MIT 'seeing machine' offers hope to blind

An MIT poet has developed a small, relatively inexpensive "seeing machine" that can allow people who are blind, or visually challenged like her, to access the Internet, view the face of a friend, "previsit" unfamiliar buildings and more.

Recently the machine received positive feedback from 10 visually challenged people with a range of causes for their vision loss who tested it in a pilot clinical trial. The work was reported in Optometry, the Journal of the American Optometric Association, earlier this year.

The work is led by Elizabeth Goldring, a senior fellow at MIT's Center for Advanced Visual Studies. She developed the machine over the last 10 years, in collaboration with more than 3O MIT students and some of her personal eye doctors. The new device costs about $4,000, low compared to the $100,000 price tag of its inspiration, a machine Goldring discovered through her eye doctor.

Goldring's adventures at the intersection of art and high technology began with a visit to her doctor, Lloyd Aiello, head of the Beetham Eye Institute of the Joslin Diabetes Center. At the time, Goldring was blind. (Surgeries have since restored vision in one eye).

To better examine her eyes, Aiello asked her to go to the Schepens Eye Research Institute at Harvard, where technicians peered into her eyes with a diagnostic device known as a scanning laser opthalmoscope, or SLO. With the machine they projected a simple image directly onto the retina of one eye, past the hemorrhages within the eye that contributed to her blindness. The idea was to determine whether she had any healthy retina left.

It turns out that she did, and was able to see the image - a stick figure of a turtle. But the turtle wasn't very interesting, Goldring said. So she asked if they could write the word "sun" and transmit that through the SLO. "And I could see it!" she said. "That was the first time in several months that I'd seen a word, and for a poet that's an incredible feeling."

She went on to use the device for many other visual experiences. For example, she developed a "visual language" consisting of short words that incorporate graphics and symbols that convey the meaning of words and make them easier to see and read.

But although the SLO held promise as more than a diagnostic device, it had serious drawbacks. In addition to the prohibitive cost, the SLO is large and bulky. Goldring determined to develop a more practical machine for the broader blind public.

She did so by collaborating over the past several years with Rob Webb, the machine's inventor and a senior scientist at the Schepens Eye Research Institute; Aiello; Dr. Jerry Cavallerano, an optometrist at Joslin; William Mitchell, former dean of MIT's School of Architecture and Planning and now a professor in the Program in Media Arts and Sciences; the late Steve Benton, an acclaimed optical physicist and MIT professor; and former MIT affiliate James Cain.

She has also worked with dozens of MIT graduate students and undergraduates, including Sylvia Gonzalez (S.B. 2003) and Shima Rayej (S.B. 2004), who helped design and construct the seeing machine.

"We essentially made the new machine from scratch," Goldring said. While still allowing the projection of images, video and more onto a person's retina, the new desktop device costs much less than its predecessor in part because it doesn't include the diagnostic feedback of the SLO. The new seeing machine also replaces the laser of the SLO with light-emitting diodes, another source of high-intensity light that is much cheaper. Like its inspiration, the seeing machine is designed to be used by one eye.

The pilot clinical trial of the seeing machine involved visually impaired people recruited from the Beetham Eye Institute. All participants had a visual acuity of 20/70 or less in the better-seeing eye. A person with 20/70 vision can see nothing smaller than the third line from the top of most eye charts. Most participants, however, had vision that was considered legally blind, meaning they could see nothing smaller than the "big E" on a standard eye chart.

With her weak eye, Goldring can distinguish between light and dark and she can see hand movement, although not individual fingers. She cannot recognize faces or read.

Subjects "had a wide range of cause for vision loss, including diabetic retinopathy, macular degeneration (the fastest growing cause of blindness), and visual field loss," said Cavallerano, a coauthor of the paper and another of Goldring's doctors.

Participants used the machine to view 10 examples of Goldring's visual language. A majority - six - interpreted all 10 "word-images" correctly. "They responded really well to the visual language," Goldring said. "One woman told me she would love to see recipes written that way."

They also used the machine to navigate through a virtual environment, raising the potential for "previewing" unfamiliar buildings a person wants to visit.

Goldring explained that visually challenged people are often terrified of going to new places. "There's a fear of missing simple visual cues, steps and not being able to decipher elevator buttons." (She noted that less than 10 percent of the blind read Braille.) Further, bystanders who aim to help - "there are five steps there; it's the third door on the left" - are often wrong, especially people with good vision, Goldring said. "If you are visually challenged, if you see something once using the machine, you remember."

Participants explored the virtual environment - which represented the inside of an MIT building - via a joystick that allowed them to move forward, backward and sideways.

All of the participants reported that the machine "may have the potential to assist their mobility in unfamiliar environments," according to the Optometry article. Concluded Goldring: "A couple of them said they'd tried every seeing aid available (magnifying devices, etc.), and this was by far the best, even in this rough, rough shape."

Goldring and colleagues are now working toward a large-scale clinical trial of a color seeing machine (the device tested in the pilot trial was black and white). With the color version, participants can explore a museum gallery containing some of Goldring's art. When a person gets close enough to a piece, the work is explained in Goldring's voice.

Source : Massachusetts Institute of Technology

Discovery may speed forest biotechnology

Researchers have discovered the genetic controls which cause trees to stop growing and go dormant in the fall, as well as the mechanism that causes them to begin flowering and produce seeds – a major step forward in understanding the basic genetics of tree growth.

The findings were made by scientists from the Swedish University of Agricultural Sciences, Oregon State University and two other institutions, and published in the journal Science. They represent a significant fundamental advance in explaining the annual growth cycles and reproduction of trees.

By knowing the genes that control these processes, it should be possible to genetically engineer trees that flower and reproduce more quickly. The long, slow growth of trees before they produce seed has been a major stumbling block towards the types of breeding that has been common with annual crop plants, and this may open the door to important advances in intensive forestry and fruit tree improvement.

Information of this type, researchers say, may also help scientists better predict how some types of trees and tree populations will respond to climate change.

"Before this we never really knew what genes were involved in the initiation of tree flowering or the cessation of growth in the fall," said Steven Strauss, a professor of forest genetics at OSU. "At least in theory, it may now be possible to dramatically speed up tree breeding programs and strategies.

"Trees grow for a long time before they begin to produce seed, several years and sometimes decades," he said. "Because of that, a lot of breeding approaches common with short-lived species that flower rapidly, such as corn and wheat, have been too slow to be practical."

A remaining obstacle, Strauss said, is public understanding of the nature and safety of genetic engineering with trees, which has led to limited interest in the field by private industry and sometimes unwieldy regulations by government agencies. These genes could be used just to speed up conventional breeding, and then removed prior to commercial plantings, he said. However, the level of regulation and concern about genetic engineering may prevent even this application.

In this research, scientists studied the genes CO and FT that were first isolated from the annual plant Arabidopsis. The genes in that plant are responsible for the day-length regulation of flowering. They discovered that the same genes had been conserved through millions of years of separate evolution and also performed similar functions in aspen trees.

To their surprise, however, the researchers found that the CO/FT combination also controlled the cessation of vegetative tree growth in the fall – something that Arabidopsis plants, which die after a single growing season, do not need to do.

These processes, scientists say, reflect a critical tradeoff between tree growth and survival. Temperate trees have to stop growing and go dormant in the winter or they literally freeze to death.

"From an evolutionary perspective, it's easy to understand why forest trees don't flower and produce seed and pollen earlier," Strauss said. "When they are young, the trees that survive need to focus their energy on growth and height in order to compete for sunlight with other trees, and only later in their life do they divert energy to produce seed."

Strauss noted that for the same reasons, any releases of such early-flowering genes into wild populations are very unlikely to be of ecological concern, as trees bearing them would have a competitive disadvantage when growing with wild forest trees, and thus would not spread to any significant degree.

It also appears that the CO/FT genetic combination is critical to help trees adapt to local conditions, the researchers found. They studied aspen trees from different populations, and found that trees adapted to colder northern climates shut down growth earlier in the summer to prepare for long, harsh winters. The genetic mechanisms that adapt trees to these conditions and control it are so strong that trees will behave about the same even if they are transplanted to warmer regions, the scientists say.

For applied research, Strauss said, researchers can now induce activation of the FT gene earlier, so that trees will reproduce at much younger ages – months instead of years - and better lend themselves to conventional genetic manipulation. It could be possible, he said, to more rapidly breed some desirable traits, and then, via normal sexual crosses, remove the FT gene to leave behind trees that no longer have it, nor reproduce abnormally early.

In other cases, a modestly strong FT gene might be left in place to provide sustained benefits, such as earlier or more heavily flowering fruit tree varieties. Especially in situations where conventional approaches are ineffective, the gene could provide a new option for modifying flower and fruit production, which fruit tree breeders do routinely.

A better understanding of these processes could also provide information about how trees may react and adapt to climate change, or perhaps identify tree populations based on their DNA that are most at risk. Such populations might benefit from accelerated breeding or transplantation to aid their survival. This would give ecologists and conservation geneticists more tools to work with, Strauss said.

Source : Oregon State University

Researchers led by a University of Missouri-Columbia professor of reproductive biotechnology have reported success in freezing and preserving swine em

Researchers led by a University of Missouri-Columbia professor of reproductive biotechnology have reported success in freezing and preserving swine embryos that were created by in vitro techniques and that carried modified genetic material. After thawing and transfer to a surrogate mother, some of the embryos went on to produce live piglets with new genetic traits.

In a paper posted today (May 3, 2006) on the Web site of Biology of Reproduction--Papers in Press, a team headed by Dr. Randall Prather, co-director of the National Swine Resource and Research Center, note that their technique could prove valuable in allowing genetically enhanced swine to be transported as embryos across the country and throughout the world.

Because many embryos are needed to produce a successful pregnancy in surrogate female pigs, this new procedure will enable workers to collect an adequate number of altered embryos and store them until they can be transplanted to a surrogate.

Swine embryos have been difficult to freeze and preserve because of their sensitivity to cold due to a high level of lipids in the cells of the embryos. It was expected that it would be even more difficult to freeze and preserve swine embryos that had been produced by in vitro methods.

Dr. Prather's team overcame the obstacles to freezing swine embryos by first removing lipids from unfertilized eggs before fertilizing them with muscle cells from a male pig containing modified genetic material. The resulting embryos were then frozen at the blastocyst stage.

Upon thawing, embryos were transferred to surrogate female swine. Embryos placed in the oviducts of two surrogates led to pregnancies that produced two piglets in one litter and eight piglets in another.

Testing confirmed that the piglets carried the modified genetic material and that the new gene had altered the fatty-acid content in tissues from the piglets.

With ten piglets from 163 frozen and preserved embryos, the researchers feel that their procedure appears to work well, although further studies will be needed to refine the technique.

Dr. Prather and his team expect that freezing and preserving swine embryos will enable wide dissemination of swine with genetic traits that are commercially valuable and also important for biomedical research involving this increasingly relevant animal model for human disorders.

Source : Society for the Study of Reproduction

Heal thyself: Systems biology model reveals how cells avoid becoming cancerous

Researchers at the University of California, San Diego and three other institutions have described for the first time a web of inter-related responses that cells use to avoid becoming diseased or cancerous after being exposed to a powerful chemical mutagen. The group led by UCSD bioengineering professor Trey Ideker describe in the May 19 issue of Science an elaborate system of gene control that is triggered by chemical damage to DNA.

"This research sheds light on the complexity of DNA repair, and offers an example of how the cellular process stimulates other pathways," said David Schwartz, director of the National Institute of Environmental Health Sciences (NIEHS), one of the agencies which funded the study. "This new knowledge has great potential for the development of new therapeutic agents to combat a broad spectrum of diseases, including cancer, neurodegenerative diseases, and premature aging."

Researchers involved in the study agreed that their findings could eventually be used to develop drugs to boost DNA repair in response to environmental toxins and possibly treat inherited degenerative diseases such as xeroderma pigmentosum, a disease in which the body's ability to repair DNA damage caused by ultraviolet light is disabled, ataxia telangiectasia, a progressive, neurodegenerative childhood disease, Werner syndrome, a premature aging disorder, and others.

"DNA damage is a basic physiological process that is important to coping with environmental toxins and a number of congenital diseases," said Ideker, the senior author of the paper. "Over the past several decades, scientists have discovered many parts of the DNA-damage-repair machinery, but what has been missing until now is a 'systems biology' approach that explains how all the parts function together to enable a cell to repair its DNA while under routine assault."

UCSD post-doctoral fellow Christopher T. Workman, Ph.D. candidate Craig Mak, and technicians Scott McCuine and Maya Agarwal analyzed the effect of exposure of yeast cells to MMS (methyl-methanesulfonate), a chemical known to cause DNA damage in a manner similar to that of certain mutagens in tobacco smoke. The alkylation injury caused by MMS results in small kinks in the otherwise smoothly curving double helix of DNA. Cells rapidly identify the damage, stop dividing, excise the damaged DNA, and use several alternate methods to substitute a clean copy of genetic material.

"It's almost as if cells have something akin to a computer program that becomes activated by DNA damage, and that program enables the cells to respond very quickly," said Mak. "And this program is easily recognizable as operating in everything from yeasts to humans and mice to fruit flies."

Researchers have previously identified hundreds of genes involved in repairing MMS damage. However, they have been mystified by another group of genes whose expression is sharply affected by DNA damage, but which appear to play no role in repairing the damage itself.

Ideker's team uncovered a tangled network of interactions of 30 transcription factors with more than 5,000 yeast genes. A transcription factor is a protein that, either alone or in combination with other transcription factors, binds to one or more genes to affect the expression of that gene or genes. The discovery by Ideker's group of a huge network of transcription factor-gene interactions was made possible by new biotechnology tools that provide comprehensive analysis of cells, like a passerby suddenly being able to monitor all the telephone calls made within a city.

The team discovered that part of the interaction network was involved, as expected, in repairing damaged DNA. However, they were surprised to find that a much larger part of the network is involved in modulating the expression of genes not directly related to DNA repair, such as genes involved in cell growth and division, protein degradation, responses to stress, and other metabolic functions. Ideker and others have theorized that when a cell's DNA is damaged, the cell may be programmed to also stop dividing and perform a variety of housekeeping chores while it repairs its DNA. If true, the model may demystify the long-standing question of why DNA damage influences the expression of hundreds of genes not involved in the actual repair process.

"What we quickly realized is that we had uncovered not just a model of DNA repair, but a blueprint of how the initial event of DNA damage is transmitted by these transcription factors to repair processes and all the other important functions of the cell," said Ideker. "With this model now in hand, we'd like to take a much closer look at the cell's response to environmental toxins. We'd like to understand what goes wrong in certain congenital diseases involving DNA repair, and we'd also like to understand how the model plays a role in various cancers."

Source : University of California - San Diego

GENETIC ACCLIMATION FOR FREEZING TOLERANCE

GENETIC ACCLIMATION FOR FREEZING TOLERANCE
Kan Wang

A late spring cold wind-current or early fall frost can cause severe damage to crop yield. A number of strategies using recombinant DNA technology and genetic transformation has been utilized to enhance crop freezing tolerance in recent years1,2. These approaches include the overexpression of biosynthetic enzymes for osmoprotectants (such as mannitol, proline, treholose, or glycine betaine), the constitutive expression of stress-induced proteins (such as late embryogenesis abundant [LEA] proteins or heat shock proteins [HSPs]), altering the enzyme activity of antioxidants (such as superoxide dismutase [SOD] or glutathione S-transferase [GST]) that are involved in the detoxification of active oxygen species (AOS) accumulated during the stress environment, and expression of transcriptional factors (such as dehydration-responsive element [DRE] or CRT-binding factors [CBFs]) that bind to water deficit and cold responsive genes. Recently, it was reported that overexpression of a plasma membrane-associated phospholipase Dδ could enhance freezing tolerance in Arabidopsis3. While most work utilizes Arabidopsis as a model system, we carried out experiments on maize, a frost-sensitive crop plant originated from subtropical regions. The freezing tolerance enhancement described here involves the constitutive expression of a protein kinase in an oxidative stress signaling pathway4.

Many plant species increase their tolerance to cold or freezing temperature after they are exposed to a sub-optimal temperature. This process is called cold acclimation. Exposure to acclimation temperature causes many changes, including mild oxidative stress in plants, which can consequently induce chilling tolerance. At the molecular level, extensive alteration in gene expression has been observed during this process. Oxidative stress generates and accumulates active oxygen species such as H2O2 in plants, which triggers the activation of a mitogen-activated protein kinase (MAPK) cascade. The activation of the MAPK pathway induces production of a number of stress responsive proteins, such as heat shock proteins (HSPs), which in turn protect plants from stresses.

The MAPK signal transduction pathway is conserved among different organisms. It is usually activated only upon stress conditions. However, in some cold stress conditions, plants may be severely damaged before they even get a chance to turn on their protective mechanisms. Our hypothesis was then, if a plant was acclimated genetically, namely, its stress-induced pathways or proteins were turned on without first being stressed, could it withstand sudden severe stress such as subzero freezing temperatures?

We introduced a tobacco MAP kinase kinase kinase gene (NPK1) into maize through Agrobacterium-mediated transformation. The cDNA fragment encoding a 268-amino acid catalytic domain of NPK1, which is under a constitutive CaMV 35S promoter, was shown previously to enhance tolerance to freezing, salt, and heat stresses in transgenic tobacco5. Two dozen transgenic NPK1 maize lines were generated. According to the NPK1 gene transcript levels in R1 plants, we categorized maize lines into high, medium, and low expressers. Two events, A4-9 and A4-15, representing the medium and high levels of gene expression, respectively, were used for freezing analysis.

We performed two types of freezing tests for these transgenic plants: graduated freezing and constant freezing. In the graduated freezing test, the temperature of the growth chamber was set at –1oC and continually decreased at the rate of 1ºC per hour until it reached a temperature of –6oC, while in the constant freezing test, the temperature was set at –5ºC. Maize plants were grown under normal growth conditions (25ºC, 14 hr day length) to the three-leaf stage before they were subjected to freezing treatments. Cellular damage of treated seedlings due to freeze-induced membrane lesions was estimated by measuring electrolyte leakage (EL) from the leaves of treated plants. The higher the EL, the more severe the damage to the plant membrane, thus indicating that samples had less tolerance to freeze challenging. Considering the possibility of genetic variation among these transgenic events, we used the null segregants from each transgenic event as the negative control. We observed that leaf EL increased with a decrease in environmental temperature. When the temperature dropped to –4ºC, the EL of negative segregants increased extensively, indicating that severe membrane damage had been caused by freezing stress. The EL of transgenic plants of A4-9 and A4-15, on the other hand, did not increase until the temperature dropped to –5ºC and –6ºC, respectively. This result indicates that these transgenic maize events were able to tolerate up to 2ºC lower freezing temperature than their negative control siblings.

The increased freezing tolerance in transgenic plants of events A4-15 and A4-9 were confirmed in the constant freezing test. The EL of A4-15 transgenic plants did not increase until 5 hours at –5ºC temperature. The EL of A4-15 negative control siblings, however, increased to 57% and 90% after 3 and 4 hours of –5ºC treatment, respectively. This result indicates that transgenic A4-15 plants can survive 1–2 more hours than their negative control siblings at a temperature of –5ºC. A similar difference in freezing tolerance between transgenic plants and their non-transgenic siblings was observed in event A4-9 in which transgenic plants survived for 3 hours at –5ºC, while the negative siblings survived for 1 hour.

To understand the mechanism of freezing tolerance in NPK1 transgenic maize plants, we measured total soluble sugar content (TSC). An increase in TSC was positively correlated with enhanced freezing tolerance in plants. It is believed that soluble sugars function as cryoprotectants and osmolytes that protect cells from freezing damage. In our study, NPK1-expressing transgenic plants had higher TSC both under non-acclimated (25ºC) and cold-acclimated (4ºC, 24 or 48 hrs) conditions compared to their negative non-transgenic siblings in all treatments. Cold acclimations significantly increased TSC levels in all plants. Under normal growth conditions (non-acclimated), event A4-9 contained significantly higher total soluble sugar content compared to its null segregants (P<0.02). It is interesting that the increase of TSC in transgenic plants was not tightly correlated with NPK1 transgene expression level or freezing tolerance performance in our case. It is possible that while the NPK1 transgene induced cold-acclimation-like biochemical processes that elevated TSC, factors other than the NPK1 transgene also affected sugar levels in the maize seedlings.

We also conducted microarray analysis to investigate whether enhanced freezing tolerance in NPK1 transgenic maize was due to the activation of MAPK cascades resulting from oxidative stress. Using a fiber-optic BeadArray™ technology, we compared the expression levels of several stress-induced genes between transgenic and non-transgenic plants with or without cold acclimation. The fiber-optic array uses randomly ordered, self-assembled arrays of beads for parallel analysis of complex biological samples6. Since the miniature fiber optic arrays that interrogate hundreds to over one thousand targets are built into a 96- or 384-array matrix that matches microtiter plates, it allows multiple assays to be carried out rapidly and efficiently. Twenty-eight maize EST sequences based on the protein sequences of putative stress-related Arabidopsis and tobacco orthologues, together with a housekeeping gene (18S rRNA) and the transgene NPK1, were chosen for analysis. The expression of three genes, GST (glutathione S-transferase), HSP17.8 (small heat shock protein), and PR1 (pathogenesis-related), was up-regulated (> 1.5) in NPK1 transgenic plants under either normal or cold-acclimated conditions. Two of these genes, GST and HSP17.8, are involved in oxidative signaling pathways5. While constitutive expression of transgene NPK1 up-regulated the gene expression of GST and HSP17.8, cold acclimation treatment (4ºC, 48 hr) did not additionally increase their transcript levels.

As discerned from array analysis, about 50% of stress-induced genes tested in our study showed no significant increase in NPK1 transgenic maize lines. One explanation is that the transgene NPK1 expression level may be too low to up-regulate these stress related genes. It is also possible that these genes were only transiently induced and our assay condition did not capture their expression at the right moments.

We have generated transgenic maize plants that constitutively express a tobacco MAP kinase kinase kinase gene (NPK1) with enhanced freezing tolerance. In field evaluation of agronomic performance of 22 events, we detected no significant differences in plant heights and leaf numbers between transgenic plants and their non-transgenic segregants, suggesting that expression of transgene NPK1 did not affect maize growth under normal field conditions. Our results demonstrate that maize freezing tolerance level could be enhanced through a genetic acclimation (instead of cold acclimation) process in which stress-induced proteins for plant protection is achieved upon the activation of the oxidative signaling pathway through manipulation of the MAPK cascade.

References

1. Cushman JC, & Bohnert HJ (2000) Genomic approaches to plant stress tolerance. Curr. Opin. Plant Biol. 3: 117-124

2. Iba K (2002) Acclimative response to temperature stress in higher plants: Approaches of gene engineering for temperature tolerance. Annul Rev. Plant Biol. 53: 225-245

3. Li W, Li M, Zhang W, Welti R, & Wang, X (2004) The plasma membrane-bound phospholipase Dδ enhances freezing tolerance in Arabidopsis thaliana. Nat. Biotechnol 22, 427-433

4. Shou H, Bordallo P, Fan J-B, Yeakley JM, Bibikova M, Sheen J, & Wang K (2004) Expression of an active tobacco MAP kinase kinase kinase enhances freezing tolerance in transgenic maize. Proc. Natl. Acad. Sci. (USA) 101, 3298-3303

5. Kovtun, Y, Chiu, WL, Tena, G, & Sheen, J (2000) Functional analysis of oxidative stress-activated mitogen-activated protein kinase cascade in plants. Proc. Natl. Acad. Sci. 97, 2940-2945

6. Yeakley JM, Fan J-B, Doucet D, Luo L, Wickham E, Ye Z, Chee MS, & Fu XD. (2002) Profiling alternative splicing on fiber-optic arrays. Nat. Biotechnol 20, 353-358

Kan Wang
Department of Agronomy
Iowa State University
kanwang@iastate.edu