Can Hobbyists and Hackers Transform Biotechnology?

For most of us, managing our health means visiting a doctor. The more serious our concerns, the more specialized a medical expert we seek. Our bodies often feel like foreign and frightening lands, and we are happy to let someone with an MD serve as our tour guide. For most of us, our own DNA never makes it onto our personal reading list.

Biohackers are on a mission to change all that. These do-it-yourself biology hobbyists want to bring biotechnology out of institutional labs and into our homes. Following in the footsteps of revolutionaries like Steve Jobs and Steve Wozniak, who built the first Apple computer in Jobs’s garage, and Sergey Brin and Larry Page, who invented Google in a friend’s garage, biohackers are attempting bold feats of genetic engineering, drug development, and biotech research in makeshift home laboratories.

In Biopunk, journalist Marcus Wohlsen surveys the rising tide of the biohacker movement, which has been made possible by a convergence of better and cheaper technologies. For a few hundred dollars, anyone can send some spit to a sequencing company and receive a complete DNA scan, and then use free software to analyze the results. Custom-made DNA can be mail-ordered off websites, and affordable biotech gear is available on Craigslist and eBay.

via Can Hobbyists and Hackers Transform Biotechnology? – Technology Review.

Advertisement

New study into bladder regeneration heralds organ replacement treatment

Researchers in the United States have developed a medical model for regenerating bladders using stem cells harvested from a patient’s own bone marrow. The research, published in STEM CELLS, is especially relevant for paediatric patients suffering from abnormally developed bladders, but also represents another step towards new organ replacement therapies.

The research, led by Dr Arun Sharma and Earl Cheng from the Feinberg School of Medicine at Northwestern University and Children’s Memorial Research Center, focused on bone marrow mesenchymal stem cells (MSCs) taken from the patient. Previously studies into the regenerative capacity of cells in bladders have focused on animal models, but these have translated poorly in clinical settings.

Scientists find potential strategy to eliminate poisonous protein from Alzheimer brains

Scientists at the Gladstone Institute of Neurological Disease (GIND) have identified a new strategy to destroy amyloid-beta (AB) proteins, which are widely believed to cause Alzheimer’s disease (AD). Li Gan, PhD, and her coworkers discovered that the activity of a potent AB-degrading enzyme can be unleashed in mouse models of the disease by reducing its natural inhibitor cystatin C (CysC).

Chemists devise self-assembling ‘organic wires’

From pacemakers constructed of materials that so closely mimic human tissues that a patient’s body can’t discern the difference to devices that bypass injured spinal cords to restore movement to paralyzed limbs, the possibilities presented by organic electronics read like something from a science fiction novel.

Derived from carbon-based compounds (hence the term “organic”), these “soft” electronic materials are valued as lightweight, flexible, easily processed alternatives to “hard” electronics components such as metal wires or silicon semiconductors. And just as the semiconductor industry is actively developing smaller and smaller transistors, so, too, are those involved with organic electronics devising ways to shrink the features of their materials, so they can be better utilized in bioelectronic applications such as those above.

Gene therapy restores vision to mice with retinal degeneration

Massachusetts General Hospital (MGH) researchers have used gene therapy to restore useful vision to mice with degeneration of the light-sensing retinal rods and cones, a common cause of human blindness. Their report, appearing in the Oct. 14 Proceedings of the National Academy of Sciences, describes the effects of broadly expressing a light-sensitive protein in other neuronal cells found throughout the retina.

New class of antibiotics may lead to therapy for drug-resistant tuberculosis

Researchers are hot on the trail of a whole new class of broad-spectrum antibiotics, according to a new report in the October 17th issue of the journal Cell, a Cell Press publication.

The discovery holds promise at a time when a quarter of all deaths worldwide are the result of bacterial infectious diseases, and yet more and more disease-causing bacteria are growing resistant to currently available antibiotics. What’s more, the antibiotics under study in this report may offer a more effective and shorter course of treatment for tuberculosis (TB), a disease that is carried by one in three people in the world and that is particularly difficult to treat with today’s antibiotics.

Computer model reveals cells’ inner workings

After spending years developing a computational model to help illuminate cell signaling pathways, a team of MIT researchers decided to see what would happen if they “broke” the model.

The results, reported in the Oct. 17 issue of the journal Cell, reveal new ways in which cells process chemical information and could indicate how to maximize the effectiveness of disease treatments such as chemotherapy.

Could Dr. House be replaced by a computer?

Scientists know that different normal and diseased tissues behave differently. But a method that tells them just how they do so may one day give medical science a new way to fight obesity, hypertension, diabetes and other dangerous disorders of the metabolism.

Until now, scientists had to rely on basic observations at the cellular level, since they lacked information about the metabolic processes of individual organs, such as the liver, heart and brain.

But a new computational approach developed by computer scientists Tomer Shlomi, Moran Cabili and Prof. Eytan Ruppin from the Blavatnik School of Computer Science at Tel Aviv University may help science gain a clearer overall picture of the metabolic processes in our different tissues.

Border control: Study shows how proteins permit entry to a cell

The means by which proteins provide a ‘border control’ service, allowing cells to take up chemicals and substances from their surroundings, whilst keeping others out, is revealed in unprecedented molecular detail for the first time today (16 October) in Science Express.

Bioengineers build first-ever multi-input ‘plug-and-play’ synthetic RNA device

Engineers from the California Institute of Technology (Caltech) have created a “plug-and-play” synthetic RNA device–a sort of eminently customizable biological computer–that is capable of taking in and responding to more than one biological or environmental signal at a time.

In the future, such devices could have a multitude of potential medical applications, including being used as sensors to sniff out tumor cells or determine when to turn modified genes on or off during cancer therapy.

Researchers successfully reprogram keratinocytes attached to a single hair

The first reports of the successful reprogramming of adult human cells back into so-called induced pluripotent stem (iPS) cells, which by all appearances looked and acted liked embryonic stem cells created a media stir. But the process was woefully inefficient: Only one out of 10,000 cells could be persuaded to turn back the clock.

Now, a team of researchers led by Juan Carlos Izpisúa Belmonte at the Salk Institute for Biological Studies, succeeded in boosting the reprogramming efficiency more than 100fold, while cutting the time it takes in half. In fact, they repeatedly generated iPS cells from the tiny number of keratinocytes attached to a single hair plucked from a human scalp.

Nanotechnology boosts war on superbugs

This week Nature Nanotechnology journal (October 12th) reveals how scientists from the London Centre for Nanotechnology (LCN) at UCL are using a novel nanomechanical approach to investigate the workings of vancomycin, one of the few antibiotics that can be used to combat increasingly resistant infections such as MRSA. The researchers, led by Dr Rachel McKendry and Professor Gabriel Aeppli, developed ultra-sensitive probes capable of providing new insight into how antibiotics work, paving the way for the development of more effective new drugs.

Scientists eliminate viral vector in stem cell reprogramming

Previously, Dr. Shinya Yamanaka of Kyoto University and the Gladstone Institute of Cardiovascular Disease, had shown that adult cells can be reprogrammed to become embryonic stem cell–like using a cancer-causing oncogene as one of the four genes required to reprogram the cells, and a virus to transfer the genes into the cells. In the last year, Dr. Yamanaka and other labs showed that the oncogene, c-Myc, is not needed. However the use of viruses that integrate into the genome prohibit use of iPS cells for regenerative medicine because of safety concerns: its integration into the cell’s genome might activate or inactivate critical host genes.

Now Dr. Yamanaka’s laboratory in Kyoto has eliminated the need for the virus. In a report published this week in Science, they showed that the critical genes can be effectively introduced without using a virus. The ability to reprogram adult cells into iPS cells without viral integration into the genome also lays to rest concerns that the reprogramming event might be dependent upon viral integration into specific genomic loci that could mediate the genetic switch.

Scientists develop sensitive nanowire disease detectors

Yale scientists have created nanowire sensors coupled with simple microprocessor electronics that are both sensitive and specific enough to be used for point-of-care (POC) disease detection, according to a report in Nano Letters.

The sensors use activation of immune cells by highly specific antigens — signatures of bacteria, viruses or cancer cells — as the detector. When T cells are activated, they produce acid, and generate a tiny current in the nanowire electronics, signaling the presence of a specific antigen. The system can detect as few as 200 activated cells.

Can genetic information be controlled by light?

DNA, the molecule that acts as the carrier of genetic information in all forms of life, is highly resistant against alteration by ultraviolet light, but understanding the mechanism for its photostability presents some puzzling problems. A key aspect is the interaction between the four chemical bases that make up the DNA molecule. Researchers at Kiel University have succeeded in showing that DNA strands differ in their light sensitivity depending on their base sequences. Their results are reported by Nina Schwalb and colleagues in the current issue of the journal Science appearing on October 10, 2008.

The role of stem cells in renewing the cornea

A group of researchers in Switzerland has published a study appearing in the Oct 1 advance online edition of the Journal Nature that shows how the cornea uses stem cells to repair itself.

Using mouse models they demonstrate that everyday wear and tear on the cornea is repaired from stem cells residing in the corneal epithelium, and that more serious repair jobs require the involvement of other stem cells that migrate from the limbus, a region between the cornea and the conjunctiva, the white part of the eye.

When a light goes on during thought processes

Thought processes made visible: An international team of scientists headed by Mazahir Hasan of the Max Planck Institute for Medical Research in Heidelberg has succeeded in optically detecting individual action potentials in the brains of living animals.

The scientists introduced fluorescent indicator proteins into the brain cells of mice via viral gene vectors: the illumination of the fluorescent proteins indicates both when and which neurons are communicating with each other. This new method enables the observation of brain activity over a period of many months and provides new ways of identifying, for example, the early onset of dysfunction in neurological disorders such as Alzheimer’s and Parkinson’s. The fluorescent proteins could also provide scientists with information about the ways in which normal aging processes affect nerve cell communication (Nature Methods, September 2008).

Nanodiamond drug device could transform cancer treatment

A Northwestern University research team has developed a promising nanomaterial-based biomedical device that could be used to deliver chemotherapy drugs locally to sites where cancerous tumors have been surgically removed.

The flexible microfilm device, which resembles a piece of plastic wrap and can be customized easily into different shapes, has the potential to transform conventional treatment strategies and reduce patients’ unnecessary exposure to toxic drugs. The device takes advantage of nanodiamonds, an emergent technology, for sustained drug release.

Many receptor models used in drug design may not be useful after all

It may very well be that models used for the design of new drugs have to be regarded as impractical. This is the sobering though important conclusion of the work of two Leiden University scientists published in Science this week. The editorial board of the renowned journal even decided to accelerate the publication on the crystal structure of the adenosine A2A receptor via Science Express. Together with an expert team at the Scripps Institute (La Jolla) led by crystallographer Ray Stevens, Ad IJzerman and postdoctoral fellow Rob Lane worked on the structure elucidation of this protein, which is one of caffeine’s main targets in the human body, and a key player in Parkinson’s disease.

New method for creating inducible stem cells is remarkably efficient

Some of the most challenging obstacles limiting the reprogramming of mature human cells into stem cells may not seem quite as daunting in the near future. Two independent research papers, published by Cell Press in the September 11th issue of the journal Cell Stem Cell, describe new tools that provide invaluable platforms for elucidating the molecular, genetic, and biochemical mechanisms associated with reprogramming. The new findings also offer considerable hope toward making the reprogramming process more therapeutically relevant.

Consortium develops new method to manipulate genetic material

A multi-institutional team of researchers, including scientists at the University of Minnesota Medical School, have developed a powerful tool for genomic research and medicine. The robust method will allow researchers to generate synthetic enzymes that can target and manipulate DNA sequences for inactivation or repair.

New nano device detects immune system cell signaling

Scientists have detected previously unnoticed chemical signals that individual cells in the immune system use to communicate with each other over short distances.

The signals the researchers detected originated in dendritic cells – the sentinels of the immune system that do the initial detection of microscopic invaders – and were received by nearby T-cells, which play a number of crucial roles in the immune system, including coordination of attacks on agents that cause disease or infection.

artist

An artist’s rendering of the completed MTN shows cells trapped inside as signals travel to them. (Source: Vanderbilt)

3D Animation explaining basics of the human genome

A dynamic 3D computer animated video takes you “inside” for a close-up look at how we’re made.  3D modeling and animation created by Bill Baker, Bakedmedia, Inc. and Mike Fisher for the National Human Genome Research Institute.

Stem Cells Restore Muscle In Mice With Muscular Dystrophy

Researchers at the Joslin Diabetes Center have demonstrated for the first time that transplanted muscle stem cells can both improve muscle function in animals with a form of muscular dystrophy and replenish the stem cell population for use in the repair of future muscle injuries.

Scientists have developed a new method for making biological ‘chips’

Protein chips – or ‘protein arrays’ as they are more commonly known – are objects such as slides that have proteins attached to them and allow important scientific data about the behaviour of proteins to be gathered.

Functional protein arrays could give scientists the ability to run tests on tens of thousands of different proteins simultaneously, observing how they interact with cells, other proteins, DNA and drugs.

Dean Kamen’s Amazing Robotic “Luke” Arm

Segway inventor Dean Kamen is looking to re-invent the prosthetic arm. IEEE Spectrum caught up with Kamen and one of his “test pilots,” to see the robotic arm (named after Luke Skywalker’s articficial limb) in action.

Genes That Control Embryonic Stem Cell Fate Identified

Scientists have identified about two dozen genes that control embryonic stem cell fate. The genes may either prod or restrain stem cells from drifting into a kind of limbo, they suspect. The limbo lies between the embryonic stage and fully differentiated, or specialized, cells, such as bone, muscle or fat.

By knowing the genes and proteins that control a cell’s progress toward the differentiated form, researchers may be able to accelerate the process — a potential boon for the use of stem cells in therapy or the study of some degenerative diseases, the scientists say.

Antibody Engineering Cuts the Collateral Damage of Cancer Drugs

Killing cancer cells, while leaving normal tissue unscathed, is almost impossible.

Nanotechnology may do the trick, but big pharmaceutical companies are far from embracing that strategy. In the meantime, highly-engineered biological molecules will fill the void.

Researchers converts biodiesel byproduct into omega-3 fatty acids

The typical American diet often lacks omega-3 fatty acids despite clinical research that shows their potential human health benefits. Zhiyou Wen, assistant professor of biological systems engineering in Virginia Tech’s College of Agriculture and Life Sciences, found a way to grow these compounds using a byproduct of the emerging biodiesel industry.

Coatings to help medical implants connect with neurons

Plastic coatings could someday help neural implants treat conditions as diverse as Parkinson’s disease and macular degeneration.

The coatings encourage neurons in the body to grow and connect with the electrodes that provide treatment.

Slipping through cell walls, nanotubes deliver high-potency punch to cancer tumors in mice

The problem with using a shotgun to kill a housefly is that even if you get the pest, you’ll likely do a lot of damage to your home in the process. Hence the value of the more surgical flyswatter.

Cancer researchers have long faced a similar situation in chemotherapy: how to get the most medication into the cells of a tumor without “spillover” of the medication adversely affecting the healthy cells in a patient’s body.

Now researchers at Stanford University have addressed that problem using single-walled carbon nanotubes as delivery vehicles. The new method has enabled the researchers to get a higher proportion of a given dose of medication into the tumor cells than is possible with the “free” drug-that is, the one not bound to nanotubes-thus reducing the amount of medication that they need to inject into a subject to achieve the desired therapeutic effect.

New study shows compounds from soy affect brain and reproductive development

Two hormone-like compounds linked to the consumption of soy-based foods can cause irreversible changes in the structure of the brain, resulting in early-onset puberty and symptoms of advanced menopause in research animals, according to a new study by researchers at North Carolina State University. The study is important in determining how these compounds can cause reproductive health problems, as well as in providing a key building block for how to treat these problems.

Being a control freak aids dividing cells

Micromanagers may generate resentment in an office setting, but they get results in your body. New data indicate that a dividing cell takes micromanagement to the extreme, tagging more than 14,000 different sites on its proteins with phosphate, a molecule that typically serves as a signal for a variety of biological processes.

This preponderance of signals suggests that the cell may become a control freak during the division process, regulating each of its parts, no matter how obscure. It may take extreme measures to ensure that each “daughter” receives a full complement of cellular material. The new data—published online in PNAS—open unexplored frontiers to developmental biologists, cancer researchers, and others who study cell growth and proliferation.

Researchers Unveil Near-complete Protein Catalog For Mitochondria

Imagine trying to figure out how your car’s power train works from just a few of its myriad components: It would be nearly impossible. Scientists have long faced a similar challenge in understanding cells’ tiny powerhouses — called “mitochondria” — from scant knowledge of their molecular parts.

Now, an international team of researchers has created the most comprehensive “parts list” to date for mitochondria, a compendium that includes nearly 1,100 proteins. By mining this critical resource, the researchers have already gained deep insights into the biological roles and evolutionary histories of several key proteins. In addition, this careful cataloging has identified a mutation in a novel protein-coding gene as the cause behind one devastating mitochondrial disease.

Supercomputer explores biochemical landscape to find memory switches

Switches are a part of daily life, from snoozing your alarm, turning on the coffee maker, firing up your car engine, and so on until we turn off the lights at night. Researchers have now cataloged even more templates of possible switches within a living cell than we use throughout our day.

A colorful "map" of switches within cells was created by Naren Ramakrishnan at Virginia Tech and Upinder S. Bhalla at the National Centre for Biological Sciences in India, using Virginia Tech’s SystemX supercomputer. Every little square in the picture is a "switch." The lines indicate the relationship between the switches.

Synthetic molecules may be less expensive alternative to therapeutic antibodies

Researchers at UT Southwestern Medical Center have developed a simple and inexpensive method to screen small synthetic molecules and pull out a handful that might treat cancer and other diseases less expensively than current methods.

In one screen of more than 300,000 such molecules, called peptoids, the new technique quickly singled out five promising candidates that mimicked an antibody already on the market for treating cancer. One of the compounds blocked the growth of human tumors in a mouse model.

Caltech bioengineers develop ‘microscope on a chip’

Researchers at the California Institute of Technology have turned science fiction into reality with their development of a super-compact high-resolution microscope, small enough to fit on a finger tip. This “microscopic microscope” operates without lenses but has the magnifying power of a top-quality optical microscope, can be used in the field to analyze blood samples for malaria or check water supplies for giardia and other pathogens, and can be mass-produced for around $10.

Researchers correct decline in organ function associated with old age

As people age, their cells become less efficient at getting rid of damaged protein — resulting in a buildup of toxic material that is especially pronounced in Alzheimer’s, Parkinson’s disease, and other neurodegenerative disorders.

Now, for the first time, scientists at the Albert Einstein College of Medicine of Yeshiva University have prevented this age-related decline in an entire organ — the liver — and shown that, as a result, the livers of older animals functioned as well as they did when the animals were much younger. Published in the online edition of Nature Medicine, these findings suggest that therapies for boosting protein clearance might help stave off some of the declines in function that accompany old age.

Excellent animation explaining the mechanism of RNAi technology

This superb animation from Youtube explains the RNA interference mechanism that recently won the Nobel prize for its discovery. The original video is from the journal Nature.

Designer RNA fights high cholesterol

Small, specially designed bits of ribonucleic acid (RNA) can interfere with cholesterol metabolism, reducing harmful cholesterol by two-thirds in pre-clinical tests, according to a new study by researchers at UT Southwestern Medical Center in collaboration with Alnylam Pharmaceuticals and the Massachusetts Institute of Technology.

In a study that appears online today and in an upcoming issue of the Proceedings of the National Academy of Sciences, researchers found that a single dose of a small interfering RNA (siRNA), a chemical cousin of DNA, lowered cholesterol levels up to 60 percent in rodents, with the effects lasting for weeks.

Scientists overcome nanotech hurdle

When you make a new material on a nano scale how can you see what you have made? A team of scientists has made a significant step toward overcoming this major challenge faced by nanotechnology scientists.

With new research published today (13 August) in ChemBioChem, the team from the University of Liverpool, The School of Pharmacy (University of London) and the University of Leeds, show that they have developed a technique to examine tiny protein molecules called peptides on the surface of a gold nanoparticle. This is the first time scientists have been able to build a detailed picture of self-assembled peptides on a nanoparticle and it offers the promise of new ways to design and manufacture novel materials on the tiniest scale – one of the key aims of nanoscience.

New evidence of battle between humans and ancient virus

For millennia, humans and viruses have been locked in an evolutionary back-and-forth — one changes to outsmart the other, prompting the second to change and outsmart the first. With retroviruses, which work by inserting themselves into their host’s DNA, the evidence remains in our genes. Last year, researchers at Rockefeller University and the Aaron Diamond AIDS Research Center brought an ancient retrovirus back to life and showed it could reproduce and infect human cells. Now, the same scientists have looked at the human side of the story and found evidence that our ancestors fought back against that virus with a defense mechanism our bodies still use today.

First-Ever Recording of Blood Vessel Development During the Formation of an Organ

 

A new microscope system that can take 3-D pictures of an embryonic mouse organ over 24 to 48 hours has shown Duke Medical Center researchers the first glimpse of the formation of blood vessels during development.

Among other things, a team lead by cell biologist Blanche Capel, Ph.D., has found a previously unknown mechanism in the formation of blood vessels that may help scientists better understand how a tumor rallies a blood supply to its aid.

Scientists create ‘designer enzymes’

Chemists from UCLA and the University of Washington have succeeded in creating “designer enzymes,” a major milestone in computational chemistry and protein engineering.

Designer enzymes will have applications for defense against biological warfare, by deactivating pathogenic biological agents, and for creating more effective medications.

Craig Venter: On the verge of creating synthetic life

Can we create new life out of our digital universe?” asks Craig Venter. And his answer is, yes, and pretty soon. He walks the TED2008 audience through his latest research into “fourth-generation fuels” — biologically created fuels with CO2 as their feedstock. His talk covers the details of creating brand-new chromosomes using digital technology, the reasons why we would want to do this, and the bioethics of synthetic life. A fascinating Q&A with TED’s Chris Anderson follows .  

Researchers make first direct observation of 3-D molecule folding in real time

All the crucial proteins in our bodies must fold into complex shapes to do their jobs. These snarled molecules grip other molecules to move them around, to speed up important chemical reactions or to grab onto our genes, turning them “on” and “off” to affect which proteins our cells make.

Military-grade gel-based liquid bandages: new frontline wound treatment

The GelSpray Liquid Bandage is a major advance in the management and care of combat casualty and civilian wounds. Much like epoxy is dispensed in household kits, the dressing is applied with a dual syringe that releases two polymer ingredients. These polymers react rapidly upon mixing to form a gel-based dressing that frontline combat soldiers can apply to their own wounds. The dressing conforms to the wound geometry, adheres to intact skin but not directly to the injured tissue, and resists abrasion.n. 

Lab-on-a-Chip Breaks Protein-Expression Bottleneck

The Nucleic Acid Programmable Protein Array (NAPPA) was developed at the Harvard Institute of Proteomics and led to the spin-out of Auguron about a year ago. The firm says this technology enables proteins from any gene in the genome to be generated on microchips from surface printed DNA.

New MIT tool probes brain circuits

Researchers at the Picower Institute for Learning and Memory at MIT report in the Jan. 24 online edition of Science that they have created a way to see, for the first time, the effect of blocking and unblocking a single neural circuit in a living animal.

This revolutionary method allowed Susumu Tonegawa, Picower Professor of Biology and Neuroscience, and colleagues to see how bypassing a major memory-forming circuit in the brain affected learning and memory in mice.

Newly Engineered Genetic Switches Enhance Production Of Proteins, Pharmaceuticals

Bacteria have evolved complex mechanisms called quorum sensing systems that provide for cell-to-cell communication, an adaptation that allows them to wait until their population grows large enough before mounting an attack on a host or competing for nutrients. Lianhong Sun, a chemical engineer at the University of Massachusetts Amherst, has engineered one of these systems to create genetic switches that could lower the cost of producing therapeutic proteins and pharmaceuticals.