. But in an ideal world, there would be patients coming through a funnel with no names or faces or money attached. Whoever is at the table makes the best decision.
The path forward is likely in the academic, nonprofit space, Vitraello said. She is initiating talks with the National Institutes of Health, the largest public funder of biomedical research, as well as research institutions, the FDA and the pharmaceutical industry. An estimated 1.3 million people with rare genetic diseases could potentially benefit from a treatment like Milas, she said.
There are 1.3 million kids that are dying that have no other treatment, no pharma company is going to help them, there is nothing that we can do, and now suddenly, weve opened up a pathway for that, she said Tuesday at the hospital in Aurora, as Mila rested following her injection. The only way to get it is to have more academic institutions treat more kids one, two, five, 10. Open it up.
The goal is that kids with flaws in their DNA could receive precision medicine sooner, halting neurological diseases before they steal the ability to walk, talk, eat or see.
Mila was a perfectly healthy child the first three years of her life. She was learning to ski, went hiking with her parents and had a vocabulary advanced beyond her years.
Her mom noticed the subtle changes before anyone the way she pulled books close to her face because she couldnt see, how her feet turned inward, that she began bumping into things and fell for no reason, how she stuttered sometimes but it wasnt like typical stuttering.
Vitarello brought her to 100 doctors and therapists from the East Coast to the West and in Canada, many of whom told her to calm down and that her daughter seemed fine. I had doctors tell me I was pretty much crazy. Very top level doctors told me to chill out, she said. Well, I wasnt going to chill out. I just kept going.
By age 7, Mila was having trouble walking and eating and was going blind. Her body was wracked with multiple seizures each day.
I spent three years trying to figure out what was wrong with her, Vitarello said. I basically gave up and brought her to the ER at Childrens Colorado.
Mila was admitted and her case assigned to Dr. Austin Larson, a geneticist whose main job at the hospital is to figure out whats wrong with patients who have an undiagnosed disease. An MRI found that the part of Milas brain that is responsible for balance, the cerebellum, was smaller than expected. But it was a genetic test that for the first time gave Vitarello a name for Milas illness: Batten disease, and a specific type of Batten that is so rare, just 25 people in the world are known to have it.
The disease occurs when both of a childs two CNL7 genes are mutated one mutation from each parent.
Larson was able to identify the defective gene from Milas father, but could not find one from her mother. At the time, Childrens Colorado along with most places didnt have the technology to search that deeply into Milas DNA through whole-genome sequencing, and Larson warned Milas family that it was likely impossible to find a clinical lab that could. She would need a researcher.
Vitarello turned to Facebook, begging for help for Mila but also so she could find out if her son, who was 2 at the time and completely healthy, had the same devastating disease that was taking away her daughter.
I was going to get nowhere with Mila unless I just opened up my story fully, to everyone, her mom said.
Dr. Larson had given her enough information and the right words to make a plea. A Boston physician saw her message and connected her with Dr. Timothy Yu, a neurogeneticist at Boston Childrens.
At the same time, the FDA had just approved a new drug called Spinraza, the first drug to treat a separate genetic condition called spinal muscular atrophy. The drug, injected into the fluid around the spinal cord, helped babies in clinical trials improve head control, sitting and standing.
The way Spinraza was designed was a game-changer for medicine and key in helping Mila. Yu and his team in Boston wondered if they could make a similar drug for the Colorado girl.
The Boston team spent days staring at screens of Milas DNA sequences until they discovered the other piece of the genetic puzzle in addition to the gene mutation from her father, Mila had inherited extra genetic material from her mother. The combination meant that, in the most basic terms, Mila had a sequence of broken DNA in her cells.
The drug created only for Mila contains little pieces of synthetic genetic material that search for a specific 22-letter sequence and cover it up so that her cells cannot read it. We are taking a Band-Aid and sticking it onto that part, said Dr. Scott Demarest, a pediatric neurologist at Childrens Colorado and a specialist in rare genetic epilepsies. That is literally what is happening. It is sticking to that spot so that the cell skips over that and goes to the next part that is correct.
The only difference between Spinraza and milasen is the genetic sequence inside the drugs send Band-Aids to different addresses.
After discovering the genetic flaw, Yu in Boston and Larson in Colorado called Milas mom together to give her the news. Her son did not have either of the recessive genes, and her daughter had both.
It was a huge mix of extreme happiness and, within the same second, just extreme falling-to-the-floor sadness for Mila, Vitarello recalled. My daughter had gotten both of the bad mutations and my son had gotten both of the good ones.
Next, Vitarello had to persuade a drugmaker to make a drug for one, and the FDA to allow doctors to inject it in her daughters spinal fluid.
The stars aligned, she says, still in disbelief.
Milas team made it happen by emphasizing that although this drug had the potential to work only on one person, the process could become a blueprint for other patients. Only the DNA sequence in the medicine would change.
They persuaded a drug manufacturer in California, TriLink Biotechnologies, to make Milas drug. And the FDA agreed to speed up the clinical trial process by allowing Yu to test the drug on rats at the same time Mila was receiving her first dose. The doctor had first tested it on Milas skin cells.
Milasen is technically now in clinical trial a trial of one patient involving two childrens hospitals.
The night before Milas first injection in January 2018, as Vitarello went for a run in subzero Boston, she told herself she was OK with whatever happened. Mila was out of time. Vitarello had seen the descriptions online and knew where Mila was headed.
My daughters trajectory of not treating her was so black and white, Vitarello said. Everyone always wonders what is going to happen to your life. When you have a rare disease, you can see exactly what is going to happen to your child ahead of time and its not a good thing.
I figured the worst-case scenario was not her dying, it was her being in pain, Vitarello said, recalling that she asked Yu to tell the FDA that she thought the drugs potential benefits outweighed the risk. I said, If my daughter dies on the spot, Im OK with that.
Instead, the injections that first year seemed to stop the diseases progression. Mila quit eating through a g-tube and started eating her moms pureed food again. She could hold up her head and her upper body, and her walking improved. Her seizures decreased from 30 a day to two or three.
Quality of life, those are huge, Vitarello said.
Now in the second year of treatment, some of Milas symptoms have declined, but not as steeply as other children with her disease. Milas team has upped her doses and started injecting them every two months instead of every three, but they have no precedent to follow.
They could find out years from now that they were giving Mila 1,000 times too little, her mother said.
I honestly dont know if it was in time for Mila, Vitarello said. She was really progressed when she received her treatment. There is still hope.
The key to saving more children from rare genetic diseases is diagnosing them earlier ideally at birth.
What if we found this three years sooner? Larson asked. I think about that a lot. What would it have taken to have found this the first time that (Vitarello) took Mila to a physician and said, I am concerned about the subtle difference in the way she walks?
The answer is it takes having a very broad test and being very good at interpreting that very broad swath of information.
Science is a ways off from being able to detect diseases as rare as Milas in newborns. But breakthroughs are coming for other genetic diseases.
Starting in January, spinal muscular atrophy will become one of 38 genetic diseases newborn babies are screened for via blood tests, said Raphe Schwartz, chief strategy officer for Childrens.
Childrens intends to take what it has learned through Milas case, partner with other institutions and use it to help more children, Schwartz said. What we learn reveals the roadmap for the future, he said. The future ones we do are more effective and less expensive over time.
There is a sense of urgency, but also caution.
We want to make sure we are doing it right, we are doing it safely, we are doing it for kids who are going to benefit the most, Demarest said. There are ethical challenges around it. We need to be very thoughtful and careful that we are doing this the right way, but were also doing it in a way that allows this to be a reality for kids as soon as possible and for as many as possible.
For now, Vitarello is grateful that Mila can receive her treatments in Colorado. Until September, they were traveling to Boston every other month for 10 days, but now they can leave home after breakfast on treatment days and return by dinner.
On Tuesday, Vitarello recited Goldilocks and the Three Bears and sang camp songs while Mila, bundled in blankets, received the 10-minute injection in her lower back, which Vitarello said doesnt seem to hurt Mila. They celebrated Milas 9th birthday last week, and her little brother, now 5, picked out a squishy toy and a sequined mermaid for her birthday presents.
Im faced with a huge amount of sadness around this, but at the same time, its making such a huge difference that it gives a lot of purpose to her life and it gives a lot of purpose to my life, Vitarello said. We are still fighting hard for Mila. But I can see this making a much bigger impact.
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This miracle drug was designed and manufactured for just one person a 9-year-old Boulder girl - The Colorado Sun
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Human genome | Britannica
Posted: November 20, 2019 at 5:49 am
Human genome, all of the approximately three billion base pairs of deoxyribonucleic acid (DNA) that make up the entire set of chromosomes of the human organism. The human genome includes the coding regions of DNA, which encode all the genes (between 20,000 and 25,000) of the human organism, as well as the noncoding regions of DNA, which do not encode any genes. By 2003 the DNA sequence of the entire human genome was known.
The human genome, like the genomes of all other living animals, is a collection of long polymers of DNA. These polymers are maintained in duplicate copy in the form of chromosomes in every human cell and encode in their sequence of constituent bases (guanine [G], adenine [A], thymine [T], and cytosine [C]) the details of the molecular and physical characteristics that form the corresponding organism. The sequence of these polymers, their organization and structure, and the chemical modifications they contain not only provide the machinery needed to express the information held within the genome but also provide the genome with the capability to replicate, repair, package, and otherwise maintain itself. In addition, the genome is essential for the survival of the human organism; without it no cell or tissue could live beyond a short period of time. For example, red blood cells (erythrocytes), which live for only about 120 days, and skin cells, which on average live for only about 17 days, must be renewed to maintain the viability of the human body, and it is within the genome that the fundamental information for the renewal of these cells, and many other types of cells, is found.
The human genome is not uniform. Excepting identical (monozygous) twins, no two humans on Earth share exactly the same genomic sequence. Further, the human genome is not static. Subtle and sometimes not so subtle changes arise with startling frequency. Some of these changes are neutral or even advantageous; these are passed from parent to child and eventually become commonplace in the population. Other changes may be detrimental, resulting in reduced survival or decreased fertility of those individuals who harbour them; these changes tend to be rare in the population. The genome of modern humans, therefore, is a record of the trials and successes of the generations that have come before. Reflected in the variation of the modern genome is the range of diversity that underlies what are typical traits of the human species. There is also evidence in the human genome of the continuing burden of detrimental variations that sometimes lead to disease.
Knowledge of the human genome provides an understanding of the origin of the human species, the relationships between subpopulations of humans, and the health tendencies or disease risks of individual humans. Indeed, in the past 20 years knowledge of the sequence and structure of the human genome has revolutionized many fields of study, including medicine, anthropology, and forensics. With technological advances that enable inexpensive and expanded access to genomic information, the amount of and the potential applications for the information that is extracted from the human genome is extraordinary.
Since the 1980s there has been an explosion in genetic and genomic research. The combination of the discovery of the polymerase chain reaction, improvements in DNA sequencing technologies, advances in bioinformatics (mathematical biological analysis), and increased availability of faster, cheaper computing power has given scientists the ability to discern and interpret vast amounts of genetic information from tiny samples of biological material. Further, methodologies such as fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH) have enabled the detection of the organization and copy number of specific sequences in a given genome.
Understanding the origin of the human genome is of particular interest to many researchers since the genome is indicative of the evolution of humans. The public availability of full or almost full genomic sequence databases for humans and a multitude of other species has allowed researchers to compare and contrast genomic information between individuals, populations, and species. From the similarities and differences observed, it is possible to track the origins of the human genome and to see evidence of how the human species has expanded and migrated to occupy the planet.
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BioEssays Editor: ‘Junk’ DNA Full of Information! Including Genome-Sized Genomic Code – Discovery Institute
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How many times have we heard it claimed that the vast majority of the human genome is junk and therefore could not have been designed? Even in the face of overwhelming evidence from the ENCODE project and numerous other studies showing that most of our genome has biochemical function, most evolutionists still maintain that our genomes are largely junk. But a few brave scientists, including some rare evolutionists, have been willing to buck that trend.
In a new article at Advanced Science News That Junk DNA Is Full of Information! Andrew Moore, the Editor-in-Chief of the respected biology journal BioEssays, comments on a new BioEssays paper. The paper finds that our DNA contains overlapping layered dual-function pieces of information, including a genomic code that spans virtually the entire genome in order to defin[e] the shape and compaction of DNA into the highly-condensed form known as chromatin. More about that paper in just a moment. It was written by leading Italian biologist Giorgio Bernardi who played a major role in the discovery of isochores. Isochores are important in this story. But for now, lets look at Moores essay. It has something worth mentioning in almost every paragraph.
Moore starts by saying that it should not be surprising that there is more function in the genome than we initially expected:
It should not surprise us that even in parts of the genome where we dont obviously see a functional code (i.e., one thats been evolutionarily fixed as a result of some selective advantage), there is a type of code, but not like anything weve previously considered as such.
From an intelligent design (ID) perspective, Moore is absolutely correct: finding more function in the genome should not surprise us. But Moore is not an ID proponent; hes clearly writing from an evolutionary perspective. Even as he describes extensive function in our genome, he frequently adds evolutionary narrative gloss just to remind you what side hes on. But within the evolutionary perspective, his support for mass genomic functionality does not represent the majority. There is a long history of evolutionary biologists predicting that non-protein-coding DNA is largely junk. (See Post-ENCODE Posturing: Rewriting History Wont Erase Bad Evolutionary Predictions.) As one example, in 1980 Francis Crick and Leslie Orgel wrote that Much DNA in higher organisms is little better than junk, and it would be folly in such cases to hunt obsessively for its function. Numerous similar claims have been made over the years.
Though clearly evolution-based, Moores perspective stands out in an important way: it is open to seeing coordinated function across the entire genome. Moore thus proposes an idea with which ID proponents would heartily agree:
And what if it [this other code] were doing something in three dimensions as well as the two dimensions of the ATGC code? A paper just published in BioEssays explores this tantalizing possibility
So there are multiple layers of information in DNA controlling cellular processes that operate in multiple dimensions. Not only that, but as Moore explains, these codes are frequently overlapping within our DNA sequence:
One of the intriguing things about DNA sequences is that a single sequence can encode more than one piece of information depending on what is reading it and in which direction viral genomes are classic examples in which genes read in one direction to produce a given protein overlap with one or more genes read in the opposite direction (i.e., from the complementary strand of DNA) to produce different proteins. Its a bit like making simple messages with reverse-pair words (a so-called emordnilap). For example: REEDSTOPSFLOW, which, by an imaginary reading device, could be divided into REED STOPS FLOW. Read backwards, it would give WOLF SPOTS DEER.
Though highly specified and difficult to produce by chance, overlapping codes are demonstrably present in our DNA. Proponents of intelligent design have long identified overlapping genes as a signature of design. For example, one chapter in the volume Biological Information: New Perspectives argues that Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation. The chapter observes that, DNA sequences are typically poly-functional with overlapping protein-coding sequences which can contribute to multiple overlapping codes simultaneously. But the likelihood of producing such information-rich, tightly constrained sequences by chance is exceedingly low: it is difficult to understand how poly-functional DNA could arise through random isolated mutations.
How do overlapping codes relate to the current situation? Moore explains that these dual-function pieces of information are found throughout our genome where DNA can both encode proteins and simultaneously define a genomic code:
For two distinct pieces of information to be encoded in the same piece of genetic sequence we would, similarly, expect the constraints to be manifest in biases of word and letter usage the analogies, respectively, for amino acid sequences constituting proteins, and their three-letter code. Hence a sequence of DNA can code for a protein and, in addition, for something else. This something else, according to Giorgio Bernardi, is information that directs the packaging of the enormous length of DNA in a cell into the relatively tiny nucleus. Primarily it is the code that guides the binding of the DNA-packaging proteins known as histones. Bernardi refers to this as the genomic code a structural code that defines the shape and compaction of DNA into the highly-condensed form known as chromatin.
This genomic code is thus a genome-wide feature, woven throughout our DNA, including portions of the genome that evolutionists have typically assumed had no function. This code is defined by the GC content of a stretch of DNA the level of base pairs that are guanine-cytosine (hence GC) rather than adenine-thymine. In protein-coding DNA, the third base-pair in codons can often vary from AT/TA to CG/GC without affecting the amino acid being specified. Evolutionists have presumed that the precise nucleotide in this third base pair was irrelevant, so long as the codon was synonymous, and that variation in the third nucleotide represented an unimportant non-functional feature. But Moore explains that the third nucleotide in a codon can have great functional importance apart from merely specifying the amino acid, and could actually help define this genomic code, which overlaps with the protein-code:
Protein-coding sequences are also packed and condensed in the nucleus particularly when theyre not in use (i.e., being transcribed, and then translated into protein) but they also contain relatively constant information on precise amino acid identities, otherwise they would fail to encode proteins correctly: evolution would act on such mutations in a highly negative manner, making them extremely unlikely to persist and be visible to us. But the amino acid code in DNA has a little catch that evolved in the most simple of unicellular organisms (bacteria and archaea) billions of years ago: the code is partly redundant. For example, the amino acid Threonine can be coded in eukaryotic DNA in no fewer than four ways: ACT, ACC, ACA or ACG. The third letter is variable and hence available for the coding of extra information. This is exactly what happens to produce the genomic code, in this case creating a bias for the ACC and ACG forms in warm-blooded organisms. Hence, the high constraint on this additional code which is also seen in parts of the genome that are not under such constraint as protein-coding sequences is imposed by the packaging of protein-coding sequences that embody two sets of information simultaneously.
Moores evolutionary bias is evident here as he repeatedly adds narrative gloss, ascribing functional aspects of our genome to evolution, rather than simply describing the functional nature of DNA and leaving evolution out of it. But the substance of what hes saying identifies function in an aspect of the genome that evolutionists have frequently ignored as junk.
He goes on to explain that this genomic code is not limited to protein-coding sequences, overlapping with the code that specifies protein sequences. The code also persists throughout giant portions of our genome, characterized by repetitive sequences that evolutionary scientists have, again, frequently ignored as junk. Read the following carefully, and try to filter out the gloss. It basically admits that these massive segments of our genome are functional:
But didnt we start with an explanation for non-coding DNA, not protein-coding sequences? Yes, and in the long stretches of non-coding DNA we see information in excess of mere repeats, tandem repeats and remnants of ancient retroviruses: there is a type of code at the level of preference for the GC pair of chemical DNA bases compared with AT. As Bernardi reviews, synthesizing his and others groundbreaking work, in the core sequences of the eukaryotic genome, the GC content in structural organizational units of the genome termed isochores increased during the evolutionary transition between so-called cold-blooded and warm-blooded organisms. And, fascinatingly, this sequence bias overlaps with sequences that are much more constrained in function: these are the very protein-coding sequences mentioned earlier, and they more than the intervening non-coding sequences are the clue to the genomic code. In eukaryotic genomes, the GC sequence bias proposed to be responsible for structural condensation extends into non-coding sequences, some of which have identified activities, though less constrained in sequence than protein-coding DNA. There it directs their condensation via histone-containing nucleosomes to form chromatin.
What we see here is that major portions of our genome, traditionally viewed as junk, are actually full of information in excess of mere repeats, tandem repeats and remnants of ancient retroviruses because there is a type of code at the level of preference for the GC pair of chemical DNA bases compared with AT. The purpose of the code, in short, is to direct DNA-packing in the nucleus.
The genomic code is largely defined by huge GC-biased portions of the genome called isochores. When you hear the word isochore, think of humongous portions of our genome characterized by repetitive sequences of DNA that most evolutionists have typically ignored as junk, but that ID proponents have predicted as probably having function.
Giorgio Bernardis paper in BioEssays provides an extensive discussion of the literature. It shows that isochores have functional importance and that the GC level of isochores defines a vital genomic code. Bernardi explains:
[T]he genomic code, which is responsible for the pervasive encoding and molding of primary chromatin domains (LADs and primary TADs, namely the gene spaces/spatial compartments) resolves the longstanding problems of non-coding DNA, junk DNA, and selfish DNA leading to a new vision of the genome as shaped by DNA sequences.
Bernardis view is that most of the genome is functional, contradicting the typical junk DNA perspective:
By the end of the 1980s, our knowledge of the isochore organization of the human genome had not only rejected what had been called the bean-bag view of the genome, that is, a collection of genes randomly scattered over vast expanses of junk DNA; but it had also indicated that the genome is an integrated structural, functional, and evolutionary system. This view arose from a comparative study of vertebrate genomes, centered on the analysis of their compositional patterns, namely of the compositional distributions of large DNA segments, coding sequences, and introns.
Thus, the presence of GC-rich isochores leads us to reject the junk DNA view. It indicates that the genome is an integrated structural, functional, and evolutionary system. Ignoring Bernardis evolutionary gloss, which wrongly assumes that integrated structural and functional systems can arise by blind evolutionary mechanisms, his statement is exactly what ID theory would expect. Bernardi continues explaining how we know that isochores are functional and carry the genomic code which overlaps with the genetic code:
The functional importance of isochores was already evident in the 1980s because of the correlations of their GC levels with all the genome properties tested. It was later confirmed by investigations carried out in the 1990s. The first indications that the base composition of isochores was under constraint came from the strong correlations between the composition of interspersed repeats, such as the GC-poor LINES and GC-rich SINES, and the composition of the GC-poor and GC-rich isochores, respectively, in which those sequences were located. The next step was the extension of the compositional correlations to genes (exons, introns, codon positions) located in GC-poor and GC-rich isochores, correlations that affect codon usage and amino acid composition of the encoded proteins. These points were subsequently reinforced, leading to the proposal that a genomic code was responsible for the compositional correlations just mentioned. As shown in Table S3, Supporting Information, the genomic code was further extended in the following years to include the sequence distributions, the functional properties associated with GC-poor and GC-rich isochores, and the structure and nuclear location of interphase chromatin.
Only recent investigations showed, however, that the genomic code: 1) is a structural code in that it directly encodes and molds chromatin structures and defines nucleosome binding; 2) is pervasive because it applies to the totality of the genome; 3) overlaps the genetic code and constrains it, by affecting the composition (but not the function) of coding sequences (and contiguous non-coding sequences), codon usage, and amino acid composition of the encoded proteins, as already mentioned.
Moores article, describing Bernardis findings, concludes strikingly:
These regions of DNA may then be regarded as structurally important elements in forming the correct shape and separation of condensed coding sequences in the genome, regardless of any other possible function that those non-coding sequences have: in essence, this would be an explanation for the persistence in genomes of sequences to which no function (in terms of evolutionarily-selected activity), can be ascribed (or, at least, no substantial function).
We may marvel at such complicated structures and ask but do they need to be quite so complicated for their function? Well, maybe they do in order to condense and position parts of the protein in the exact orientation and place that generates the three-dimensional structure that has been successfully selected by evolution. But with a knowledge that the genomic code overlaps protein coding sequences, we might even start to become suspicious that there is another selective pressure at work as well
Moore doesnt specify what the other selective pressure is, but clearly he sees the functionally important genomic code as pervasive throughout the genome. So heres what we have: evolutionary scientists proposing that most of our genomes sequence has functional importance because it carries a genomic code, controlling the three-dimensional packing in the nucleus. This code even overlaps with the genetic code in protein-coding DNA. Such a perspective directly contradicts the evolutionary paradigm of a genome flooded with junk.
Why would evolutionary scientists like Moore and Bernardi step outside that paradigm? The answer is simple: Their views are driven by the data. Moore or rather, more power to them!
Photo byAnn Kathrin BoppviaUnsplash.
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Biomedical Engineering Researcher to Explore Immune System Impact on Genome Engineering – University of Arkansas Newswire
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A biomedical engineering faculty member has received a $50,000 award to pursue a new line of research into the immune systems role in genome engineering.
Christopher Nelson, assistant professor of biomedical engineering, earned the funding through the American Society of Gene and Cell Therapys Career Development program. Nelson holds the 21stCentury Professorship in Biomedical Engineering.
His research program is adapting genome editing technologies to treat genetic disease. Genetic diseases are caused by a change in the DNA sequence away from the normal sequence. Nelsons research involves modifying DNA by using molecular scissors, known as CRISPR, to make precise genome modifications with a goal of fixing disease-causing mutations.
The ASGCT award adds a new direction to Nelsons research that will explore how the immune system impacts emerging genome engineering therapies.
This line of research is important to the field, as high-profile failures in the past warn that the immune system plays a critical role in the success or failure of biomolecular therapies, Nelson said.
Nelsons previous research in animal models of muscular dystrophy has shown the bodys immune response to CRISPR may provide an additional barrier to translating genome editing therapies to clinical use, he said. That work was published inNature Medicineearlier this year.
The immune response to delivery vehicles or genome editing technologies could prevent successful gene editing or cause a dangerous host response, Nelson said. Full characterization of these risks and strategies to avoid a host response are needed for clinical development.
The project will launch new lines of work in Nelsons lab by providing preliminary data for future research related to immune cell biology and immune tolerance.
Raj Rao, head of the department of biomedical engineering, said the award is an important step for Nelsons research.
I am extremely proud of Chris for receiving the ASGCT Career Development Award and for pursuing this potentially transformative project that seeks to better understand the impact of cutting-edge gene editing technologies on the immune system, he said.
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Is genome sequencing the answer to rare diseases? – Hyderus Cyf
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Rare diseases despite the infrequency that the name confers cumulatively affect around 350 million people worldwide. This figure includes roughly seventy million Indians. Could genome sequencing prove to be the tool that begins to spark medical innovation and diagnosis for the millions affected by such disorders?
The Economic Times notes a recent case in which genome sequencing has proven to be an effective means of diagnosis for conditions classified as rare diseases. A woman, who was at the time three months pregnant, came to see a paediatrician at Government Medical College in Kozhikode wanting to know if there was a way to find out if her unborn child could develop a rare immune disease her firstborn was suffering from.
The article notes that the white blood cells in her six year-old daughters body behaved abnormally, leading to organ infections and rimpaired growth. Doctors, so far, had been unable to cure the girl, she said. While the name of the condition is never revealed in the article, many rare diseases also fall under the categorisation of autoimmune disorders, such as Ashersons syndrome.
The woman underwent an antenatal procedure to retrieve genetic material from the unborn child. This was analysed and compared to genetic testing performed on the six-year-old daughter. The tests brought the welcome news that the womans baby would not have the same genetic disorder as her previous child.
This test had the luxury of comparing directly to a relative. However, most testing has to be compared to databases with one major drawback. No reliable genetic information of Indians is available and for research, our scientists have to rely on gene data banks from the US and the UK or of Caucasians, said Council of Scientific and Industrial Research (CSIR) director-general Shekhar C. Mande.
As of now, Indian genomes only represent 0.2 percent of the global genetic databanks. The current majority of genomes around 96 percent are of European ancestry. Ignoring the study of Indian genes leaves what could be a medical goldmine all but untapped.
Previous genomic studies conducted in India have uncovered genes exclusive to the Indian population that present a unique risk in developing diabetes. Knowledge of risks such as these can allow for the Indian medical system, as well as government policy, to be better informed when making decisions regarding disease prevention and treatment.
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Is genome sequencing the answer to rare diseases? - Hyderus Cyf
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