Sunscreen Saves Superhero Gene

Oct. 8, 2013 — Next time your kids complain about putting on sunscreen, tell them this: Sunscreen shields a superhero gene that protects them from getting cancer.

It is widely accepted that sunscreen stops you from getting burnt but to date there has been academic debate about the effectiveness of sunscreen in preventing skin cancers.

Now QUT has undertaken a world-first human study to assess the impact of sunscreen at the molecular level.

Researchers found sunscreen provides 100 per cent protection against all three forms of skin cancer: BCC (basal cell carcinoma); SCC (squamous cell carcinoma); and malignant melanoma.

Lead researcher Dr Elke Hacker, from QUT's AusSun Research Lab, said sunscreen not only provided 100 per cent protection against the damage that can lead to skin cancer but it shielded the important p53 gene, a gene that works to prevent cancer.

"As soon as our skin becomes sun damaged, the p53 gene goes to work repairing that damage and thereby preventing skin cancer occurring.

"But over time if skin is burnt regularly the p53 gene mutates and can no longer do the job it was intended for -- it no longer repairs sun damaged skin and without this protection skin cancers are far more likely to occur."

The study, published in the Pigment Cell & Melanoma Researchjournal, looked at the impact of sunlight on human skin, both with and without sunscreen, and found no evidence of UV-induced skin damage when proper application of sunscreen (SPF30+) had been applied to exposed area.

"Melanoma is the most lethal form of skin cancer with research showing damage of melanocytes -- the pigment-producing cells of the skin -- after sun exposure plays a role in the development of skin cancer," Dr Hacker said.

Dr Hacker said the study, funded by Cancer Council Queensland, involved 57 people undergoing a series of skin biopsies to determine molecular changes to the skin before and after UV exposure and with and without sunscreen.

"Firstly we took small skin biopsies of people's unexposed skin. We then exposed two skin sites to a mild burning dose of UV light, one site was applied with sunscreen and the other was not. We again took biopsies of both sites.

"After 24 hours, we took another set of biopsies and compared the skin samples.

"What we found was that, after 24 hours where the sunscreen had been applied, there were no DNA changes to the skin and no impact on the p53 gene," she said.

Dr Hacker said this was a significant finding.

"In Australia we have strong standards around sunscreens and their ability to protect against erythema (redness of skin)," Dr Hacker said.

"But this research looks beyond the redness to determine whether UV exposure when using sunscreen causes molecular changes to the skin, as these changes have been linked to BCC, SCC and malignant melanoma.

"When there are changes in the molecular structure it can enhance skin cancer development."

Dr Hacker said the study also provided a baseline measurement of molecular responses to UV exposure, which would now be used to investigate post-sun exposure treatments, such as super sunscreens, to assist in the repair of sun damaged skin.

Dr Hacker is a member of the Institute of Health Biomedical Innovation.

Cancer Council Queensland spokesperson Katie Clift said the research reinforced the SunSmart message in Queensland -- which has the highest rates of skin cancer in the world.

"It's imperative that all Queenslanders adopt SunSmart habits every day that they're out and about in the Sunshine State, no matter the season," Ms Clift said.

"Cancer Council Queensland recommends using SPF30 or above broad-spectrum, water-resistant sunscreen, and reapplying sunscreen every two hours.

"Applying sunscreen correctly is important. Adults should apply more than half a teaspoon of sunscreen to each arm and the face, neck and ears -- and just over one teaspoon to each leg, and front and back of the torso.

"It's also important to complement sunscreen with sun protective clothing, a broad-brimmed hat, to seek shade and slide on wraparound sunglasses for best protection."

DNA microarray

A DNA microarray (also commonly known as gene chip, DNA chip, or biochip) is a collection of microscopic DNA spots attached to a solid surface.

Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome.

For more information about the topic DNA microarray, read the full article at Wikipedia.org, or see the following related articles:

Protein microarray

A protein microarray is a piece of glass on which different molecules of protein have been affixed at separate locations in an ordered manner thus forming a microscopic array.

These are used to identify protein-protein interactions, to identify the substrates of protein kinases, or to identify the targets of biologically active small molecules.

For more information about the topic Protein microarray, read the full article at Wikipedia.org, or see the following related articles:

Gene Regulation Differences Between Humans, Chimpanzees Very Complex

Oct. 17, 2013 — Changes in gene regulation have been used to study the evolutionary chasm that exists between humans and chimpanzees despite their largely identical DNA. However, scientists from the University of Chicago have discovered that mRNA expression levels, long considered a barometer for differences in gene regulation, often do not reflect differences in protein expression -- and, therefore, biological function -- between humans and chimpanzees. The work was published Oct. 17 inScience.

"We thought that we knew how to identify patterns of mRNA expression level differences between humans and chimpanzees that would be good candidates to be of functional importance," said Yoav Gilad, PhD, Professor of Human Genetics at the University of Chicago. "Now we see that even such mRNA patterns are not translated to the protein level. Which means that it is unlikely that they can affect a functional phenotypic difference."

For genes to be expressed, DNA must be transcribed into messenger RNA (mRNA), which then code for proteins, the biological building blocks and engines that drive cellular function. Although humans and chimpanzees share highly similar genomes, previous studies have shown that the species evolved major differences in mRNA expression levels. Many of these differences were thought to indicate areas of evolutionary divergence, thus pointing to genes important for human-specific traits.

To test this, Gilad, Jonathan Pritchard, PhD, currently at Stanford University, and their team, spearheaded by postdoctoral fellow Zia Khan, PhD, used high-resolution mass spectrometry to compare the expression levels of thousands of proteins with corresponding mRNA expression data in human and chimpanzee cell lines.

The team found 815 genes with differing mRNA expression levels but only 571 genes that differed in protein expression. In total, they identified an estimated 266 genes with mRNA differences that did not lead to changes in protein levels. They found similar results in rhesus macaque cell lines when compared to both chimpanzees and humans, confirming the trend.

"Some of these patterns of mRNA regulation have previously been thought of as evidence of natural selection for important genes in humans, but this can no longer be assumed," Gilad said.

The study raises questions over why mRNA expression levels differ between species if they do not necessarily cause protein differences. Although further study is needed, Gilad believes this study suggests that protein expression levels evolve under greater evolutionary constraint than mRNA levels, via a yet-uncharacterized compensation or buffering mechanism.

For now, research that uses mRNA expression levels as a measure of the functional importance of a gene requires reassessment, and not just in studies on evolution.

"We've gained insight into complex diseases by studying mRNA transcripts, but we also have a lot of gaping holes in our knowledge. Perhaps some of them are because of this disparity," Gilad said.

Unique Skull Find Rebuts Theories On Species Diversity in Early Humans

Oct. 17, 2013 — Paleoanthropologists from the University of Zurich have uncovered the intact skull of an early Homo individual in Dmanisi, Georgia. This find is forcing a change in perspective in the field of paleoanthropology: human species diversity two million years ago was much smaller than presumed thus far. However, diversity within the "Homo erectus," the first global species of human, was as great as in humans today.

This is the best-preserved fossil find yet from the early era of our genus. The particularly interesting aspect is that it displays a combination of features that were unknown to us before the find. The skull, found in Dmanisi by anthropologists from the University of Zurich as part of a collaboration with colleagues in Georgia funded by the Swiss National Science Foundation, has the largest face, the most massively built jaw and teeth and the smallest brain within the Dmanisi group.

It is the fifth skull to be discovered in Dmanisi. Previously, four equally well-preserved hominid skulls as well as some skeletal parts had been found there. Taken as a whole, the finds show that the first representatives of the genus Homo began to expand from Africa through Eurasia as far back as 1.85 million years ago.

Diversity within a species instead of species diversity

Because the skull is completely intact, it can provide answers to various questions which up until now had offered broad scope for speculation. These relate to none less than the evolutionary beginning of the genus "Homo" in Africa around two million years ago at the beginning of the Ice Age, also referred to as the Pleistocene. Were there several specialized "Homo" species in Africa at the time, at least one of which was able to spread outside of Africa too? Or was there just one single species that was able to cope with a variety of ecosystems? Although the early Homo finds in Africa demonstrate large variation, it has not been possible to decide on answers to these questions in the past. One reason for this relates to the fossils available, as Christoph Zollikofer, anthropologist at the University of Zurich, explains: "Most of these fossils represent single fragmentary finds from multiple points in space and geological time of at least 500,000 years. This ultimately makes it difficult to recognize variation among species in the African fossils as opposed to variation within species."

As many species as there are researchers

Marcia Ponce de León, who is also an anthropologist at the University of Zurich, points out another reason: paleoanthropologists often tacitly assumed that the fossil they had just found was representative for the species, i.e. that it aptly demonstrated the characteristics of the species. Statistically this is not very likely, she says, but nevertheless there were researchers who proposed up to five contemporary species of early "Homo" in Africa, including "Homo habilis," "Homo rudolfensis," "Homo ergaster" and "Homo erectus." Ponce de León sums up the problem as follows: "At present there are as many subdivisions between species as there are researchers examining this problem."

Tracking development of "Homo erectus" over one million years thanks to a change in perspective

Dmanisi now offers the key to the solution. According to Zollikofer, the reason why Skull 5 is so important is that it unites features that have been used previously as an argument for defining different African "species." In other words: "Had the braincase and the face of the Dmanisi sample been found as separate fossils, they very probably would have been attributed to two different species." Ponce de León adds: "It is also decisive that we have five well-preserved individuals in Dmanisi whom we know to have lived in the same place and at the same time." These unique circumstances of the find make it possible to compare variation in Dmanisi with variation in modern human and chimpanzee populations. Zollikofer summarizes the result of the statistical analyses as follows: "Firstly, the Dmanisi individuals all belong to a population of a single early Homo species. Secondly, the five Dmanisi individuals are conspicuously different from each other, but not more different than any five modern human individuals, or five chimpanzee individuals from a given population."

Diversity within a species is thus the rule rather than the exception. The present findings are supported by an additional study recently published in the PNAS journal. In that study, Ponce de León, Zollikofer and further colleagues show that differences in jaw morphology between the Dmanisi individuals are mostly due to differences in dental wear.

This shows the need for a change in perspective: the African fossils from around 1.8 million years ago likely represent representatives from one and the same species, best described as "Homo erectus." This would suggest that "Homo erectus" evolved about 2 million years ago in Africa, and soon expanded through Eurasia -- via places such as Dmanisi -- as far as China and Java, where it is first documented from about 1.2 million years ago. Comparing diversity patterns in Africa, Eurasia and East Asia provides clues on the population biology of this first global human species.

This makes Homo erectus the first "global player" in human evolution. Its redefinition now provides an opportunity to track this fossil human species over a time span of 1 million years.

Researchers rewrite an entire genome -- and add a healthy twist

Yale and Harvard have recoded the entire genome of an organism and improved a bacterium's ability to resist viruses, a dramatic demonstration of the potential of rewriting an organism's genetic code.

"This is the first time the genetic code has been fundamentally changed," said Farren Isaacs, assistant professor of molecular, cellular, and developmental biology at Yale and co-senior author of the research published Oct. 18 in the journal Science. "Creating an organism with a new genetic code has allowed us to expand the scope of biological function in a number of powerful ways."

The creation of a genomically recoded organism raises the possibility that researchers might be able to retool nature and create potent new forms of proteins to accomplish a myriad purposes -- from combating disease to generating new classes of materials.

The research -- headed by Isaacs and co-author George Church of Harvard Medical School -- is a product of years of studies in the emerging field of synthetic biology, which seeks to re-design natural biological systems for useful purposes.

In this case, the researchers changed fundamental rules of biology.

Proteins, which are encoded by DNA's instructional manual and are made up of 20 amino acids, carry out many important functional roles in the cell. Amino acids are encoded by the full set of 64 triplet combinations of the four nucleic acids that comprise the backbone of DNA. These triplets (sets of three nucleotides) are called codons and are the genetic alphabet of life.

Isaacs, Jesse Rinehart of Yale, and the Harvard researchers explored whether they could expand upon nature's handywork by substituting different codons or letters throughout the genome and then reintroducing entirely new letters to create amino acids not found in nature. This work marks the first time that the genetic code has been completely changed across an organism's genome.

In the new study, the researchers working with E. coli swapped a codon and eliminated its natural stop sign that terminates protein production. The new genome enabled the bacteria to resist viral infection by limiting production of natural proteins used by viruses to infect cells. Isaacs -- working with Marc Lajoie of Harvard, Alexis Rovner of Yale, and colleagues -- then converted the "stop" codon into one that encodes new amino acids and inserted it into the genome in a plug-and-play fashion.

The work now sets the stage to convert the recoded bacterium into a living foundry, capable of biomanufacturing new classes of "exotic" proteins and polymers. These new molecules could lay the foundation for a new generation of materials, nanostructures, therapeutics, and drug delivery vehicles, Isaacs said.

"Since the genetic code is universal, it raises the prospect of recoding genomes of other organisms," Isaacs said. "This has tremendous implications in the biotechnology industry and could open entirely new avenues of research and applications."

Other participating researchers from Yale University are Hans Aerni and Adrian Haimovich.

((M2 Communications disclaims all liability for information provided within M2 PressWIRE. Data supplied by named party/parties. Further information on M2 PressWIRE can be obtained at http://www.presswire.com on the world wide web. Inquiries to info@m2.com)).



For more stories covering the world of technology, please see HispanicBusiness' Tech Channel

New partnerships to forge synthetic biology links between UK and China

Nanowerk News) Scientific links between the UK and China in the exciting field of synthetic biology will be boosted by the announcement of five grants awarded through a Synthetic Biology China Partnering Award.

The awards, co-funded by the Biotechnology and Biological Research Council (BBSRC), the Chinese Academy of Sciences (CAS) and the Engineering and Physical Sciences Research Council (EPSRC) will provide funding to BBSRC and EPSRC supported researchers to partner and develop long term fruitful relationships with Chinese scientists.

A total of £124,000 will be provided by BBSRC and EPSRC to UK scientists, with CAS providing matched funding to Chinese researchers, for activities such as exchange of early career researchers, workshops, reciprocal access to facilities, networking and travel. The funding is provided for up to four years and it is anticipated that the partnerships will lead to new joint grant applications and high impact research.

This is the first time BBSRC and EPSRC have run a joint funding call with CAS and it is hoped that this will form a strong foundation for further joint working with China in the future.

Synthetic biology is an emerging field where engineering principles are applied in biology to design, engineer and build new biological systems.

Professor Douglas Kell, Chief Executive of BBSRC, said: "Synthetic biology is an exciting new field with enormous potential to bring benefits to people around the world in all sorts of ways, for example producing better antibiotics or manufacturing low carbon fuels.

"Co-funded initiatives such as this scheme will see British and Chinese scientists learning from each other's expertise and benefiting from the globalisation of excellent science."

Cao Jinghua, Deputy Director-General of Bureau of International Cooperation of CAS, said: "We at CAS attach great importance to international collaboration.

"The idea of this program is to put the best minds together. Together our scientists and these from the UK can advance this field more efficiently. In the progress of their cooperation, I hope they will further strengthen their linkages and collaboration, and tackle bigger challenges for the needs of mankind."

Professor David Delpy, Chief Executive of EPSRC, said: "EPSRC is pleased to be part of this joint international call which demonstrates the wide scope for synthetic biology to create impact in many academic fields. It has the potential to create new solutions to address pressing global challenges, such as the need for new fuels, better waste management and new medicines."

The funding has been awarded to:

Professor Nigel Minton, University of Nottingham

Prof Minton, of the BBSRC Sustainable Bioenergy Centre (BSBEC), will collaborate with Professor Weihong Jiang of the Key Laboratory of Synthetic Biology at the Shanghai Institute for Biological Sciences. Industrial partners Lanzatech and BaoSteel are contributing a total of £6,000 to aid work on the design of strategies and tools for producing bacteria able to make low carbon fuels and chemicals from industrial waste gas without consuming food or land resources.

Professor John Ward, University College London

Prof Ward will collaborate with Professor Zhihua Zhou at the Shanghai Institute for Biological Sciences using synthetic biology and metagenomics approaches to obtain new enzymes and build pathways for the breakdown of biomass.

Professor Nigel Scrutton, University of Manchester

Prof Scrutton will collaborate with Professor Lixin Zhang at the Chinese Academy of Sciences Institute of Microbiology to establish cooperative research on the use of synthetic biology approaches for production of high-value fine chemicals.

Dr Louise Horsfall, University of Edinburgh

Dr Horsfall will collaborate with Professor Pingsheng Liu at the Chinese Academy of Sciences Institute of Biophysics to research the potential of lipid droplets as tools for synthetic biology and test the enzymes of a bacterium called Rhodococcus opacus for their ability to degrade plant materials. The partners will also examine the ethical, legal and social implications of synthetic biology in an applied context and within international partnerships

Professor Gregory Challis, University of Warwick

Prof Challis will collaborate with Professor Shuang-Yan Tang at the Chinese Academy of Sciences Institute of Microbiology, Beijing on the development of synthetic biology approaches for the identification and structural diversification of novel antibiotics.

Source: BBSRC

CHOP's Harvest Toolkit Offers Innovative Data Discovery Resource for Biomedical Researchers

( A team of informatics experts and biomedical researchers at The Children's Hospital of Philadelphia offers a new software toolkit to help researchers explore complex data sets without having to become database technicians themselves. Harvest is an open-source highly interactive framework designed by CHOP's Center for Biomedical Informatics.)

Biomedical researchers often confront large quantities of information that may be amassed in many forms: vital signs, blood cell counts, lengthy DNA sequences, bar graphs, MRIs, patient demographics, and so much more. How do researchers assemble, access and analyze all that data without having to become specialized database technicians themselves?

A team of informatics experts and biomedical researchers at The Children’s Hospital of Philadelphia (CHOP) offers a new software toolkit to help researchers wrangle data. Their open-source, highly interactive framework called Harvest (http://harvest.research.chop.edu) is designed to let users to navigate quickly among different types and levels of data.

“We want to help researchers explore their data, not their database,” said Byron Ruth, lead developer of Harvest at CHOP’s Center for Biomedical Informatics (CBMi). Ruth is one of the co-authors of a paper introducing CBMi’s Harvest framework, appearing online today in the Journal of the American Medical Informatics Association.

Co-author Michael J. Italia added, “Research institutions typically work through their information technology staff to provide a single data warehouse that may be too general-purpose for all its projects, or develop one-off solutions on a case-by-case basis for each project.”

“Our approach in Harvest is different,” said Italia, the CBMi’s manager of Applications Research. “We decided to focus on end-users, generalizing the toolkit for application to any biomedical study with multiple collaborators, but also allowing individual software developers and data managers to customize the software for specific projects.”

Harvest, said Italia, “isn’t just shrink-wrapped, ready-to-go software.” He estimates that Harvest typically provides 80 percent of the work, leaving it to any institution’s software developer to adapt the framework to a project’s needs, in collaboration with each project’s principal investigator. Harvest is open-source, so users are free to see bug reports, check software patches, and share fixes and customizations with a wider community of users.

A key feature of Harvest is the ability to maneuver smoothly among various levels of data, from individual patient records to aggregated reports of all patients in a database, and to subpopulations in between. Users can construct queries to slice and dice data—grouping subjects, for instance, by age or ethnicity, calling up individual blood test results or MRIs, or including or excluding specific diagnoses.

One advantage of Harvest is that it provides transparency and visibility to data in a manner that is familiar to a researcher who is invested in a particular disease or project. “Harvest adopts convenient and clear interfaces to view and explore data that are increasingly used in other industries, such as social media,” said senior author and CBMi director Peter S. White, Ph.D. “We have found that this often helps users to quickly familiarize themselves with data they are seeing, which increases the likelihood that they will trust the resource, and even be incentivized to contribute to the project as it develops.”

The Harvest developers say their tool reflects the growing complexity of research in the Big Data era of electronic health records and genomic technology. In the 1980s and 1990s, much federal research followed a hypothesis-driven model, focusing on predefined measurements within a patient population. Many current databases collect vast amounts of many data types with fewer preconceived notions of what is significant. “Harvest allows users to formulate and refine questions and even explore a different view of data that wasn’t apparent or important to them a few minutes before,” said Italia.

The CBMi team originally designed Harvest to manage data from AudGenDB, an audiology database funded by the National Institute on Deafness and Other Communications Disorders.

In the current paper, the study team evaluated Harvest by running it through its paces with data from two other collections: CardioDB, which stores clinical data from 47,000 of CHOP’s pediatric cardiology patients, and OpenMRS, a public dataset holding lab results, infection status and other clinical results from electronic health records.

CBMi is now applying Harvest to more collections, including the Longitudinal Pediatric Data Resource, a long-term informatics system being created to store clinical data derived from thousands of children with conditions detected in national newborn screening programs. “Although these collections contain very different types of data, the Harvest toolkit is flexible enough to adapt to these different scenarios, while at the same time maintaining a consistent set of basic components,” added Ruth.

Harvest has been focused primarily on the end-user up to this point. Future work includes a bigger focus on software developers and applications support personnel who are responsible for setting up and maintaining Harvest applications. “However, as we think about the life cycle of a Harvest application, we want it to be as easy as possible for administrators and software developers to get Harvest into the hands of researchers,” Italia said.

The National Institutes of Health (grant DC012207) and the David Lawrence Altschuler Endowed Chair Fund at Children’s Hospital supported this research. Co-authors with Ruth, Italia and White were Jeffrey W. Pennington, Jeffrey Miller, Stacey Wrazien, Jennifer G. Loutrel, and E. Bryan Crenshaw, all from The Children’s Hospital of Philadelphia. White is the corresponding author.

“Harvest: An Open Platform for Developing Web-Based Biomedical Data Discovery and Reporting Applications,” Journal of the American Medical Informatics Association, published online Oct. 16, 2013.
http://jamia.bmj.com/content/early/2013/10/16/amiajnl-2013-001825

About The Children’s Hospital of Philadelphia: The Children’s Hospital of Philadelphia was founded in 1855 as the nation’s first pediatric hospital. Through its long-standing commitment to providing exceptional patient care, training new generations of pediatric healthcare professionals and pioneering major research initiatives, Children’s Hospital has fostered many discoveries that have benefited children worldwide. Its pediatric research program receives the highest amount of National Institutes of Health funding among all U.S. children’s hospitals. In addition, its unique family-centered care and public service programs have brought the 527-bed hospital recognition as a leading advocate for children and adolescents. For more information, visit http://www.chop.edu.

Philanthropic trust awards $2m biomedical research grants

The Ramaciotti Foundations, a philanthropic trust managed by Perpetual, last night announced the recipients of the annual Ramaciotti Awards for biomedical research.

The main award of $1 million went to the Centenary Institute's Cytometry research program, with the $50,000 Medal for Excellence going to Professor Douglas Hilton for his discoveries in blood cell production.

Also announced were 17 Equipment and Establishment grant recipients of up to $75,000 each, totalling over $1.2 million.

Perpetual's head of philanthropic services Andrew Thomas said: "This year's winners join an honour board of outstanding individuals and institutions pioneering vital frontiers for medical research.

"It is important to reflect how these people and projects have benefited from the foresight and conviction of Vera Ramaciotti who, since establishing the charitable trusts in 1970 with $6.7 million, through the Ramaciotti Foundations, has enabled over $52.5 million to be granted to biomedical research, with another $52 million invested for future contributions.

Founded in 1971, the Ramaciotti Foundations' combined capital today stands at $52 million. The Ramaciotti Awards have provided grants in the fields of molecular biology, genetics and immunology

Turning biologists into programmers

(Howard Salis is assistant professor of agricultural and biological engineering, hms17@psu.edu.)
(Synthetic life could create real benefits.)


 
For more than half a century scientists have looked on the DNA molecule as life's blueprint. Now biological engineers are beginning to see the molecule not as a static plan, but more like a snippet of life's computer code that they can program.
Penn State researchers are unraveling the mystery of how nature codes and recodes this program to address some of the world's biggest challenges, says Howard Salis, assistant professor of biological engineering and chemical engineering.
"You can engineer DNA to reprogram the metabolism of simple organisms and you can program them to make what you want, or to make it more efficiently, says Salis. "The trick is to understand how the organism interprets its DNA, and then to optimize new DNA sequences to rationally control its behavior."
This rapidly developing field, often referred to as synthetic biology, may one day allow biological engineers to design living systems just as reliably as engineers currently design and build airplanes, cars and trains, according to Salis. It also holds the key to products such as inexpensive biofuels, environmentally friendly plastics, and less expensive pharmaceuticals.
"Decoding the function of DNA -- what the DNA makes the organism do -- and then recoding it with a new human-desired function is central to synthetic biology," he says.
 
Adenine, cytosine, guanine and thymine are the chemical components of DNA. Better known by their initials, ACGT, these chemicals form the nucleotide bases of DNA and combine in a mind-boggling arrangement to specify which amino acids are needed to make certain proteins.
Biological engineers are starting to sound more like computer engineers as they begin to also look at DNA as information -- something that can be decoded and recoded -- as well as its blend of chemicals.
Salis’s group recently developed a genetic compiler software that researchers and scientists have used to predict and help control protein expressions in bacteria. So far, it has designed more than 30,000 sequences for academic and commercial researchers around the globe. The software cuts down on time-consuming trial and error and is a significant step toward unlocking biology as an advanced manufacturing platform, Salis says.
Despite the futuristic sound of synthetic biology, the idea -- and simple forms of the technology -- have been around for decades, he adds. One example of this early use of biological engineering is the use of fungi to manufacture penicillin, one of the most common forms of antibiotics -- a technique discovered in 1928. In the late 1970s, researchers used genetic engineering techniques to produce synthetic insulin that could be used to treat diabetic patients. The discovery helped replace insulin derived from pigs, which was expensive and often ineffective.
In the 2000s, better and faster computers have steadily boosted DNA sequencing and synthesis technologies, enabling the sequencing of the human genome and the synthesis of whole bacterial genomes.
Salis sees the early achievements of synthetic biology as only the beginning of ways researchers will improve upon nature's evolutionary genius.
"Evolution was the first engineer and now we are learning how to take evolution into different directions to solve humanity's problems," he says. "Since all life uses DNA, it's the same genetic code, just interpreted in different ways."

A host of applications

He and other biological engineers are busy discovering ways to turn leftover agricultural products into sustainable biofuels that can ease fuel costs and help boost energy independence. By tweaking the DNA, engineers have developed microbes that digest corn leaves and stalks, produce sugars and then convert the sugars into biofuels. Their goal is to fine-tune the microbe's genetic code to optimize biofuel production and deliver a superior, low-cost product.
"We could redesign bacterial metabolism to make it a super biofuel producer," he says.
Significant hurdles remain to make the process economical. As Salis explains, funding for biofuel projects usually traces the path of gasoline prices. As those prices increase and consumers chafe under higher costs, biofuels become more acceptable and economical, which attracts investors and venture capitalists. However, when consumers adjust to higher fuel prices, interest in finding alternative sources of energy wanes.
"The cyclical nature of research funding has greatly harmed our ability to overcome technical and economical hurdles," says Salis. "You need a long-term commitment to the project."
In addition to helping quench the world's growing demand for energy, biological engineers may use synthetic biology techniques for medicine. Salis says engineers can reprogram organisms' metabolisms to produce anti-cancer and anti-bacterial drugs.
Living organisms can be reengineered to do more than build things -- they can also be used to break things down and clean them up, he adds. Bacterial metabolisms could be programmed to digest industrial waste material and toxic chemicals, for example.
However, Salis recognizes that talk of genetically engineered microbes worries some people.
"We have been domesticating bacteria and yeast to make bread, beer and yogurt for thousands of years," he says. "When we engineer microbes to make a new drug or a new fuel, the microbe does not survive very well in the outside world."
Competition between all microbes -- natural and engineered -- will put the brakes on any microbe that tries to do one thing very well, he adds.
"One thing we do as engineers is learn how to, from a critical point of view, balance what risks to take compared to the benefits of taking those actions," he says.
In fact, his team is working on building a genetic security system to prevent genetically modified DNA from falling into the wrong hands. Engineering DNA to perfection still takes a long time and industrial espionage in biotechnology is a growing problem.
"DNA is the ultimate self-replication information storage device," says Salis. "Once you build a better DNA molecule, that's your product."

 

There’s much more to IQ than biology and DNA

(The claim by Michael Gove’s adviser Dominic Cummings that exam results are in the genes suggests he needs to take a few biology lessons)


There was a bit of a spat about my own trade last week. Intelligence, so Michael Gove’s special adviser told us, is due to genetic. Dominic Cummings is convinced that a child’s fate lies in its dna. He claims that as much as 70 per cent of academic performance is genetically derived – and that the quality of teaching, as a result, fades into the background.

That statement, and many like it, shows a fundamental misunderstanding of how biology works. Cummings is, no doubt, talking about a measure called “heritability”, the proportion of total variation in a population that is due to genetic variation. There have been endless squabbles about this, with estimates for adult Intelligence quotient varying from zero to almost 100 per cent. But his figure of 70 per cent is not far from recent estimates based on the similarity of relatives, on adoptions, and on studies of twins.

Heritability is, crucially, a statement about populations, not individuals. It certainly does not mean that seven tenths of every child’s talents reside in the double helix, and that teachers hence become irrelevant. If anything, it means the opposite.

Nature and nurture always work together. Almost everything is genetic, but we usually deal with it by changing the environment. If you have, as thousands do, an inborn error that makes it hard to deal with cholesterol and pushes up the risk of heart attacks, the treatment is to cut down on fat and take statins. Being run over by a bus might seem the ultimate piece of environmental bad luck, but genes are much involved – for men, with their pesky Y chromosomes, are at twice the risk.

Biological differences in intelligence fascinate both ends of the political spectrum, and it is difficult not to become entangled in vulgar quarrels about doctrine when discussing them. But variation in height does not have that problem. There, heritability for adults is even higher, with figures of around 80 per cent; proof, perhaps, that the vertically challenged are born to be stunted.

In fact, that is not true at all. My father knew Dylan Thomas slightly (and disliked him a lot: in his words, “a terrible snob”). Once, writing of himself in the third party, Thomas claimed: “He was of normal height; normal for Wales, that is.” Well, at five foot seven, so was I – but not any more, for since the early Fifties, the average Celt has shot up by two inches. IQ scores have risen to match.

In Wales and everywhere else, the DNA has not changed, but circumstances have. The evidence is everywhere. Second, third and fourth children are shorter, and score less well on IQ tests, than firstborn, although they share the same parents. Whatever the importance of genes, the environment (be it a school’s cook or its maths teachers) plays a major role.

A closer look shows just how misleading it is to use heritability as a key to educational policy. For both height and IQ, the measure for children is far lower than for adults, since they respond much more readily to their circumstances: the IQ of a poor child adopted into a well-off household usually rises by several points. For 10-year-olds, the heritability of IQ is, in some studies, as little as 20 per cent.

With adults, social position also plays a major part. In America, with its extremes of wealth and poverty, the heritability of IQ among the poorest tenth is a fraction of their equivalents at the other end of the income scale: their miserable circumstances allow few among them to show their potential.

For geneticists, the more we learn about DNA, the more important the environment appears. The lesson from the double helix is that we need more and better teachers, rather than wringing our hands about the unkindness of fate. A few lessons about elementary biology might be a good place to start.