Contact Us

GENTAUR Europe

 GENTAUR Europe BVBA
Voortstraat 49, 1910 Kampenhout BELGIUM
Tel 0032 16 58 90 45 
Fax 0032 16 50 90 45
This email address is being protected from spambots. You need JavaScript enabled to view it.  

Gentaur Bulgaria

 GENTAUR BULGARIA
53 Iskar Str. 1191 Kokalyane, Sofia
Tel 0035924682280 
Fax 0035929830072
This email address is being protected from spambots. You need JavaScript enabled to view it.

    GENTAUR France
    Gentaur Germany

      GmbH Marienbongard 20
    52062 Aachen Deutschland
    Tel (+49) 0241 56 00 99 68 
    Fax (+49) 0241 56 00 47 88 
    This email address is being protected from spambots. You need JavaScript enabled to view it.

    This email address is being protected from spambots. You need JavaScript enabled to view it.

     

    Gentaur London

     GENTAUR Ltd. 
    Howard Frank Turnberry House 
    1404-1410 High Road 
    Whetstone London N20 9BH 
    Tel 020 3393 8531 
    Fax 020 8445 9411
    This email address is being protected from spambots. You need JavaScript enabled to view it.

    GENTAUR Poland

     GENTAUR Poland Sp. z o.o. 

    ul. Grunwaldzka 88/A m.2

    81-771 Sopot, Poland
    Tel  058 710 33 44
    Fax 058 710 33 48 
    This email address is being protected from spambots. You need JavaScript enabled to view it.

    GENTAUR Nederland

     GENTAUR Nederland BV
    Kuiper 1 
    5521 DG Eersel Nederland
    Tel 0208-080893 
    Fax 0497-517897
    This email address is being protected from spambots. You need JavaScript enabled to view it.

    Gentaur Italy

     GENTAUR SRL IVA IT03841300167

    Piazza Giacomo Matteotti, 6, 24122 Bergamo
    Tel 02 36 00 65 93 
    Fax 02 36 00 65 94
    This email address is being protected from spambots. You need JavaScript enabled to view it.

    GENTAUR Spain

     GENTAUR Spain
    Tel 0911876558
    This email address is being protected from spambots. You need JavaScript enabled to view it.

    Genprice USA
    Gentaur Serbia

    serbiaSerbia, Macedonia FlagMacedonia, 

    montenegro-flagMontenegro, croatiaCroatia: 
    Tel 0035929830070 
    Fax 0035929830072
    This email address is being protected from spambots. You need JavaScript enabled to view it.

    GENTAUR Romania

    romGENTAUR Romania

    Tel 0035929830070 
    Fax 0035929830072
    This email address is being protected from spambots. You need JavaScript enabled to view it.

    GENTAUR Greece

    grGENTAUR Greece 

    Tel 00302111768494 
    Fax 0032 16 50 90 45

    This email address is being protected from spambots. You need JavaScript enabled to view it.

    Other countries

    Other countries
    Luxembourg +35220880274
    Schweiz Züri +41435006251
    Danmark +4569918806
    Österreich +43720880899
    Ceská republika Praha +420246019719
    Ireland Dublin +35316526556
    Norge Oslo +4721031366
    Finland Helsset +358942419041
    Sverige Stockholm +46852503438
    Magyarország Budapest +3619980547

    seal-in-search-symantec

     

     

    Displaying items by tag: RNA

    Description:

    1. Prima is an automated system for extracting DNA and RNA from blood, saliva or other biological fluid samples, solid tissues and plant samples. This workstation is based on magnetic bead technology and it is able to process up to 24 samples at a time in less than 100 minutes.

    It is possible to use one of the recommended and validated extraction kits, whose automatic protocol is already available, or to test and employ other magnetic bead-based kits or specific protocols, counting on customized management for each lab.

    1. Prima has a high throughput capacity and allows extraction of highly-pure DNA or RNA, various downstream applications can be run on this platform, such as PCR, real-time PCR, sequencing libraries, microarray, enzymatic analysis.

    Moreover, as all OMNIA workstations, Prima is very flexible so that it can be used for plate preparation and automatic pipetting to perform many protocols that can be quickly programmed.

    Main features

    • Easy and fast extraction from up to 24 blood, saliva or other biological fluid samples, tissues and plant samples without wasting of reagents or consumables
    • Use of several validated commercial kits or test of specific kits
    • High purity of extracted nucleic acid (A260/280 ratio DNA: 1.7-1.9, RNA: 1.9-2.1)
    • High performance in downstream applications such as PCR and qPCR
    • Decontamination through UV light
    • Workstation suitable for other autosampling and liquid handling protocols
    • User-friendly software with wireless remote control

     

    Manufacturer: MASMEC

     

    askus-blue

    Published in Promos

    Gentaur proteinProtein in the body can improve its ability to detect and treat viral infections such as influenza and hepatitis C. This conclusion leads a laboratory study by researchers from the University Institute of cancer in Pittsburgh, USA.
     
    To start playback in the body, the virus actually "invaded" cells and "takes" control over them.
     
    Experts explain that, despite progress in the field of vaccines and treatment diseases caused by viral infections remain among the leading causes of death in the world. According to them, there is a need for a new type of security and the new discovery appears to be promising for further studies.
     
    Scientists isolated protein of similar oligoadenylate synthetase-occurring in humans, suffering from liver cancer, prichinen of hepatitis C. When the Expert increase the levels of this protein in human cells, observed inhibition of virus replication.
     
    In later study found that murine organisms in which there is no presence of the protein are susceptible to a large extent of a viral infection, in comparison to those who have it.

    Viruses affect the ribonucleic acid (RNA), including hepatitis C, influenza and respiratory syncytial virus, using RNA as the genetic material, when played back.
     
    The types of treatment, based on the protein like oligoadenylate synthetase, can enhance the ability of cells to detect RNA, used by the virus, and thus to activate the immune system to stop its reproduction.

    Published in News
    Tuesday, 15 April 2014 09:52

    Gene editing cures rare liver disease

    CRISPR is very easy to configure and customize equipmentUsing a new system of genetic editing based on bacterial proteins by researchers from MIT cured rare liver disease caused by a single genetic mutation.

    The findings described in the edition of Nature Biotechnology, provide the first evidence that the technique of editing of a gene known as CRISPR, can reverse disease symptoms.

    CRISPR, which offers an easy way to crop the mutated DNA and replacement with the correct sequence has the potential to treat many genetic diseases, according to the research team.

    Recently developed CRISPR system relies on cellular mechanism that bacteria use to protect themselves from viral infection.

    Researchers have copied this cell system for the creation of gene-editing complexes, including DNA.

    They are cut enzyme called Cas9, bound to the RNA strand, which can be programmed to bind to a specific genomic sequence.

    Meanwhile, researchers deliver DNA template strand.

    When repairing cell damage resulting from Cas9, scientists introduced the template DNA in the genome.

    Scientists predict that this type of revision of the genome one day could help in the treatment of diseases such as hemophilia, Huntington's disease, and the like, caused by a single mutation.

    There are other systems developed on the basis of genetic editing of DNA enzymes known as nucleases, but these complexes can be expensive and difficult to assemble.

    In contrast, CRISPR is very easy to configure and customize equipment.

    Published in News

    Using PureEXO kits is much more productive than ultracentrifugation, in terms of both purity and yeild. When extracting exosomal RNA, the PureExo kit produces nearly 4 times better results than the standart ultracentifugation protocols. This was proven using the NanoDrop 8000 spectrophotometer.

    grafika ENG

    PureExo kits are not only cheaper, but also superior to other currently available kits: it guarantees 95% exosome purity and the exosomes themselves are homogeneous, spherical and intact. No more will you have to endure the countless sizes, irregular shapes and the overly damaged exosomes that other kits eventually cause.

    The purity of the yield is verified by Exosomal protein marker, which enhances the accuracy and sensitivity to detect biomarkers carried by exosomes.

    Two verions of kits are available:

    Published in Promos

    cervical-smear-test1Researchers have to develop a test with the aid of which will be able to determine the presence of cancer in the body, regardless of the type. Initially, the scientific team of Anderson Cancer Center at the University of Texas working on a quest to discover genetic mutation, which can be confirmed pancreatic cancer without the need for biopsy. The researchers found that cancer cells, like other healthy individual specific small particles known as exosomes, 1983, having "footprint" of the respective tumor.

    Exosomes are small bubbles that form in the cytoplasm and secreted by cells into the extracellular environment. They can be found in a study of various body fluids, such as blood plasma, cerebrospinal fluid, urine, saliva, breast milk even. Their size is in the range of the virus, they are larger than the low density lipoprotein (bad cholesterol molecule), but smaller than the red blood cells. Their diameter is between 30 and 100 nanometers.

    Exosomes carrying the proteins, RNA and lipids. Participate in the regulation of immune responses and are an important component of intercellular communication. Relatively recently it was found that the transferred microRNA and mRNA to specific target cells and in particular, that provide for horizontal transport of mRNA between the cells, i.e. they are carried out by means of differentiation of the cell recipient. It is believed that the nucleic acids are transferred, are involved in the epigenetic inheritance. There is evidence that protein exosomes to create favorable changes in tumor growth cell-around environment.

    Researchers from the University of Texas believes it can develop a test that decipher coded in the excuzemes. This can not only determine the presence of cancerous processes in the body, but he caught at the beginning of tumorigenesis, which will be of immense value in medical practice for early detection, diagnosis and treatment of patients.

    At this stage there is no such medical text with the help of which you can find out whether a person suffers from some kind of tumor. Medicine use multiple tests "recognize" one or another gene mutation, pointing respectively to one or another type of tumor and whether it is malignant or benign.

    To be diagnosed with a tumor disease, it is first necessary to determine if it exists, to reach it, if it is available, and finally there are always risks and costs of surgical interventions, said Dr. Raghu Kaluri team .

    According to him, the genetic analysis of exosomes will help to determine not only the presence of a tumor process in the organism, but also its identification without biopsy. Different types of cancer produce different chromosomal mutations explains it with the test will be possible to know whether the cancer, pancreatic or brain, for example.

    Such a tool will undoubtedly enhance the ability of physicians to detect cancer in its early stages and effectively treating oncological diseases are written in the Journal of Biological Chemistry. Still a lot of work on the development of the test, which is not an easy task, given that the very exosomes is still studied by science.

    Published in News

    A molecular technique that will help the scientific community to analyze-on a scale previously impossible-molecules that play a critical role in regulating gene expression has been developed by a research team led by a chemist and a plant biologist at Penn State University. The scientists developed a method that enables more-accurate prediction of how ribonucleic acid molecules (RNAs) fold within living cells, thus shedding new light on how plants-as well as other living organisms-respond to environmental conditions. A paper by the research team-led by Sarah M. Assmann, Waller Professor of Biology, and Philip Bevilacqua, professor of chemistry-is scheduled for early online publication in the journal Nature on 24 November 2013.
    "Scientists have studied a few individual RNA molecules, but now we have data on almost all the RNA molecules in a cell-more than 10,000 different RNAs," Assmann said. "We are the first to determine, on a genome-wide basis, the structures of the RNA molecules in a plant, or in any living organism."

    eterna-rna-main
    Temperature and drought are among the environmental stress factors that affect the structure of RNA molecules, thereby influencing how genes are "expressed"-how their functions are turned on or turned off. "Climate change is predicted to cause increasingly extreme and unpredictable heat waves and droughts, which would impact our food crops, in part by affecting the structures of their RNA molecules and so influencing their translation into proteins," Bevilacqua said. "The more we understand about how environmental factors affect RNA structure and thereby influence gene expression, the more we may be able to breed-or develop with biotechnological methods-crops that are more resistant to those stresses. Such crops, which could perform better under more-marginal conditions, could help feed the world's growing population."
    The scientific achievement of the Penn State research team-postdoctoral scholar Yiliang Ding, graduate students Yin Tang and Chun Kit Kwok, and Professor of Statistics Yu Zhang, along with Assmann and Bevilacqua-involved determining the structures of the varieties of RNA molecules in a plant named Arabidopsis thaliana. This plant is used worldwide as a model species for scientific research.
    Arabidopsis thaliana, commonly known as mouse-ear cress, is an ideal organism for RNA studies, the researchers say, because it is the first plant species to have its full genome sequenced and has the greatest number of genetic tools available.
    RNA is the intermediate molecule between DNA and proteins in all living things. It is a critical component in the pathway of gene expression, which controls an organism's function. Unlike the double-stranded DNA molecule, which is compressed into cells by twisting and wrapping around proteins, RNA is single stranded, and folds back on itself. The researchers set out to answer the question, How exactly does RNA fold in a cell and how does that folding regulate gene function?
    "We needed a tool to answer that question," says Bevilacqua. "That tool involves introducing a chemical into the plant that can modify some segments of the RNA but not others, which then gives a readout of the structure of the RNA. Using this technique we can figure out which classes of genes are associated with certain RNA structural traits. And we can try to understand how these RNA structural changes relate to certain biological functions."
    "Previously, researchers would query the structures of individual RNAs in a cell one by one, and it was a tedious process," says Assmann. "You can't abstract rules or generalities about how RNAs are behaving just from knowing the structures of one or a few RNAs-you can't get a pattern. Now that we have genome-wide information for a particular organism, we can start to abstract patterns of how RNA structure influences gene expression and ultimately plant function. Other scientists can query their organisms of interest and ask what rules they can abstract. Are there universal rules that will be true for all organisms for how RNA structure influences gene expression?"
    Bevilacqua adds, "Because RNA is so central in its role in gene regulation, the tools we've developed can be transferred to scientists who are working with essentially any biological system."
    Long-term potential implications of the methodology include human health-for example, how an infection-induced fever could affect the RNA structures of both humans and pathogens.

    Published in News
    Wednesday, 20 November 2013 09:19

    Super antibodies almost won HIV

    In AIDS patients as there is only one hope - to antiretroviral therapy, which is based on drugs that prevent HIV from reproducing. Genome recorded in the virus RNA and thus enter the cell it with reverse transcriptase enzyme (reverse transcriptase) makes a copy of its own DNA template RNA. Then, this DNA was self proteins cells begin RNA viral clone. If, for example, to suppress the work of the reverse transcriptase of the virus, it can not reproduce.

    But even cocktails of antiretroviral drugs only help to translate the acute phase of the disease chronic. Such therapy can not do anything with the virus, which floats in the blood or in the cell is dormant. Therefore, researchers are looking for a way to get rid of the virus, rather than just suppressing its ability to reproduce. (By the way, the usual anti-HIV therapy is theoretically allows to get rid of the virus, but only under special conditions, and such cases are, unfortunately, rare.)

    630b-teratoma-service-ipsc-transgenic-mouse-dr4-stem-cell-differentiation-neural-stem-cells-rat-models-gene

    HIV and human lymphocyte

    When it comes to completely banish HIV, all agree that the best anti tool to be found here. On the one hand, it's simple: just find the immunoglobulins, which would learn viral envelope protein have been associated with him and would have signaled an immune killer cells that this complex must be destroyed. The problem, however, is that HIV has enormous variability, and antibodies usually catch only a certain proportion of the virus particles, for the same protein they endowed with a number of differences that make antibodies do not see it.

    However, our immune system is still able to cope with such a variety of the virus , creating a broad-spectrum antibodies . The fact that the immune system can produce immunoglobulins that recognize more than 90 % of the species of HIV , scientists discovered in 2010, and this discovery , of course, has given all hope that AIDS is about to fall . But over time it became clear that such antibodies are rare and a huge amount of time , then only in response to a real infection - that is to provoke a synthesis of a vaccine of killed pathogen will not work.

    Nevertheless, scholars have continued to work with the likes of antibodies. And not so long ago have found universal antibodies that appear much earlier and look simpler than those observed before - however, proved their versatility and low. But be sure to make yourself immune to produce such antibodies? The experiments showed the two research groups - Deaconess Medical Center Beth Israel and the National Institute of Allergy and Infectious Diseases (both - USA) - immunoglobulins broad-spectrum, just introduced into the blood, effectively reduce the level of HIV.

    858b-teratoma-service-ipsc-transgenic-mouse-dr4-stem-cell-differentiation-neural-stem-cells-rat-models-gene

    HIV between epithelial cells (bottom) and lymphocyte (top)

    Immediately it should be said that the group of Dan Baruch (Dan Barouch) and Malcolm Martin (Malcolm Martin) experimented with monkeys: macaques infected with simian-human hybrid HIV, which multiply in monkeys, but looked like a human virus. He served as a weapon against a broad-spectrum antibodies obtained from patients with AIDS.

    Dan Baruch and his colleagues used a cocktail of three types of antibodies, and, as the researchers write in Nature, in the week of the virus level down so that it can not be detected! A similar result was also when used instead of a mixture of immunoglobulins only one of their kind. Once the content of such antibodies in the blood began to decline, the concentration of the virus rose again, but some monkeys it was still indistinguishably low even without the introduction of additional portions of antibodies.

    In another study carried out by Malcolm Martin and his colleagues, we are talking about the same thing , but here researchers have used different types of antibodies against HIV. Again, the concentration of the virus in macaques fell for seven days prior to the indiscernible ( again: undetectable !) Level and remained so for 56 days, until the antibodies do not begin to fade. Then it all depended on how much virus was originally in monkeys , if small, following the disappearance of virus antibodies remained under the control of its own immunity of animals , and if it was originally much, the level began to rise.

    Thus, as emphasized by the researchers, the virus disappeared from both the blood and other tissues, and no resistance to the administered antibodies, it appeared. (However, there was one exception: when the second study administered only one antibody and experimental monkey was a 3-year experience of cohabitation with the virus, it has a sustained viral strain.)

    In both cases, scientists are not too long treated the virus with human antibodies because they were afraid that the immune system begins to resent monkeys against foreign immune proteins , and perhaps that was the reason that in most cases, the virus recovered . That is, it is not clear whether it is possible to make the effect of the " long-playing ". All this is clear only after a clinical trial , and as for the results described above , the enthusiasm of researchers can understand the first time in a living organism could so much lower level of viremia (alas , previous experiments with antibodies that were placed on humans and mice had a very unimpressive results ) .

    What's next? The cost of antibodies is much higher than the anti-retroviral drugs, and to treat them more difficult. But the authors of the work suggest that such antibodies should be connected to conventional anti-HIV drugs: it will reduce the cost of treatment, and is likely to increase its efficiency - if antibodies to add substances harmful to reproduction of the virus in the cell.

    Published in News

    madetoorderaProtein synthesis in the extensions of nerve cells, called dendrites, underlies long-term memory formation in the brain, among other functions. "Thousands of messenger RNAs reside in dendrites, yet the dynamics of how multiple dendrite messenger RNAs translate into their final proteins remain elusive," says James Eberwine, PhD, professor of Pharmacology, Perelman School of Medicine at the University of Pennsylvania, and co-director of the Penn Genome Frontiers Institute.
    Dendrites, which branch from the cell body of the neuron, play a key role in the communication between cells of the nervous system, allowing for many neurons to connect with each other. Dendrites detect the electrical and chemical signals transmitted to the neuron by the axons of other neurons. The synapse is the neuronal structure where this chemical connection is formed, and investigators surmise that it is here where learning and memory occur.
    Previous studies in the Eberwine lab have shown that translation of messenger RNAs (mRNAs) into proteins occurs in dendrites at focal points called translational hotspots. Local protein synthesis in dendrites, not in the cell body of nerves, provides the ability to respond rapidly and selectively to external stimuli. This ability is especially important in neurons that have highly polarized cell morphology, meaning one end of the cell has a very different shape from the other end.
    In dendrites and axons these rapid structural and functional changes occur concurrently – their length, size, shape, and number change to suit the needs of neuronal cell body communication.
    These structural and chemical changes – called synaptic plasticity—require rapid, new synthesis of proteins. Cells may use different rates of translation in different types of mRNA to produce the right amounts and ratios of required proteins.
    Knowing how proteins are made to order – as it were - at the synapse can help researchers better understand how memories are made. Nevertheless, the role of this "local" environment in regulating which messenger RNAs are translated into proteins in a neuron's periphery is still a mystery.
    Eberwine, first author Tae Kyung Kim, PhD, a postdoc in the Eberwine lab, and colleagues including Jai Yoon Sul, PhD, assistant professor in Pharmacology, showed that protein translation of two dendrite mRNAs is complex in space and time, as reported online in Cell Reports this week.
    "We needed to look at more than one RNA at the same time to get a better handle on real- world processes, and this is the first study to do that in a live neuron," Eberwine explains.
    At Home in the Hippocampus
    The team looked at two RNAs that make proteins that bind to glutamate, the dominant neurotransmitter in the brain. Using rat hippocampus neurons the researchers found a heterogeneous distribution of translational hotspots along dendrites for the two mRNAs.
    This finding indicates that RNA translation is dictated by translational hotspots, not solely when RNA is present. A translational hot spot is characterized by where translation is occurring in a ribosome at any one time in a discrete spot. Since hotspots are not uniform, understanding individual hotspot dynamics is important to understanding learning and memory.
    "It's not always one particular RNA that dominates at a translation hotspot versus another type of RNA," says Eberwine. "Since there are 1,000 to 3,000 different mRNA types present in the dendrite overall, but not 1,000 to 3,000 different translational hot spots, do the mRNAs 'take turns' being translated in space and time at the ribosomes at the hotspots?"
    The researchers engineered the glutamate receptor RNAs to contain different fluorescent proteins that are independently detectable, as well as a photo-switchable protein to determine when new proteins were being made. In the case of the photo-switchable protein studies, when an mRNA for the glutamate receptor protein is marked green, it means it has already been translated.
    When a laser is passed over the green protein, it changes to red as a way of tagging when it has been been translated, and new proteins synthesized at that hotspot would be green, which is visible by the appearance of yellow fluorescence (green + red, as measured by light on the visible spectrum). These tricks of the light allow the team to keep track of newly made proteins over time and space.
    "This is the first time this method of protein labeling has been used to measure the act of translation of multiple proteins over space and time in a quantitative way," says Eberwine. "We call it quantitative functional genomics of live cell translation."
    "Our results suggest that the location of the translational hotspot is a regulator of the simultaneous translation of multiple messenger RNAs in nerve cell dendrites and therefore synaptic plasticity," says Sul.
    Laying the Groundwork
    Almost 10 years ago, the Eberwine lab discovered that nerve-cell dendrites have the capacity to splice messenger RNA, a process once believed to take place only in the nucleus of cells. Here, a gene is copied into mRNA, which possesses both exons (mature mRNA regions that code for proteins) and introns (non-coding regions). mRNA splicing works by cutting out introns and merging the remaining exon pieces, resulting in an mRNA capable of being translated into a specific protein.
    The vast array of proteins within the human body arises in part from the many ways that mRNAs can be spliced and reconnected. Specifically, splicing removes pieces of intron and exon regions from the RNA. The resulting spliced RNA is made into protein.
    If the RNA has different exons spliced in and out of it, then different proteins can be made from this RNA. The Eberwine lab was successful in showing that splicing can occur in dendrites because they used sensitive technologies developed in their lab, which permits them to detect and quantify RNA splicing, as well as the translated protein in single isolated dendrites.
    Understanding the dynamics of RNA biology and protein translation in dendrites promises to provide insight into regulatory mechanisms that may be modulated for therapeutic purposes in neurological and psychiatric illnesses. The directed development of therapeutics requires this detailed knowledge, says Eberwine.

    Published in News

    ahiddengenetScientists routinely seek to reprogram bacteria to produce proteins for drugs, biofuels and more, but they have struggled to get those bugs to follow orders. But a hidden feature of the genetic code, it turns out, could get bugs with the program. The feature controls how much of the desired protein bacteria produce, a team from the Wyss Institute for Biologically Inspired Engineering at Harvard University reported in the September 26 online issue of Science.
    The findings could be a boon for biotechnologists, and they could help synthetic biologists reprogram bacteria to make new drugs and biological devices.
    By combining high-speed "next-generation" DNA sequencing and DNA synthesis technologies, Sri Kosuri, Ph.D., a Wyss Institute staff scientist, George Church, Ph.D., a core faculty member at the Wyss Institute and professor of genetics at Harvard Medical School, and Daniel Goodman, a Wyss Institute graduate research fellow, found that using more rare words, or codons, near the start of a gene removes roadblocks to protein production.
    "Now that we understand how rare codons control gene expression, we can better predict how to synthesize genes that make enzymes, drugs, or whatever you want to make in a cell," Kosuri said.
    To produce a protein, a cell must first make working copies of the gene encoding it. These copies, called messenger RNA (mRNA), consist of a specific string of words, or codons. Each codon represents one of the 20 different amino acids that cells use to assemble proteins. But since the cell uses 61 codons to represent 20 amino acids, many codons have synonyms that represent the same amino acid.
    In bacteria, as in books, some words are used more often than others, and molecular biologists have noticed over the last few years that rare codons appear more frequently near the start of a gene. What's more, genes whose opening sequences have more rare codons produce more protein than genes whose opening sequences do not.
    No one knew for sure why rare codons had these effects, but many biologists suspected that they function as a highway on-ramp for ribosomes, the molecular machines that build proteins. According to this idea, called the codon ramp hypothesis, ribosomes wait on the on-ramp, then accelerate slowly along the mRNA highway, allowing the cell to make proteins with all deliberate speed. But without the on-ramp, the ribosomes gun it down the mRNA highway, then collide like bumper cars, causing traffic accidents that slow protein production. Other biologists suspected rare codons acted via different mechanisms. These include mRNA folding, which could create roadblocks for ribosomes that block the highway and slow protein production.
    To see which ideas were correct, the three researchers used a high-speed, multiplexed method that they'd reported in August in The Proceedings of the National Academy of Sciences.
    First, they tested how well rare codons activated genes by mass-producing 14,000 snippets of DNA with either common or rare codons; splicing them near the start of a gene that makes cells glow green, and inserting each of those hybrid genes into different bacteria. Then they grew those bugs, sorted them into bins based on how intensely they glowed, and sequenced the snippets to look for rare codons.
    They found that genes that opened with rare codons consistently made more protein, and a single codon change could spur cells to make 60 times more protein.
    "That's a big deal for the cell, especially if you want to pump out a lot of the protein you're making," Goodman said.
    The results were also consistent with the codon-ramp hypothesis, which predicts that rare codons themselves, rather than folded mRNA, slow protein production. But the researchers also found that the more mRNA folded, the less of the corresponding protein it produced—a result that undermined the hypothesis.
    To put the hypothesis to a definitive test, the Wyss team made and tested more than 14,000 mRNAs – including some with rare codons that didn't fold well, and others that folded well but had no rare codons. By quickly measuring protein production from each mRNA and analyzing the results statistically, they could separate the two effects.
    The results showed clearly that RNA folding, not rare codons, controlled protein production, and that scientists can increase protein production by altering folding, Goodman said.
    The new method could help resolve other thorny debates in molecular biology. "The combination of high-throughput synthesis and next-gen sequencing allows us to answer big, complicated questions that were previously impossible to tease apart," Church said.
    "These findings on codon use could help scientists engineer bacteria more precisely than ever before, which is tremendous in itself, and they provide a way to greatly increase the efficiency of microbial manufacturing, which could have huge commercial value as well," said Wyss Institute Founding Director Don Ingber, M.D., Ph.D. "They also underscore the incredible value of the new automated technologies that have emerged from the Synthetic Biology Platform that George leads, which enable us to synthesize and analyze genes more rapidly than ever before."

    Published in News

    newroleforprPioneering new research from a team of Indiana University Bloomington biologists has shown for the first time that a protein which has been long known to be critical for the initiation of protein synthesis in all organisms can also play a role in the regulation of gene expression in some bacteria, and probably land plants as well.
    The protein, called translation initiation factor 3, or IF3, is one of three proteins that make up the core structure of the machinery needed to guide the joining of messenger RNAs and ribosomes as protein translation commences. These three proteins have been widely considered to simply operate in a constitutive manner and play little, if any, role in regulating the expression of genes.
    The new findings, from the laboratory of David M. Kehoe, professor of biology in the Indiana University Bloomington College of Arts and Sciences, reveals that IF3, in addition to its well-accepted function during translation initiation, also regulates the expression of genes that encode components of the photosynthetic machinery in response to changes in the color of light in the surrounding environment, a process known as "chromatic acclimation."
    These photosynthesis genes produce red-pigmented proteins called phycoerythrin in cyanobacteria when the cells are grown in green light and allow these organisms to efficiently absorb the predominant ambient light color for photosynthesis. The team uncovered the novel function of IF3 while searching for mutants that incorrectly regulated phycoerythrin. The discovery of this mutant was at first surprising, because in all other bacteria that have been examined, mutations in infC (the gene that encodes IF3) are lethal.
    The team solved this puzzle by uncovering a second infC gene in Fremyella diplosiphon, the model organism for the study of light color responsiveness in cyanobacteria. While both IF3s, which have been named IF3a and IF3b, can act in the traditional role of translation initiation, only IF3a was found to also regulate photosynthetic gene expression.
    By exploring the genomes of hundreds of prokaryotes and eukaryotes in collaboration with members of the laboratory of Indiana University Distinguished Professor and Class of 1955 Professor Jeffrey Palmer, the group identified a wide range of species whose genomes appear to have the potential to encode multiple IF3s, with one organism apparently encoding five distinct IF3 family members. And since almost none of these species are capable of chromatic acclimation, Kehoe believes that multiple IF3s must be used to regulate a wide range of environmental and perhaps developmental responses in both prokaryotes and eukaryotes.
    "Particularly interesting was our finding that IF3 families exist in a number of plant species, including commercially important crops," Kehoe said. "This means that new approaches to the modification of traits in agriculturally significant plant species may be possible by manipulating the expression patterns of different IF3 family members."
    The discovery has generated excitement for an additional reason. Historically, scientists have had a difficult time studying IF3 because it is so essential for translation initiation that it can not be altered without causing death. In fact, it remains one of the few proteins involved in translation for which no effective antibiotic has been developed. But the ability of the Kehoe team to delete either of the two infC genes in F. diplosiphon without causing lethality will allow the group to modify both IF3a and IF3b at will.
    "Now that we know that F. diplosiphon contains two functionally different IF3s, and that each is nonessential, we have a unique opportunity to enhance our understanding of how the structural features of IF3 are related to its function," Kehoe said. "Advancing our understanding of the role of IF3 in translation is likely to provide opportunities to develop new antibiotics that are targeted to this class of proteins."
    "A unique role for translation initiation factor 3 in the light color regulation of photosynthetic gene expression" is now available in early online editions of the Proceedings of the National Academy of Sciences. Co-authors with Kehoe and Palmer were Andrian Gutu, a former Ph.D. student in the Kehoe lab who is now a Howard Hughes Medical Institute Postdoctoral Fellow at Harvard University; April Nesbit, a former postdoctoral researcher in the Kehoe lab who is now a lecturer at Purdue Northwest; and Andrew Alverson, a former postdoctoral fellow in the Palmer lab who is now a faculty member at the University of Arkansas. Primary funding for the work was provided by the National Science Foundation, with support provided to Nesbit by the National Institutes of Health.

    Published in News
    Page 1 of 3