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Wednesday, August 23, 2017

The Introduction of Namibian National Database's project.

Sunday, July 2, 2017

Genomic Enrollment


Research coordinators from the Million Veteran Program (MVP) at the Central Western Massachusetts VA explain the program to a veteran during an outreach event. (Veterans Affairs Department photo)
Genes and military service:

Stars and Stripes | 2 Jul 2017 | 
A large-scale Department of Veterans Affairs project to research how veterans' genes and military service affect their health surpassed 580,000 participants Friday during an enrollment event at American Legion headquarters in downtown Washington, D.C.
The Million Veteran Program was designated the largest genomic database in the world when it reached 500,000 participants last August. Project leaders plan to use the information to research conditions such as diabetes, cancer, Gulf War illness, heart disease, kidney disease, schizophrenia, bipolar disorder and post-traumatic stress disorder. But the project could face an uncertain future based on President Donald Trump's proposed 2018 VA budget, veterans with the American Legion said.The budget proposal specifically states that using the Million Veteran Program to advance precision medicine would be a "particular goal" in 2018. But the budget would cut the funding allotted to medical research.The American Legion has testified to lawmakers about their concerns.
"We noticed that in the [fiscal] 2018 budget that $18 [million] had been stripped out from [the Information Technology] appropriation for all of VA research," said Joe Plenzler, a spokesman for the American Legion. The total amount in that fund was $20 million, he said.
"We are very concerned about the long-term impacts on cutting-edge research projects like the Million Veteran Program. This research is important and will help develop precision therapies that will benefit veterans and the American people in every legislative district," Plenzler said. "We're heading in the wrong direction here. These cuts will limit the amount of research that can be done using the [Million Veteran Program] resource, and that's a mistake." Gerardo Avila and Roscoe Butler, the last two veterans to voluntarily enroll at the Friday event, put the database over the 580,000 mark. VA staff asked them about their medical and military history and collected blood samples.
The Million Veteran Program began collecting data in 2011, and it has the goal of reaching 1 million participants by 2020 or 2021, said Sumitra Muralidhar, the program director. "Our ultimate goal was really to be able to provide improved and personalized health care to veterans, and to the population at large eventually," she said. "We're changing the paradigm of medicine. Traditionally, a doctor checks your symptoms and makes a diagnosis based on that. The future is a holistic picture, looking at DNA, the molecular profile of a person and lifestyle."
The program was developed with "meager resources," Muralidhar said. "We leveraged what we already had," she said. "We've been very diligent with where we put those resources." The VA sent 4 million invitations to veterans in the mail in order to recruit participants. To participate, veterans can go to one of 65 VA medical centers across the country that are equipped to do enrollments. Veterans must be enrolled in VA health care to be eligible.
Muralidhar said she's now working with the Defense Department in an attempt to open enrollment to current servicemembers. Enrolling people earlier could help researchers better track the effects of toxic exposure in the military and improve the likelihood the servicemembers would be helped by the research. Most participants are from the Vietnam War era, in the age range of 60 to 65, Muralidhar said. Less than 2 percent are younger than 30. "We have very few younger veterans," she said. "We're going to follow people who enroll throughout their lifetimes. So if they enroll early, there's a better chance of applying what we learn from this program to them and help them. We can prevent illnesses."
Some veterans have expressed privacy concerns with providing their information to the program. Muralidhar insisted the information is kept in a secure system that only a few VA employees are authorized to access.
A VA website has a list of locations enrolling veterans into the program.

Related Topics

Department of Veteran Affairs Donald Trump Defense Budget

Saturday, June 24, 2017

Catch-up with Bioengineers

                                                                               Medical Biosensor 



Researchers at the University of Texas at Dallas have developed a wearable diagnostic biosensor that can detect three interconnected, diabetes-related compounds -- cortisol, glucose and interleukin-6 -- in perspired sweat for up to a week without loss of signal integrity. The team envisions that their wearable devices will contain a small transceiver to send data to an application installed on a cellphone.
Credit: University of Texas at Dallas
Researchers at The University of Texas at Dallas are getting more out of the sweat they've put into their work on a wearable diagnostic tool that measures three diabetes-related compounds in microscopic amounts of perspiration.
"Type 2 diabetes affects so many people. If you have to manage and regulate this chronic problem, these markers are the levers that will help you do that," said Dr. Shalini Prasad, professor of bioengineering in the Erik Jonsson School of Engineering and Computer Science. "We believe we've created the first diagnostic wearable that can monitor these compounds for up to a week, which goes beyond the type of single use monitors that are on the market today."
In a study published recently in Scientific Reports, Prasad and lead author Dr. Rujute Munje, a recent bioengineering PhD graduate, describe their wearable diagnostic biosensor that can detect three interconnected compounds -- cortisol, glucose and interleukin-6 -- in perspired sweat for up to a week without loss of signal integrity.
"If a person has chronic stress, their cortisol levels increase, and their resulting insulin resistance will gradually drive their glucose levels out of the normal range," said Prasad, Cecil H. and Ida Green Professor in Systems Biology Science. "At that point, one could become pre-diabetic, which can progress to type 2 diabetes, and so on. If that happens, your body is under a state of inflammation, and this inflammatory marker, interleukin-6, will indicate that your organs are starting to be affected."
Last October, Prasad and her research team confirmed they could measure glucose and cortisol in sweat. Several significant advances since then have allowed them to create a more practical, versatile tool.
"We wanted to make a product more useful than something disposable after a single use," Prasad said. "It also has to require only your ambient sweat, not a huge amount. And it's not enough to detect just one thing. Measuring multiple molecules in a combinatorial manner and tracking them over time allows us to tell a story about your health."
One factor that facilitated their device's progress was the use of room temperature ionic liquid (RTIL), a gel that serves to stabilize the microenvironment at the skin-cell surface so that a week's worth of hourly readings can be taken without the performance degrading over time.
"This greatly influences the cost model for the device -- you're buying four monitors per month instead of 30; you're looking at a year's supply of only about 50," Prasad said. "The RTIL also allows the detector to interface well with different skin types -- the texture and quality of pediatric skin versus geriatric skin have created difficulties in prior models. The RTIL's ionic characteristics make it somewhat like applying moisturizer to skin."
Prasad's team also determined that their biomarker measurements are reliable with a tiny amount of sweat -- just 1 to 3 microliters, much less than the 25 to 50 previously believed necessary.
"We actually spent three years producing that evidence," Prasad said. "At those low volumes, the biomolecules expressed are meaningful. We can do these three measurements in a continuous manner with that little sweat."
Prasad envisions that her wearable devices will contain a small transceiver to send data to an application installed on a cellphone.
"With the app we're creating, you'll simply push a button to request information from the device," Prasad said. "If you measure levels every hour on the hour for a full week, that provides 168 hours' worth of data on your health as it changes."
That frequency of measurement could produce an unprecedented picture of how the body responds to dietary decisions, lifestyle activities and treatment.
"People can take more control and improve their own self-care," Prasad said. "A user could learn which unhealthy decisions are more forgiven by their body than others."
Prasad has emphasized "frugal innovation" throughout the development process, making sure the end product is accessible for as many people as possible.
"We've designed this product so that it can be manufactured using standard coating techniques. We made sure we used processes that will allow for mass production without adding cost," Prasad said. "Our cost of manufacturing will be comparable to what it currently takes to make single-use glucose test strips -- as little as 10 to 15 cents. It needs to reach people beyond America and Europe -- and even within first-world nations, we see the link between diabetes and wealth. It can't simply be a small percentage of people who can afford this."
Prasad was motivated to address this specific problem in part by her own story.
"South Asians, like myself, are typically prone to diabetes and to cardiovascular disease," Prasad said. "If I can monitor on a day-to-day basis how my body is responding to intake, and as I age, if I can adjust my lifestyle to keep those readings where they need to be, then I can delay getting a disease, if not prevent it entirely."
For Prasad, the latest work is a fulfilling leap forward in what has already been a five-year process.
"We've been solving this problem since 2012, in three phases," Prasad said. "The initial concept for a system level integration of these sensors was done in collaboration with EnLiSense LLC, a startup focused on enabling lifestyle based sensors and devices. In the market, there's nothing that is a slap-on wearable that uses perspired sweat for diagnostics. And I think we are the closest. If we find the right partner, then within a 12-month window, we hope to license our technology and have our first products in the market."

Story Source:
Materials provided by University of Texas at Dallas visit the main source for more information.

Wednesday, November 2, 2016

DNA App Software


There is a part of you that you’ve never met before!


DNA App software and online store for genetic data will not only make the process of  DNA sequencing cheaper, but of course could revolutionized everything we never imagining,since everyone have possibility to know his or her health risks and predispositions, with these knowledge health workers such as doctors and geneticists may afford to avert many diseases just before manifestation. Thank to the human genomic project (HGP) that has finished sequencing some DNA libraries. The complete sequenced data in (HGP) will make this intriguing idea of developing genetic cloud system and application software.  Our genomes contains information about our health risks(phathogenesis), our physical traits(phenotype), and whom we’re related to like ancestry (genotype). Dr. Justin Kao the cofounder of Helix biotech ,a San Francisco based company that last summer secured more than $100 million in a quest to create the first ever “app store” for genetic information. Helix company has team up with another biotechnology corporate called Illumina,the leading manufacturer of ultrafast DNA sequencing machines.

Helix and Illumina have some ideas to collect a spit sample from anyone who buys a DNA app, sequence and analyze the customers’ genes, and then digitize the findings so they can be accessed by software developers who want to sell other apps. Helix calls this idea “sequence once, query often.” The company says customers will find these apps on websites and possibly in their Android and Apple app stores. With its ties to Illumina, Helix thinks it can eble to decode the entire person’s genome about 20,000 genes and a few other bits at just lower cost of about $100, about one-fifth of what it costs other companies. If Helix spent less in such project could afford its second gambit: to generate and store this type of data for all customers, even if they initially make only one specific genetic query.The engine to power the app store is being assembled a mile from Illumina’s San Diego headquarters, in a building where workmen were still bending sheet metal and laying floor tiles in January. Several miles of data cables strung through the ceiling will be connected to a large farm of sequencing machines, able to process the DNA from a million samples a year. Illumina’s  CEO,
Jay Flatley, also chairman of Helix, has said it could be the largest sequencing center ever on planet.

Helix plans to launch the store this year or next. Customers will control their data by deciding who sees it. There’s even a “nuclear button” to erase every A, G, C, and T. But key details are still being sorted out. Will people be able to download their DNA information and take it elsewhere? Probably, yes though they might pay extra for the privilege. One company that already lending assistance to Helix is Good Start Genetics based in Cambridge, Massachusetts, that offers pre-conception testing. These DNA tests tell parents-to-be if they share a risk for passing on a serious genetic condition, such as cystic fibrosis. Jeffrey Luber, Good Start’s head of business development, says it hopes to reach a larger audience with an app that can report a few important risks.

A looming question mark is the U.S. Food and Drug Administration (FDA), which has kept close tabs on gene tests and will decide how much information Helix apps can reveal. Right now, says Keith Stewart, director of the Center for Individualized Medicine at the Mayo Clinic, most apps that return real medical information for people and reveal the chance of cancer, say, not just how much Neanderthal is in your DNA would need agency approval, or at least a doctor in the loop. “The bottom line is : What are the regulatory constraints on information that is truly useful.
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Further sources:



Credit: Given to Javier JaĆ©n and Senior Editor Antonio Regalado (MIT Biomedicines review)
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Tuesday, October 25, 2016

X-Rays' Machines Damage DNA


The bad effects of Chemotherapy Regimen:

Scientists under the chief researcher Dr. Peter Campbell at Wellcome Trust Sanger Institute, London have, for the first time, found how X-rays and other radioactive particles that normally emitted by common therapeutic devices in hospitals and clinics, of which were presumed to treat cancer tumors could further again worsening health condition in humans by damaging DNA.  Not so many cancer patients are so lucky enough to live when they  randomly go through these chemotherapy regimens. It has officially recorded now that the X-rays' energy-waves are not  selective, the chemotherapy it kill every living cell includes cancerous tumour and health ones. Thanks, to those ongoing medical researches that eventually reveal the bad effects of chemotherapy system. Researchers at Wellcome Trust Sanger Institute in UK have already identified the degree of damage in human cells which cause by ionising radiation, such as gamma rays,X-rays and radioactive particles used in every clinical applications. The new medical studies found that the Chemotherapy is not only lead to the elimination of tumours alone but the same radiation particles used in the process could cause cancer simultaneously. 

This traditional and randomness type of treatment can overwhelm DNA repairing mechanism in health living cells and leading to more health implications.   "we studied the genomes of cancers caused by radiation in comparison to tumours that arose spontaneously," said Peter Campbell. 


Your DNA Health Matters:
Radiation can damage anyone's DNA. Radiation is a high-powered particles or energy.  Luckily, our cells are very good at repairing the spontenous damage so it takes a lot of radiation to do permanent harm. Damaged DNA matters because your DNA has the instructions for making and running you. If these instructions get damaged, it can sometimes affect how well you run.  Like any good instructions, the ones in DNA are written up with letters adenine (A)cytosine (C)guanine (G) and thymine (T) that tells your cells what to do. These instructions are written in a language called the genetic code. 

The high energy of radiation or prolong in radioactive environment can mess up the instructions by changing those biological letters. It can also tear the DNA by displace some of these letters or bring them closer together. This would be like ripping out anything from part of a page to a whole chapter of your personal instruction manual. These changes can have a real impact on a cell or a person if the cell can't fix it in time.  Like any instructions, some mistakes can be tolerated. And luckily for us, our DNA has a lot of white space where a bit of damage is fine. When these parts get hit, our instructions are hardly affected at all. But when critical DNA gets hit and doesn't get fixed, problems like cancers can happen. Or problems can be passed down to the next generation. As I said though, our cells are really good at fixing these mistakes so it usually isn't a problem unless our cells get overwhelmed by too much radiation. This is an example whenever doctors exposing cancer patient constantly on chemotherapy regimen.

Actually, to lecturing you how radiation affects our DNA. One way is by breaking the long string of letters apart. This can happen to just one or both of the strands. If double strand breaks don't get fixed, then part of your DNA can be deleted, duplicated or stuck. Any of these problems can cause cancers and other genetic disorders. Double strand breaks can also be big problems for you and even your future kids' chromosomes.

UV radiation:
Too much sunlight can damage your DNA by messing up the base pairing. UV light will often make two T's that are next to each other to clog together making something called a dimer. Our cells have ways to fix this problem but if there is too many TT pairs, your cells can't deal very well with it. Some cells with lots of thymine dimers will die. You've seen this happen if your skin ever peeled after a sunburn. Cells that can't fix themselves and don't die could become cancerous. Melanoma is a common UV-induced skin cancer. Your cells have amazing ways of repairing "damaged"  but you can help them out by avoiding radiation when possible. Wear your sunscreen and try to stay away from uranium mines and sources.  

Conclusion it is advisable to avoid chemotherapy and opt other alternative form of treatments that are more holific in its medical approach. 

The blog news in this article is well researched and you can read more at:

Friday, October 7, 2016

Bioforensics:

Human Microbiomes: A new study conducted at Harvard University School of Public Health researches shows that the microbial communities we carry inside our bodies and as well outside the bodies which known as the Human Microbiomes have the potential to identify an individuals, much like a fingerprint. Researchers demonstrated that personal microbiomes contain enough distinguishable biological features so unique to construct the outer phenotype of a person. The study, rigorously show that by identifying people using microbiome-recorded database is very feasible in near future. The research surprisingly indicate that those unique microbial inhabitants, could raise potential privacy concerns for any subject directed in human microbiome research projects.
"Linking a human DNA sample to a DNA Database has became a basic for forensic genetics, which is now a decades-old field. The Bioforensic has moved on, and in this study it shown that the same sort of linking is possible using DNA sequences of microbes that inhabiting inside and outside human body without touching human's DNA. "This technique has opened the door to harvest microbiome's DNA samples and develop special databases, which has the potential to expose the information of the host, for example infections, which are detectable from the microbiome sample itself," said Eric Franzosa, a leading research fellow in the Department of Biostatistics at Harvard Chan. Franzosa. The scientists used publicly available microbiome data produced through the Human Microbiome Project (HMP), which surveyed microbes from the stool, saliva, skin, and other body substances, the samples collected from 242 individuals over a month.



The researchers also adapted a classical computer science algorithm to combine stable and distinguishing sequence features from individuals' initial microbiome samples and place them into individual-specific "codes." They then compared the codes to microbiome samples collected from the same individuals' at follow-up visits. The results showed that the codes were unique among hundreds of individuals, and that a large fraction of individuals' microbial "fingerprints" remained stable over a one-year sampling period. The codes constructed from gut samples were particularly stable, with more than 80% of individuals identifiable up to a year after the sampling period.



Wednesday, October 5, 2016

A Biological DNA Circuit

A biological cell's DNA can recall its primordial history: The biologists and engineers at MIT design new synthetic biology circuits that combine memory and logic. The biological chip allows scientists to program cells to perform some novel functions such as fluorescing in response to a particular chemical or producing drugs in response to disease markers.



Very soon this new development will prompt the technical revolution from Digital computers to analog computers, a cell circuit can able to translates electrical instructions that naturally written in the cell's genes into a language more intelligible to humans by that human beings and machines "computers" will communicating to each others. The breakthrough in science and biology could help pave the way to highly efficient, highly accurate analog simulations of entire organs. In recent years, analog computers have proven to be much more efficient at simulating biological systems than digital computers.
Timothy Lu is  Associate Professor of Biological Engineering and Electrical Engineering and Computer Science. He is also the senior author of the new study, which appears in the 22 July issue of Science.  In 2013, Lu and other colleagues designed cell circuits that could perform a logic function and then store a memory of the event by encoding it within the cell's DNA. The  machine circuits that they designed  rely on enzymes called recombinases. When activated by a specific input in the cell, such as a chemical signal, recombinases either delete or invert a particular stretch of DNA, depending on the orientation of two DNA target sequences known as recognition sites. The stretch of DNA between those sites may contain recognition sites for other recombinases that respond to different inputs. Flipping or deleting those sites alters what will happen to the DNA if a second or third recombinase is later activated. Therefore, a cell's history can be determined by sequencing its DNA.

Biological circuits:

 Using this special language, the researchers already programmed 60 circuits on span with different functions, and 45 of them worked correctly the first time they were tested. Many of the biological circuits were designed to measure some environmental conditions, such as oxygen level or glucose concentration, and they all respond accordingly. Another circuit was designed to rank three different inputs and then respond based on the priority of each one. Another advantage of this technique is its speed,“It would take years to build these types of circuits" said Voigt.

This blog news presented and written by E.A. Nambili Samuel whom also is a Bio-medical Engineering student at Cyprus International University,Turkey.

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