Monday, 30 June 2008

Weekly BioNews 23 - 30 June 2008

- New paradigm for cell-specific gene delivery



June 23, 2008 01:45 AM


Researchers from Northwestern University and Texas A & M University have discovered a new way to limit gene transfer and expression to specific tissues in animals. In studies to determine how plasmids enter the nuclei of non-dividing cells, the group previously identified a region of a smooth muscle cell-specific promoter that was able to mediate nuclear targeting of any plasmid carrying this sequence uniquely in cultured smooth muscle cells but in no other cell type. In their current study to appear in the July 08 issue of Experimental Biology and Medicine, the team, led by Drs. David Dean and Jennifer Young from the Department of Medicine at Northwestern University, in collaboration with Warren Zimmer from Texas A & M University, now demonstrate that such restriction of nuclear entry using this specific DNA sequence can be used in blood vessels of living animals to direct gene transfer and expression specifically to smooth muscle cells. They have also developed a novel gene delivery approach for the vasculature that uses an electric field to transiently permeabilize the plasma membrane of cells to allow entry of DNA. Thus, this work establishes the control of nuclear entry of gene therapy vectors as a novel approach to target genes and gene expression to desired cell types in the body.


Vascular smooth muscle proliferative diseases, including atherosclerosis and restenosis, are among the leading causes of morbidity and mortality in the US. Gene therapy may represent an important alternative for the treatment and prevention of these proliferative diseases of the vasculature. It can be highly cell-specific, mimic or restore normal in vivo function, and can be permanent or transient depending on vector design. Currently, a number of gene delivery systems for use on the arterial wall are being studied, but as yet their low efficiency in gene transfer and lack of cell-specific targeting and expression are major limitations...






- Gene silencer and quantum dots reduce protein production to a whisper



June 23, 2008 04:10 PM


More than 15 years ago scientists discovered a way to stop a particular gene in its tracks. The Nobel Prize-winning finding holds tantalizing promise for medical science, but so far it has been difficult to apply the technique, known as RNA interference, in living cells.



Now scientists at the University of Washington in Seattle and Emory University in Atlanta have succeeded in using nanotechnology known as quantum dots to address this problem. Their technique is 10 to 20 times more effective than existing methods for injecting the gene-silencing tools, known as siRNA, into cells.


"We believe this is going to make a very important impact to the field of siRNA delivery," said Xiaohu Gao, a UW assistant professor of bioengineering and co-author of a study published online this week in the Journal of the American Chemical Society.


"This work helps to overcome the longstanding barrier in the siRNA field: How to achieve high silencing efficiency with low toxicity," said co-author Shuming Nie, a professor in the Wallace H. Coulter Department of Biomedical Engineering, jointly affiliated with the Georgia Institute of Technology and Emory University.


Other co-authors are Maksym Yezhelyev and Ruth O'Regan at Emory and Lifeng Qi at the UW.
Short pieces of RNA, the working copy of DNA, can disable production of a protein by silencing, or deactivating, a stretch of genetic code. Research laboratories regularly use the technique to figure out what a particular gene does. In the body, RNA interference could be used to treat conditions ranging from breast cancer to deteriorating eyesight.


The recent experiments used quantum dots, fluorescent balls of semiconductor material just six nanometers across (lining up 9,000 dots end to end would equal the width of a human hair). Quantum dots' unique optical properties cause them to emit light of different colors depending on their size. The dots are being developed for cellular imaging, solar cells and light-emitting diodes.


This paper describes one of the first applications of quantum dots to drug delivery.


Each quantum dot was surrounded by a proton sponge that carried a positive charge. Without any quantum dots attached, the siRNA's negative charge would prevent it from penetrating a cell's wall. With the quantum-dot chaperone, the more weakly charged siRNA complex crosses the cellular wall, escapes from the endosome (a fatty bubble that surrounds incoming material) and accumulates in the cellular fluid, where it can do its work disrupting protein manufacture...





A fluorescent image of the cell taken 15 minutes after introducing the quantum dot-siRNA complex. At this early stage the particles are in the cell membrane. (Credit: Image courtesy of University of Washington)





- Stopping flagella movement



Date: 23/06/2008
It has been long been known that bacteria swim by rotating their tail-like structure called the flagellum. (See the swimming bacteria in the figure.) The rotating motion of the flagellum is powered by a molecular engine located at the base of the flagellum. Just as engaging the clutch of a car connects its gear to its engine and delivers power to its wheels, engaging the molecular clutch of a bacterium connects its gear to its engine and delivers power to its flagellum.Now, a paper appearing in the June 20 issue of Science describes, for the first time, how the flagellum's rotations are stopped so that bacteria stop moving. Here's how the stopping mechanism works: while a bacterium is swimming, it releases a protein (shown in red in the stationary bacterium in the figure) that flows between its gear and engine. The presence of this protein detaches the bacterium's gear from its engine and thereby stops the delivery of power to its flagellum. This process is analogous to disengaging the clutch of a car, which detaches its gear from its engine and thereby stops the delivery of power to its wheels.

Stopping flagella movement


Once the delivery of power to bacterium's flagellum stops, the flagellum stops rotating, and the bacterium's swimming ends.


An improved understanding of how flagella work may give nanotechnologists ideas about how to regulate tiny engines of their own creation. The flagellum is one of nature's smallest and most powerful motors. The flagellum of some bacteria can, for example, rotate more than 200 times per second, driven by 1,400 piconewton-nanometres of torque. That's quite a bit of (miniature) horsepower for a machine whose width stretches only a few dozen nanometres.








- Researchers develop neural implant that learns with the brain



June 24, 2008 04:07 PM


Devices known as brain-machine interfaces could someday be used routinely to help paralyzed patients and amputees control prosthetic limbs with just their thoughts. Now, University of Florida researchers have taken the concept a step further, devising a way for computerized devices not only to translate brain signals into movement but also to evolve with the brain as it learns.


Instead of simply interpreting brain signals and routing them to a robotic hand or leg, this type of brain-machine interface would adapt to a person's behavior over time and use the knowledge to help complete a task more efficiently, sort of like an assistant, say UF College of Medicine and College of Engineering researchers who developed a model system and tested it in rats.


Until now, brain-machine interfaces have been designed as one-way conversations between the brain and a computer, with the brain doing all the talking and the computer following commands. The system UF engineers created actually allows the computer to have a say in that conversation, too, according to findings published this month online in the Institute of Electrical and Electronics Engineers journal IEEE Transactions on Biomedical Engineering.


"In the grand scheme of brain-machine interfaces, this is a complete paradigm change," said Justin C. Sanchez, Ph.D., a UF assistant professor of pediatric neurology and the study's lead author. "This idea opens up all kinds of possibilities for how we interact with devices. It's not just about giving instructions but about those devices assisting us in a common goal. You know the goal, the computer knows the goal and you work together to solve the task."


Scientists at UF and other institutions have been studying and refining brain-machine interfaces for years, developing and testing numerous variations of the technology with the goal of creating implantable, computer-chip-sized devices capable of controlling limbs or treating diseases.


The devices are programmed with complex algorithms that interpret thoughts. But the algorithms, or code, used in current brain-machine interfaces don't adapt to change, Sanchez said.


"The status quo of brain-machine interfaces that are out there have static and fixed decoding algorithms, which assume a person thinks one way for all time," he said. "We learn throughout our lives and come into different scenarios, so you need to develop a paradigm that allows interaction and growth."


To create this type of brain-machine interface, Sanchez and his colleagues developed a system based on setting goals and giving rewards...






- Embryo regeneration



Date: 26/06/2008


More than 80 years have passed since the German scientist Hans Spemann conducted his famous experiment that laid the foundations for the field of embryonic development. After dividing a salamander embryo in half, Spemann noticed that one half - specifically, the half that gives rise to the salamander's 'belly' (ventral) starts to wither away. However, the other 'back' (dorsal) half that develops into its head, brain and spinal cord, continues to grow, regenerating the missing belly half and develops into a complete, though be it smaller, fully functional embryo. Spemann then conducted another experiment, where this time, he removed a few cells from the back half of one embryo and transplanted them into the belly half of a different embryo. To his surprise, this gave rise to a Siamese twin embryo where an extra head was generated from the transplanted cells. Moreover, although the resulting embryo was smaller than normal, all its tissues and organs developed in the right proportions irrespective of its size, and functioned properly. For this work, Spemann received the Nobel Prize in Physiology or Medicine in 1935.But how does this happen? How exactly is the half embryo able to maintain its tissues and organs in the correct proportions despite being smaller than a normal sized embryo?


Despite many years of research, this question has remained unanswered - until now. More than 80 years since Spemann's classic experiment, Profs. Naama Barkai, Benny Shilo and research student Danny Ben-Zvi of the Weizmann Institute of Science's Molecular Genetics Department, together with Prof. Abraham Fainsod of the Hebrew University-Hadassah School of Medicine, Jerusalem, have finally discovered the mechanisms involved.


Previous studies have shown that the growth and development of cells and organs within the embryo is somehow linked to a special group of substances called morphogens. These morphogens are produced in one particular area within the embryo and then spread throughout the entire embryo in varying concentrations. Scientists then began to realise that the fate of embryo cells, that is to say, the type of tissue and organ they are eventually going to develop into, is determined by the concentration of morphogen that they come into contact with. But this information does not answer the specific question as to how proportion is maintained between organs?


The idea for the present research came about when Weizmann Institute scientist Prof. Naama Barkai and her colleagues developed a mathematical model to describe interactions that occur within genetic networks of an embryo.






- Evolution Of Fruit Size In Tomato



ScienceDaily (June 28, 2008)


Domesticated tomatoes can be up to 1000 times larger than their wild relatives. How did they get so big?


In general, domesticated food plants have larger fruits, heads of grain, tubers, etc, because this is one of the characteristics that early hunter-gatherers chose when foraging for food. In addition to size, tomatoes have been bred for shape, texture, flavor, shelf-life, and nutrient composition, but it has been difficult to study these traits in tomatoes, because many of them are the result of many genes acting together. These genes are often located in close proximity on chromosomal regions called loci, and regions with groups of genes that influence a particular trait are called quantitative trait loci (QTLs).


When a trait is influenced by one gene, it is much simpler to study, but quantitative traits, like skin and eye color in humans or fruit size in tomatoes, cannot be easily defined just by crossing different individuals. Now, with genome sequencing and genomics tools, chromosomal regions with QTLs can be mapped and cloned more easily than in the past. These genomic maps can also be compared across plant genomes to identify similar genes in other species. With this knowledge, breeders can improve tomato varieties as well as other less well known food plants in the family Solanaceae.


Dr. Steven D. Tanksley and his colleagues, Bin Cong and Luz S. Barrero, are studying QTLs that influence fruit size. Dr. Barrero, of the Corporación Colombiana de Investigación Agropecuaria (CORPOICA), Colombia, will be presenting this work at a symposium on the Biology of Solanaceous Species at the annual meeting of the American Society of Plant Biologists in Mérida, Mexico (June 29, 2008).


Tomato (Solanum lycopersicum) is a member of the Solanaceae or nightshade family, which also includes potato, eggplant, tobacco, and chili peppers. The center of origin and diversity of tomato and other solanaceous species is in the northern Andes, where endemic wild populations of these species still grow. Tanksley and his colleagues have been employing the data emerging from the International Tomato Genome Sequencing Project as well as the tools of structural genomics to clone and characterize the major gene and QTL responsible for extreme fruit size during tomato domestication--fas.


The first QTL, fw2.2, was the first ever cloned in plants and may have been the site of one of the earliest mutations in tomato that led to its selection by humans and subsequent domestication. The size of tomato fruit can vary up to 30% as a result of variation at this locus alone. Cloning and sequencing of this locus reveals that the wild type protein codes for a repressor of cell division. When the control sequence is mutated, the repressor protein is not expressed or only very little, leading to higher cell division during fruit development and, consequently, larger fruits.


However, fw2.2 and associated genes related to cell-cycle control and cell division are not solely responsible for extreme fruit size. Two other loci-- locule-number and fasciated (fas)-- influence fruit size indirectly by affecting the number of carpels, the female parts of the flower that will become seed chambers in the fruit. Most wild tomatoes have only 2-4 locules (ovary chambers) while domesticated varieties can have 8 or more, and it appears that increase in locule number can increase fruit size by 50%. The data indicate that, of the two loci, fas has the larger effect. Tanksley and his colleagues used positional cloning to isolate the fas locus....


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