Contrary to predictions, males of high genetic quality are not very successful when it comes to fertilizing eggs.

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Contrary to predictions, males of high genetic quality are not very successful when it comes to fertilizing eggs. A new study on seed beetles by Swedish and Danish scientists Göran Arnqvist and Trine Bilde shows that when a female mates with several males, the males of low genetic quality are the most successful in fertilizing eggs. The study is published in this week's issue of Science.

In almost all animals, females mate with several different males, despite the fact that a single mating is often sufficient to fertilize her eggs. Multiple mating also carries costs to females, such as the risk of catching sexually transmitted diseases.
One commonly held belief is that this behaviour may allow females to choose the sperm of the male with highest genetic quality to fertilize her eggs. Professor Göran Arnqvist from the Department of Ecology and Evolution, Uppsala University and associate professor Trine Bilde from the Department of Biological Sciences, University of Aarhus, have tested this possibility directly for the first time and shown that it is not true.
Their study on seed beetles shows that, contrary to predictions, males of low genetic quality are more successful in fertilizing eggs. Males who gained the highest share of paternity were actually males with low genetic quality. These males also fathered offspring that did less well.
"The results support the suggestion that genes that are good for males may often be bad for their mates. Therefore, in beetles at least, multiple mating does not award females with genetic benefits," says Göran Arnqvist.
Source: Uppsala University (news : web)

Long-standing Mystery Of How Plants Make Eggs Solved

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ScienceDaily (June 4, 2009) — A long-standing mystery surrounding a fundamental process in plant biology has been solved by a team of scientists at the University of California, Davis.

The group’s groundbreaking discovery that a plant hormone called auxin is responsible for egg production has several major implications.
First, this is the first definitive report of a plant hormone acting as a morphogen, that is, a substance that directs the pattern of development of cells based on its concentration.
Also, the study’s results provide tantalizing new insights into the evolutionary pathway that flowering plants took 135 million years ago when they split off from gymnosperms, the “naked-seeded” plant group that includes conifers, cycads and ginkgo trees.
Finally, the group used their discovery to make additional egg cells within plant reproductive structures, raising the prospects that these techniques may someday be used for enhancing the reproduction and fertility of crop plants.
“So the sequence becomes clear now,” said Venkatesan Sundaresan, the UC Davis professor of plant biology and plant sciences who led the study. “The plant triggers auxin synthesis at one end of the female reproductive unit called the embryo sac, creating an auxin gradient. The eight nuclei in the sac are then exposed to different levels of auxin, but only the nucleus in the correct position in the gradient becomes an egg cell. And that cell is subsequently fertilized to make the next generation.”
A paper describing the study was published June 4 in the journal Science’s online site, Science Express, in advance of its publication in the journal later this month.
Development of sperm and egg cells in plants
In humans and other animals, the germ cells for production of eggs and sperm are established at birth. But cells in flowering plants are assigned more or less randomly to become reproductive units when the plant reaches sexual maturity. Within the flower, sperm cells are produced by pollen at the tips of stamens, while egg cells develop in ovules, tiny structures embedded in the ovary at the base of the pistil.
At the start of the process of egg-cell development, a “mother cell” in the ovule divides several times, in a sequence involving both meiosis and mitotic divisions. These divisions result in the creation of an oblong, cell-like structure called the embryo sac, which contains eight nuclei, three of which are clustered near the open end of the ovule.
Within hours cell membranes start forming, eventually, creating seven cells: the all-important egg cell near the ovule opening where pollen will enter, and six other supporting cells, with essential functions for seed formation.
“The big question in our field for the past 50 years or more has been: How does this process happen in such a beautifully orchestrated pattern?” Sundaresan said. “It’s been clear that there’s a program here telling the plants exactly what to do, and that it is working not on cells, but on nuclei.”
Auxin concentrations determine fate of nuclei
Two years ago Sundaresan and a postdoctoral fellow in his laboratory, Gabriela Pagnussat, used genetic tools to shift the position of a single nucleus at one end of an embryo sac in the plant Arabidopsis. When they examined the mature sac, they found that it had produced two egg cells instead of one.
Sundaresan recognized that a pattern shift like this was similar to the response that had been reported two decades earlier in Drosophila fruit flies in experiments that provided the first direct evidence for the existence of morphogens.
This prompted him to begin searching for a substance in Arabadopsis that might be acting as a morphogen. When the group discovered that auxin was accumulating at the open end of the ovule, they turned their attention to this ubiquitous hormone, which is known to play myriad signaling roles in plant growth and behavioral processes. (The hormone’s existence was first guessed by Charles Darwin when he was studying how plants grow towards light.)
After many tests, Sundaresan and his group found that during embryo sac formation, auxin concentrations did indeed follow a gradient, with the highest levels occurring in the ovule at the end of the embryo sac where the pollen enters and lowest levels occurring at the opposite end of the sac.
To test the theory that this gradient was determining the fate of nuclei in the sac, Sundaresan and his group created a series of genetically manipulated Arabadopsis plants. In some plants they ratcheted up production of auxin in the embryo sac, and in others they decreased the sac’s sensitivity to auxin, creating the same effect that a decline in auxin would make.
When they examined these experimental plants, their hypothesis was confirmed: Auxin concentrations determined the fate of the nuclei. Knowing whether auxin levels were high or low, it became possible to predict the appearance or disappearance of egg cells at different positions within the embryo sac.
Finally, the group employed a long series of bio-manipulative techniques to determine that the auxin gradient they had discovered within the embryo sac was due to on-site synthesis rather than transport from a source outside the sac.
“What we have found about the way auxin works here is amazing,” Sundaresan said. “The idea that you can have a small molecule like this being maintained in a gradient within this eight-nucleate structure through synthesis alone is mind-boggling.”
Implications for flowering plant evolution
Development of the embryo sac is arguably the key element in the evolution from gymnosperms to flowering plants, also known as angiosperms.
Yet the fossil record reveals very little about the stages that led from gymnosperm seed production to angiosperm seed production when the transition occurred around 135 million years ago. The rapid expansion of flowering plants and their eventual domination of the Earth’s vegetation was called “an abominable mystery” by Darwin.
By elucidating the mechanism of embryo sac development, Sundaresan and his team have opened the door to new work into the evolutionary pathway between these two major plant groups. The discovery supports what is known as the modular theory, which posits that the first angiosperms underwent a drastic reduction of their female reproductive unit compared to the gymnosperms, allowing flowering plants to reproduce more efficiently and eventually supplant their naked-seeded forebears.
Most remarkably, perhaps, the new work suggests that the eight nuclei of the angiosperm embryo sac have retained developmental plasticity in their evolution from gymnosperms. “It’s amazing that even though the split supposedly happened over a hundred million years ago,” Sundaresan said, “all these nuclei still have the capacity to become egg cells.”
Collaborators in the study are lead author Gabriela Pagnussat and Monica Alandete-Saez, who were postdoctoral researchers with Sundaresan when they did the work, and John L. Bowman, a professor of plant biology at UC Davis at the time of the study, now at Monash University in Melbourne, Australia.
The work was supported by grants from the National Science Foundation.
Adapted from materials provided by University of California - Davis.

Biotechnology: Engineered Moss Can Produce Human Proteins

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ScienceDaily (May 11, 2009) — ETH Zurich researchers have shown that mosses and humans share unexpected common characteristics. These evolutionary relics could be useful in the production of therapeutic proteins.

At first glance, mosses and human beings have little in common. The moss Physcomitrella patens is small, pale green, immobile, and uses sunlight as its energy source. Humans are large, mobile, and need to obtain energy by eating vegetable or animal foods.
Transferring mammalian genes into moss
This made the result of the experiments carried out by researchers in the group led by Martin Fussenegger, Professor of Chemical and Bioengineering at ETH Zurich, all the more astonishing. In collaboration with researchers at the University of Freiburg im Breisgau, the PhD student Marc Gitzinger carried out tests to see what happens when unmodified human or mammalian genes are inserted into the moss genome. They transferred the foreign, unmodified genes into the moss and discovered that the moss was easily able to manufacture the proteins encoded therein.
This cannot be taken for granted, since the same process does not work when a mammalian gene is implanted into what are known as “higher” flowering plants. The reason is that sections of the start and finish sequences of the genes of animals, plants, fungi and bacteria are considerably different. They are responsible for ensuring that a gene in the organism is recognized as such, and the proteins encoded by it are produced in the correct amount and are released from the cell. The more remote the relationship between living organisms, the greater the difference between these sequences. This is why biotechnologists must normally adapt them to a foreign organism before transplanting a gene into it. The researchers were astonished to find that this was not necessary in the case of the moss.
Moss as a generalist
The explanation given for this by Ralf Reski, Professor of Plant Biotechnology at the University of Freiburg im Breisgau, is that the moss has remained a generalist. It underwent the last major modification about 450 million years ago when it changed from living in water to a life on land, adapting to the new living conditions and then remaining unaltered for millions of years, both in its appearance and at a genetic level.
The process used by the moss to produce its proteins is less sophisticated than in “higher” organisms. In contrast to the moss, these latter organisms underwent major further developments and specializations over the course of 450 million years. On the other hand, the moss clearly retained – for millions of years – the ability to read foreign genes such as those from mammals and thus also from humans, and to translate them into proteins, probably without ever having made any use of this capability during these 450 million years.
A cost-effective alternative to mammalian cells
Today, the moss Physcomitrella patens and its ability to manufacture mammalian proteins could help to satisfy the large worldwide demand for therapeutic proteins. One well-known example is insulin, which enables diabetics to control their blood sugar level.
Nowadays, therapeutic proteins are mainly manufactured in mammalian cells, which are very expensive to culture. They need to be maintained at body temperature with a continuous supply of nutrients and oxygen, and the production process is costly. At present, global production capacity cannot match the demand. Because of the difficulties involved in handling them, production is possible only in industrialized countries.
In contrast, the moss Physcomitrella patens is comparatively undemanding. It needs water, a couple of nutrient salts and some light to allow it to flourish and produce proteins. This makes it convenient and simple to handle in a bioreactor, and, in the future, it might enable even less developed nations to satisfy their requirement for therapeutic proteins. However, further research will be needed before the moss can be used to produce therapeutic proteins on an industrial scale.
Journal reference:
Gitzinger et al. Functional cross-kingdom conservation of mammalian and moss (Physcomitrella patens) transcription, translation and secretion machineries. Plant Biotechnology Journal, 2009; 7 (1): 73 DOI: 10.1111/j.1467-7652.2008.00376.x
Adapted from materials provided by ETH Zurich.

How Cells Move: Cooperative Forces Boost Collective Mobility Of Cells

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ScienceDaily (May 11, 2009) — Research by scientists in Spain and their colleagues offers for the first time an experimental answer to the question of how cells move during biological processes as diverse as the development, metastasis, or regeneration of tissues.

The work addresses the issue of collective mobility of cells, that is to say, how cells are moved within tissues, and what is the prevalent form of movement inside living organisms.
"Research into collective cell mobility is very active due to the direct implications it has on fields such as embryologic development, organ regeneration, and cancer. For example, if we could find a way to control cell mobility during metastasis, cancer would be a curable disease in the majority of cases," says Dr. Xavier Trepat, senior researcher of the cellular and respiratory biomechanics group and researcher in the Department of Physiological Sciences at the University of Barcelona, and in the Networking Biomedical Research Centre for respiratory diseases (CIBER).
Up until now, scientists had proposed various mechanisms to explain collective cell migration. One hypothesis for example, suggests that the cells move collectively due to the existence of “leader” cells, which stretch out in the rest of the group, like a train pulls carriages behind it. Another hypothesis suggests that each cell moves independently to those around it, like cars on the motorway during a traffic jam, or like soldiers in a military parade. “We have rejected both these possibilities,” says Trepat.
According to his research, collective cell mobility is the result of a cooperative process in which each cell contributes to the movement of the group, stretching to those around it. “It is a mechanism similar to a tug-of-war game, in which two teams pull a rope by its extremes and the team that pulls the hardest wins. During the game, each player generates force and transmits it to the rope, so that the tension in the rope is the sum of the forces generated by each member of the team. Cells do the same. Each cell generates force to stretch to its neighbours in the direction of the movement» explains the researcher.
Journal reference:
Xavier Trepat, Michael R. Wasserman, Thomas E. Angelini, Emil Millet, David A. Weitz, James P. Butler & Jeffrey J. Fredberg. Physical forces during collective cell migration. Nature Physics, 2009; DOI: 10.1038/nphys1269
Adapted from materials provided by Universidad de Barcelona, via AlphaGalileo.

Sexually Transmitted Infections: Transistors Used To Detect Fungus Candida Albicans

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ScienceDaily (May 11, 2009) — The Nanosensors group from the Universidad Rovira i Virgili has created a biosensor, an electrical and biological device, which is able to selectively detect the Candida albicans yeast in very small quantities of only 50 cfu/ml (colony-forming units per millilitre).

"The technique uses field-effect transistors (electronic devices that contain an electrode source and a draining electrode connected to a transducer) based on carbon nanotubes and with Candida albicans-specific antibodies", Raquel A. Villamizar, lead author of the study said.
The Candida samples, which can be obtained from blood, serum or vaginal secretions, are placed directly on the biosensor, where the interaction between antigens and antibodies changes the electric current of the devices. This change is recorded and makes it possible to measure the amount of yeast present in a sample.
"Thanks to the extraordinary charge transference properties of the carbon nanotubes, the fungus detection process is direct, fast, and does not require the use of any marker", remarks Villamizar, who is co-author of a study that provides details of the biosensor and was published recently in the journal Sensors and Actuators B: Chemical.
To date, conventional diagnosis of Candida has been carried out using microbial cultures, serological tests, PCR molecular biology techniques (polymerase chain reactions used to amplify DNA), or immunoassays such as ELISA (Enzyme Linked Inmunoabsorbent Assay).
These techniques require long analysis times and sometimes give rise to false positives and negatives. ELISA also requires the use of markers (compounds that must be added to detect the presence of yeast by fluorescence and other techniques).
The new carbon nanotubes biosensor, however, "makes it possible to improve some of the quality parameters of the traditional methods, for example the speed and simplicity of measurements, and it is an alternative tool that could be used in routine sample analysis", explains Villamizar.
The researcher adds that by using this biosensor "it will be possible in future to obtain a rapid diagnosis of infection with this pathogen, which will help to ensure administration of the correct prophylactic treatments".
The Candida albicans fungus exists naturally in the skin, mouth, the mucous membranes lining the digestive tract, and the respiratory and genitourinary systems. This yeast can cause anything from simple mycosis of the skin to complicated cases of candidiasis. It is much more commonly found in patients suffering from immunodeficiency, tumours, diabetes and lymphomas, among other diseases.
Journal reference:
Villamizar et al. Improved detection of Candida albicans with carbon nanotube field-effect transistors. Sensors and Actuators B Chemical, 2009; 136 (2): 451 DOI: 10.1016/j.snb.2008.10.013
Adapted from materials provided by Plataforma SINC.

DNA Sequencing Becomes Much Quicker

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http://www.sciencedaily.com/releases/2007/10/071015093528.htm

Science Daily — A new technique that combines gene chip technology with the latest generation of gene sequencing machines to allow fast and accurate sequencing of selected parts of the genome has been developed by researchers from the Human Genome Sequencing Center at Baylor College of Medicine in Houston and NimbleGen Systems, Inc., a Wisconsin-based company recently purchased by Roche Applied Science.
"This new technology will replace polymerase chain reaction (PCR) for many purposes," said Dr. Richard Gibbs, director of the HGSC and senior author of the report. "If the aim is to sequence a whole genome for everybody, this is a huge step in that direction."
The report, which appears in Nature Methods, describes the use of microarrays to enrich or increase the volume of specific genomic sequences. High throughput DNA sequencing machines made by 454 Life Sciences then determine the exact genetic code of the material.
For example, if scientists were looking for a mutation in a particular cancer-causing gene (such as BRCA1 that is associated with breast and ovarian cancer), they could make a microarray that is complementary to the part of the genome in which one is interested. This takes advantage of the fact that the adenine (A) bases always attach to the thymine (T) and the cytosine (C) always attaches to the guanine (G) in reactions.
"You take the DNA and you hybridize it (allow the DNA to stick to its complement) on the chip," said Dr. George Weinstock, co-director of the HGSC. "Then you wash away everything that doesn't stick. This can enrich the portion of the genome to be studied by factors of three hundred or more."
The new process is simpler, more accurate and efficient than the multiplex PCR that was previously used to sequence portions of the genome. In one experiment, more than 6,400 exons (the part of the genetic code that carries the instructions for making proteins), were analyzed. Using the old technology this would have taken at least six months.
"We hope to be able to use this to sequence all the exons in the genome," Gibbs said.
Resequencing of genes or other genomic regions of interest is a key step in detecting mutations associated with various complex human diseases, such as cancer, asthma and heart disease. The predominant method for selection of specific genomic regions for resequencing has primarily relied on PCR (polymerase chain reaction) to enrich for specific DNA fragments.
However, PCR is limited in the length of sequence it can amplify, is difficult to scale or multiplex for the enrichment of thousands of fragments, and has limited performance in the repetitive regions typical of complex genomes, such as human. The sequence capture microarray technology bridges the gap between next-generation DNA sequencing technology and current sample preparation methods by providing an adaptable, massively parallel method for selective enrichment of genomic regions of interest. Roche NimbleGen's sequence capture technology enables high-performance targeting of thousands of specific genes or loci using a single microarray hybridization-based enrichment process.
The Nature Methods paper published by Baylor demonstrates that the sequence capture process is simpler, more accurate, more efficient and more cost-effective than the multiplex PCR that was previously used to prepare genomic samples for sequencing. In one experiment, more than 6,700 exons (the part of the genetic code that together form genes), were enriched and analyzed, as well as contiguous genomic regions of up to 5 million bases.
The study, entitled "Direct Selection of Human Genomic Loci by Microarray Hybridization," appears online (14 October 2007 ahead of print) in the journal Nature Methods.
The authors are Albert TJ, Molla MN, Muzny DM, Nazareth L, Wheeler D, Song X, Richmond TA, Middle CM, Rodesch MJ, Packard CJ, Weinstock GM, and Gibbs RA. (DOI:10.1038/NMETH1111)
Others who took part in this study include David Wheeler, Donna Muzny and Xingzhi Song of BCM and Thomas J. Albert, Michael N. Molla, Lynne Nazareth, Todd. A. Richmond, Chris M. Middle, Matthew J. Rodesch and Charles J. Packard of NimbleGen.
Funding for this work came from the U.S. National Human Genome Research Institute and the National Cancer Institute.
Note: This story has been adapted from material provided by Baylor College Of Medicine.

Fausto Intilla
www.oloscience.com

Indian Bug Is The Ancestor Of Crohn's Disease Pathogen

Source:

http://www.sciencedaily.com/releases/2007/10/071002213435.htm

Science Daily — An Indian team of researchers led by Seyed E. Hasnain of the Institute of Life Sciences (ILS), University of Hyderabad, India has found that a seemingly unknown mycobacterial organism Mycobacterium indicus pranii (MIP) could be the earliest ancestor of the 'generalist' branch of mycobacterial pathogens.
The 'generalist' bacteria infect anything from cockroaches to human and are capable of surviving in soil and water as against human adapted 'specialists' such as tubercle and leprosy bacilli. TB, a disease that killed about 1.7 million humans last year alone, is caused by a member of the Mycobacterial family of pathogens.
The finding further suggests that the prominent 'generalist' pathogen M. avium which seriously haunts AIDS patients, together with its close associate M. avium paratuberculosis (MAP), the agent of Crohn's disease in humans and Johne's disease in cattle descended from the MIP. It was also found that the MIP and the MAP bacilli initially inhabited water bodies and infected marine organisms predated by fishes finally arriving on soil through bird-droppings.
The MIP bacilli, also called as Mycobacterium w (Mw) were first isolated in India by G. P. Talwar at the All India Institute of Medical Sciences, New Delhi, in eighties and it is currently used, after an extensive and perhaps the largest clinical trial in the world, as an immunotherapeutic against leprosy in India.
The success with MIP based leprosy vaccine has led to human clinical evaluations of MIP in interventions against HIV-AIDS, psoriasis and bladder cancer in India. MIP, commercially available as 'Immuvac', is currently the focus of advanced multi-centric phase III clinical trials for its antituberculosis efficacy.
The comparative genomics study based on complete sequence of the MIP organism published in PLoS One reports observations based on the first ever whole genome sequencing project from India, carried out jointly by the ILS, the Centre for DNA fingerprinting and Diagnostics also at Hyderabad and the University of Delhi.
The study provides an important evolutionary basis for the acquisition and optimization of virulence in mycobacteria and determinants of boundaries therein. Similarly these efforts constitute a step forward in understanding the role of non-pathogenic and saprophytic mycobacteria in immunomodulation and in triggering innate immune responses. The study advocates exploitation of genetic similarity between MIP and MAP as a plausible advantage for therapeutic intervention against Crohn's and Johne's diseases.
Citation: Ahmed N, Saini V, Raghuvanshi S, Khurana JP, Tyagi AK, et al (2007) Molecular Analysis of a Leprosy Immunotherapeutic Bacillus Provides Insights into Mycobacterium Evolution. PLoS ONE 2(10): e968. doi:10.1371/journal.pone.0000968
Note: This story has been adapted from material provided by Public Library of Science.

Fausto Intilla
www.oloscience.com

Individual Differences Caused By Shuffled Chunks Of DNA In The Human Genome

Source:

http://www.sciencedaily.com/releases/2007/09/070927154931.htm

Science Daily — A study by Yale researchers offers a new view of what causes the greatest genetic variability among individuals -- suggesting that it is due less to single point mutations than to the presence of structural changes that cause extended segments of the human genome to be missing, rearranged, or present in extra copies.

"The focus for identifying genetic differences has traditionally been on point mutations or SNPs -- changes in single bases in individual genes," said Michael Snyder, the Cullman Professor of Molecular, Cellular & Developmental Biology and senior author of the study, which was published in Science Express. "Our study shows that a considerably greater amount of variation between individuals is due to rearrangement of big chunks of DNA."
Although the original human genome sequencing effort was comprehensive, it left regions that were poorly analyzed. Recently, investigators found that even in healthy individuals, many regions in the genome show structural variation. This study was designed to fill in the gaps in the genome sequence and to create a technology to rapidly identify structural variations between genomes at very high resolution over extended regions.
"We were surprised to find that structural variation is much more prevalent than we thought and that most of the variants have an ancient origin. Many of the alterations we found occurred before early human populations migrated out of Africa," said first author Jan Korbel, a postdoctoral fellow in the Department of Molecular Biophysics & Biochemistry at Yale.
To look at structural variants that were shared or different, DNA from two females -- one of African descent and one of European descent -- was analyzed using a novel DNA-based methodology called Paired-End Mapping (PEM). Researchers broke up the genome DNA into manageable-sized pieces about 3000 bases long; tagged and rescued the paired ends of the fragments; and then analyzed their sequence with a high-throughput, rapid-sequencing method developed by 454 Life Sciences.
"454 Sequencing can generate hundreds of thousands of long read pairs that are unique within the human genome to quickly and accurately determine genomic variations," explained Michael Egholm, a co-author of the study and vice president of research and development at 454 Life Sciences.
"Previous work, based on point mutations estimated that there is a 0.1 percent difference between individuals, while this work points to a level of variation between two- and five-times higher," said Snyder.
"We also found 'hot spots' -- particular regions where there is a lot of variation," said Korbel. "While these regions may be still actively undergoing evolution, they are often regions associated with genetic disorder and disease."
"These results will have an impact on how people study genetic effects in disease," said Alex Eckehart Urban, a graduate student in Snyder's group, and one of the principal authors on the study. "It was previously assumed that 'landmarks,' like the SNPs mentioned earlier, were fairly evenly spread out in the genomes of different people. Now, when we are hunting for a disease gene, we have to take into account that structural variations can distort the map and differ between individual patients."
"While it may sound like a contradiction," says Snyder, "this study supports results we have previously reported about gene regulation as the primary cause of variation. Structural variation of large of spans of the genome will likely alter the regulation of individual genes within those sequences."
According to the authors, even in healthy people, there are variants in which part of a gene is deleted or sequences from two genes are fused together without destroying the cellular activity with which they are associated. They say these findings show that the "parts list" of the human genome may be more variable, and possibly more flexible, than previously thought.
Other authors from Yale in addition to primary authors Alex E Urban and Jan Korbel, who is also affiliated with the European Molecular Biology Laboratory in Heidelberg, Germany, are Fabian Grubert, Philip Kim, Dean Palejev, Nicholas Carriero, Andrea Tanzer, Eugenia Saunders, Sherman Weissman, and Mark Gerstein. The research was funded the National Institutes of Health, a Marie Curie Fellowship, the Alexander von Humboldt Foundation, The Wellcome Trust, Roche Applied Science and the Yale High Performance Computation Center.
Citation: Science: Science Express (on line) September 28, 2007.
Note: This story has been adapted from material provided by Yale University.

Fausto Intilla

www.oloscience.com

Mystery Behind How Nuclear Membrane Forms During Mitosis Solved

Source:

http://www.sciencedaily.com/releases/2007/09/070915100302.htm

Science Daily — Just how a dividing cell rebuilds the nuclear envelope, the protective, functional wrapping that encases both the original and newly copied genetic material, has been a source of controversy for the last 20 years.

The answer matters because the architecture established during formation of the envelope is regarded as key to future regulation of gene expression.
Now scientists at the Salk Institute of Biological Studies, reporting in the September 9 advanced online edition of Nature Cell Biology, lay the debate to rest. Studying frog eggs, they discovered that the endoplasmic reticulum (ER), a key cellular organelle shaped like a network of tubes, flattens part of itself during mitosis to form a double-sided sheet, which then bends around what will become the nucleus, the control hub of the cell.
“The process is simple and elegant,” says Martin W. Hetzer, Ph.D., an assistant professor in the Molecular and Cell Biology Laboratory, who explains, “the membrane tubules are flattened as they associate with chromatin. Our model does not involve vesicle fusion.”
The most dramatic event during nuclear assembly following replication and separation of chromosomes is the reformation of the nuclear envelope, a highly structured barrier that separates the nuclear interior from the rest of the cell, say Hetzer and Daniel J. Anderson, a graduate student in Hetzer’s lab and co-author of the study. The envelope is the gateway into the nucleus and, thus, restricts access to the genome; it is composed of a concentric double membrane that is penetrated by nuclear pores, which serve as transport channels between the nucleus and the cytoplasm.
Just as chromosomes duplicate, the cell’s organelles, including the ER, also reproduce themselves. “The ER is always there and remains an intact network of tubes,” says Hetzer. In a mature cell the ER works closely with the genome, synthesizing and transporting the proteins produced under the direction of genes housed inside the nucleus.
Some scientists have believed that the ER in the sister cells help form the nuclear envelope, although proof of the process has been lacking. Others have argued that the new membrane is resurrected from bits of the “old” nuclear membrane that disintegrates when nuclear chromosomes duplicate and pull apart during mitosis.
“The problem with this theory, however, is that these fragments would then have to be fused together in the newly produced cells, and that would require massive membrane fusion and a dedicated protein machinery,” Hetzer says. “But no one has ever found it. Our data suggests that the search for this fusion machinery is now obsolete,” he says.
Hetzer and Anderson used a popular scientific model of mitosis, the eggs of Xenopus, an African frog, to determine how the nuclear envelope is restored. They found that the tubules of the ER are connected to each other in a three-way junction that allows them to constantly move and change position relative to each other.
During the early phases of mitosis, the end of the tubes bind directly to DNA found at the surface of the chromatin, the tightly bundled coil of genetic material and proteins that form chromosomes after DNA replication. Then, as mitosis proceeds, extra DNA binding proteins that reside in the ER are employed to progressively immobilize some of the tubules, flattening them out to create the nuclear membrane
“The tubules are squeezed into flat sheets that merge with each other, forming large membrane sheets that cover the entire surface of the chromatin,” Hetzer says. Why this matters, according to Hetzer, is because it is becoming increasingly clear that the nuclear envelope plays an important role in cell function.
“Anchorage of chromatin at the nuclear periphery and its three-dimensional organization within the nuclear interior helps regulate gene expression, and we know that mutations in nuclear envelope proteins cause a variety of different human diseases,” he says. “So knowing how the nuclear membrane is assembled will help us understand nuclear architecture and, in the long run, gene expression.”
The study was funded by NIH and a Pew Scholar Award.
Animation available: http://www.salk.edu/video/Sec61-U2OS-1/Sec61-U2OS-1.html
Note: This story has been adapted from a news release issued by Salk Institute for Biological Studies.

Fausto Intilla

www.oloscience.com

Synthetic Biology? Memory In Yeast Cells Synthesized

Source:

http://www.sciencedaily.com/releases/2007/09/070915081448.htm

Science Daily — Harvard Medical School researchers have successfully synthesized a DNA-based memory loop in yeast cells, findings that mark a significant step forward in the emerging field of synthetic biology.
After constructing genes from random bits of DNA, researchers in the lab of Professor Pamela Silver, a faculty member in Harvard Medical School's Department of Systems Biology, not only reconstructed the dynamics of memory, but also created a mathematical model that predicted how such a memory "device" might work.
"Synthetic biology is an incredibly exciting field, with more possibilities than many of us can imagine," says Silver, lead author of the paper to be published in the September 15 issue of the journal Genes and Development. "While this proof-of-concept experiment is simply one step forward, we've established a foundational technology that just might set the standard of what we should expect in subsequent work."
Like many emerging fields, there's still a bit of uncertainty over what, exactly, synthetic biology is. Ask any three scientists for a definition, and you'll probably get four answers.
Some see it as a means to boost the production of biotech products, such as proteins for pharmaceutical uses or other kinds of molecules for, say, environmental clean-up. Others see it as a means to creating computer platforms that may bypass many of the onerous stages of clinical trials. In such a scenario, a scientist would type the chemical structure of a drug candidate into a computer, and a program containing models of cellular metabolism could generate information on how people would react to that compound.
Either way, at it's core, synthetic biology boils down to gleaning insights into how biological systems work by reconstructing them. If you can build it, it forces you to understand it.
A team in Silver's Harvard Medical School lab led by Caroline Ajo-Franklin, now at Lawrence Berkeley National Laboratory, and postdoctoral scientist David Drubin decided to demonstrate that not only could they construct circuits out of genetic material, but they could also develop mathematical models whose predictive abilities match those of any electrical engineering system.
"That's the litmus test," says Drubin, "namely, building a biological device that does precisely what you predicted it would do."
The components of this memory loop were simple: two genes that coded for proteins called transcription factors.
Transcription factors regulate gene activity. Like a hand on a faucet, the transcription factor will grab onto a specific gene and control how much, or how little, of a particular protein the gene should make.
The researchers placed two of these newly synthesized, transcription factor-coding genes into a yeast cell, and then exposed the cell to galactose (a kind of sugar). The first gene, which was designed to switch on when exposed to galactose, created a transcription factor that grabbed on to, and thus activated, the second gene.
It was at this point that the feedback loop began.
The second gene also created a transcription factor. But this transcription factor, like a boomerang, swung back around and bound to that same gene from which it had originated, reactivating it. This caused the gene to once again create that very same transcription factor, which once again looped back and reactivated the gene.
In other words, the second gene continually switched itself on via the very transcription factor it created when it was switched on.
The researchers then eliminated the galactose, causing the first synthetic gene, the one that had initiated this whole process, to shut off. Even with this gene gone, the feedback loop continued.
"Essentially what happened is that the cell remembered that it had been exposed to galactose, and continued to pass this memory on to its descendents," says Ajo-Franklin. "So after many cell divisions, the feedback loop remained intact without galactose or any other sort of molecular trigger."
Most important, the entire construction of the device was guided by the mathematical model that the researchers developed.
"Think of how engineers build bridges," says Silver. "They design quantitative models to help them understand what sorts of pressure and weight the bridge can withstand, and then use these equations to improve the actual physical model. We really did the same thing. In fact, our mathematical model not only predicted exactly how our memory loop would work, but it informed how we synthesized the genes."
For synthetic biology, this kind of specificity is crucial. "If we ever want to create biological black boxes, that is, gene-based circuits like this one that you can plug into a cell and have it perform a specified task, we need levels of mathematical precision as exact as the kind that go into creating computer chips," she adds.
The researchers are now working to scale-up the memory device into a larger, more complex circuit, one that can, for example, respond to DNA damage in cells.
"One day we'd like to have a comprehensive library of these so-called black boxes," says Drubin. "In the same way you take a component off the shelf and plug it into a circuit and get a predicted reaction, that's what we'd one day like to do in cells."
For an animation of how to construct a synthetic memory loop see http://hms.harvard.edu/public/video/silver_illustration.mov
Full Citation: Caroline M. Ajo-Franklin(1), David A. Drubin(1), Julian A. Eskin(1), Elaine P.S. Gee(2), Dirk Landgraf(1), Ira Phillips(1), and Pamela A. Silver(1), "Rational design of memory in eukaryotic cells", Genes and Development, Volume 21, Issue 18: September 15, 2007
1-Department of Systems Biology, Harvard Medical School, 200 Longwood Ave., Boston MA 2-Harvard University Program in Biophysics, Massachusetts Institute of Technology, Cambridge, MA
Note: This story has been adapted from a news release issued by Harvard Medical School.

Fausto Intilla
www.oloscience.com