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Sasicha Manupipatpong

Divergent evolution illuminated: Light shed on reasons behind genome differences betwee... - 0 views

www.sciencedaily.com/...120329124607.htm

trna dna evolution genome differences proteins biotechnology

shared by Sasicha Manupipatpong on 01 Apr 12 - No Cached
  • divergent evolution of the genomes of different groups of species
  • three large domains: Archaea, Bacteria and Eukarya
  • genomes of each group have evolved towards distinct structures that have favored their separation
  • ...15 more annotations...
  • connection between the function of enzymes and the composition of the genomes shed light on the evolution and structure of genes
  • analyzed the distribution and abundance of transfer RNA genes
  • structure of genomes was adapted to the activity of some enzymes, which differ for Bacteria and for Eukarya and are absent in Archaea
  • activity of these enzymes modifies tRNAs, allowing them to recognize up to three distinct codons
    • Sasicha Manupipatpong
      Sasicha Manupipatpong on 01 Apr 12
       
      Prior to the study, it was understood that tRNA's have a specific anti-codon sequence which would recognize a single mRNA codon with the complementary sequence. Does this mean that the tRNA also attaches to different amino acids as well? How does the tRNA differentiate between the different amino acids it is at that moment carrying and the codon it matches with on the mRNA--does it change shape according to which amino acid is attached to it?
  • activity of the bacterial and eukaryal enzymes is different, which explains why the genomes and the gene composition of bacteria, eukarya, and archaea have diverged
  • relation between genome structure and the speed of protein synthesis from its genes
  • demonstrates how organisms have evolved in a different manner to achieve better adaptations and to have optimum protein translation efficiency
  • biotechnology as the discovery of the relevance of these modifications will allow an improvement in the industrial production of proteins
  • another parameter with which to optimize the synthesis of proteins from a gene
  • human insulin is "manufactured" in bacteria and our discovery would allow this production to be increased if we take into account the activity of these enzymes
  • relevant for the study of cancer: "it is possible that these modification enzymes are over-represented in some kinds of cancer. In fact, this would be logical because cancer cells are highly efficient in producing proteins."
  • greater the abundance of a protein in a cell the higher the number of triplets found in its gene sequence that can be read by modified tRNAs
  • don't exactly know why these enzymes appear or why they are different in bacteria and in eukaryotes but it's clear that they contribute to the separation of genomes of these two groups
  • genetic code is the same
  • what has changed is the relative importance of different codons of the code
  • Sasicha Manupipatpong on 01 Apr 12
     
    A recent study uncovers the reasons for the divergent evolution of the genomes of different species. The findings provide information about tRNA modifications which may prove useful in the field of biotechnology, specifically in the industrial production of proteins
Nitchakan Chaiprukmalakan

Missing Lincs - Science News - 6 views

www.sciencenews.org/...Missing_Lincs

shared by Nitchakan Chaiprukmalakan on 25 Mar 12 - No Cached
    • Nitchakan Chaiprukmalakan
      Nitchakan Chaiprukmalakan on 01 Apr 12
       
      Scientists are finding more information about the importance of the non coding RNAs, lincRNAs.
  • Only now have scientists begun identifying the previously invisible contractors who make sure that materials get where they are supposed to be and in the right order to build a human being or any other creature. Some of these little-known workers belong to a class of molecules called long intergenic noncoding RNAs.
  • And the lincRNAs originate in what scientists used to view as barren wastelands between protein-coding genes. But new research is showing that these formerly underappreciated workers have important roles in projects both large and microscopic.
  • ...16 more annotations...
  • In the last few years, scientists have learned that lincRNAs, as well as other RNAs that are long and noncoding but not intergenic, perform a variety of jobs. Some serve as guides showing proteins where to go, while others tether proteins to different types of RNA, or to DNA. Some work as decoys, distracting regulatory molecules from their usual assignments. Some may even have multiple roles, all the while chattering away to other RNA within cells. (It is not idle gossip; RNA communication within cells may ward off diseases such as cancer.) And as the ultimate multitaskers, lincRNAs keep proper cellular development ticking along and help define what makes mice mice and people people.
  • That archive contains about 3 billion genetic letters, far more than the genomes of less complex organisms such as roundworms and fruit flies.
  • In 2005, the research revealed that even though genes that code for proteins make up only 1.5 percent of the mouse genome, more than 63 percent of the genome’s DNA is copied into RNA. In humans the number is even higher, with up to 93 percent of the genome made into RNA, even though protein-coding genes make up less than 2 percent of the genome.
  • At first, many scientists didn’t know what to make of the excess RNA. Some thought it was overexuberance on the part of the DNA-copying machinery. But gradually researchers began to realize that many of those extra RNAs had important jobs to do.
  • Some, though, appear to act like general contractors — not hammering in the nails and pouring the foundations of cells themselves, but dictating how the job should be done.
  • One of the most famous long noncoding RNAs, known as XIST, is also one of the most hands-on. XIST is in charge of shutting down one of the X chromosomes in every single cell of women and girls
  • XIST doesn’t have a long commute to work; it coats whichever X chromosome makes it, preventing other genes on the chromosome from being activated
  • One of the most well-studied linc­RNAs, named HOTAIR, wasn’t lucky enough to get a job close to home. It is copied from DNA on chromosome 12 but has to travel to chromosome 2 to shut down several genes in a group known as the HOXD cluster, genes important for proper development of an organism
  • Not only does HOTAIR help direct development, but it is also important throughout life to help cells pinpoint their location in the body.
  • Whether promoting health or mis­directing cells, lincRNAs don’t necessarily act alone.
  • A lincRNA known as HOTTIP also works with a crew of histone modifiers, but instead of shuttering genes, HOTTIP’s crews hang grand-opening signs to attract gene-activating machinery
  • In the recipe for humans, lincRNAs are in the thick of things from the very beginning. At least 26 different lincRNAs need to be on to keep an embryonic stem cell a stem cell
  • Just how lincRNAs choose which genes to turn on and off isn’t yet known. But Pier Paolo Pandolfi, a geneticist at Beth Israel Deaconess and Harvard Medical School, suspects that the lincRNAs are whispering to each other and to other RNAs, keeping tabs on all a cell’s goings-on. Pandolfi laid out his hypothesis for how this chatter might help control protein production and other processes in the Aug. 5 Cell.
  • The Columbia team and Pandolfi’s team independently found that tweaking levels of a few messenger RNAs that distract microRNAs from PTEN messenger RNA can lead to prostate cancer or a type of brain tumor called glioblastoma. Just messing with levels of a messenger RNA from another gene known as ZEB2 throws off PTEN protein levels and can lead to melanoma in mice, Pandolfi’s group reported in another paper in the Oct. 14 Cell.
  • Losing one noncoding RNA may be disastrous for a cell, but for want of noncoding RNAs whole species may never have evolved, argues Queensland’s Mattick. He and others say the real function of lincRNAs is to give evolution a sort of molecular clay from which to mold new designs.
  • Humans have several lincRNAs that are found in no other species. Many of those RNAs are made in the brain, leading scientists to speculate that the molecules may be at least partially responsible for that important organ’s evolution.
  • Paige Prescott on 25 Mar 12
     
    Is RNA the most important molecule in the cell? There is a lot of evidence leading to new understandings of RNA and it's role in many different mechanisms within a cell.
Sasicha Manupipatpong

Identical DNA codes discovered in different plant species - 2 views

www.sciencedaily.com/...120409164426.htm

plant species identical DNA sequences medicine

shared by Sasicha Manupipatpong on 16 Apr 12 - No Cached
  • found identical sequences of DNA located at completely different places on multiple plant genomes
  • Although the scientists found identical sequences between plant species, just as they did between animals, they suggested the sequences evolved differently.
  • find identical sequences in plant DNAs
  • ...9 more annotations...
  • identical sections weren't found at the same points
  • genomes of six animals (dog, chicken, human, mouse, macaque and rat)
  • six plant species (Arabidopsis, soybean, rice, cottonwood, sorghum and grape)
  • found long strings of identical code in different species of animals' DNA
  • expect to see convergent evolution, but we don't
  • Plants and animals are both complex multi-cellular organisms that have to deal with many of the same environmental conditions, like taking in air and water and dealing with weather variations, but their genomes code for solutions to these challenges in different ways
  • could help in the development of new medicines
  • used to find identical sequential patterns in an organism's entire set of proteins
  • lead to finding new targets for existing drugs or studying these drugs' side effects
  • Sasicha Manupipatpong on 16 Apr 12
     
    A computer algorithm found identical sequences of DNA in different places of various plant species' genomes. The same has been found in animals. This could prove to be beneficial in the development of new medicines (for testing drug side effects).
Paige Prescott

Human Genome Project Science - 7 views

www.ornl.gov/...info.shtml

Genetics human genome project DNA

shared by Paige Prescott on 25 Mar 12 - Cached
  • The human genome contains 3164.7 million chemical nucleotide bases (A, C, T, and G).
  • The average gene consists of 3000 bases, but sizes vary greatly, with the largest known human gene being dystrophin at 2.4 million bases.
  • Paige Prescott on 25 Mar 12
     
    check out when the last time this page was updated.  What information has changed in the last 4 years?
Nitchakan Chaiprukmalakan

Biotechdaily - Human Mitochondrial Mutations Repaired by New Technique - 2 views

www.biotechdaily.com/...repaired_by_new_technique.html

shared by Nitchakan Chaiprukmalakan on 01 Apr 12 - No Cached
  • researchers have identified a generic approach to correct mutations in human mitochondrial DNA by targeting corrective RNAs,
  • In adults, many aging disorders have been associated with defects of mitochondrial function, including diabetes, Parkinson’s disease, cancer, heart disease, stroke, and Alzheimer’s disease.
  • The introduction of nucleus-encoded small RNAs into mitochondria is critical for the replication, transcription, and translation of the mitochondrial genome,
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  • The study defined a new role for a protein called polynucleotide phosphorylase (PNPASE) in regulating the import of RNA into mitochondria. Reducing the expression--or output--of PNPASE decreased RNA import, which impaired the processing of mitochondrial genome-encoded RNAs. Reduced RNA processing inhibited the translation of proteins required to maintain the mitochondrial electron transport chain that consumes oxygen during cell respiration to produce energy. With reduced PNPASE, unprocessed mitochondrial-encoded RNAs accumulated, protein translation was inhibited, and energy production was compromised, leading to stalled cell growth.
  • Geng Wang developed a strategy to target and import specific RNA molecules encoded in the nucleus into the mitochondria and, once there, to express proteins needed to repair mitochondrial gene mutations.
  • First, the researchers had to find a way to stabilize the reparative RNA so that it was moved out of the nucleus and then localized to the mitochondrial outer membrane. This was accomplished by modifying an export sequence to direct the RNA to the mitochondrion. Once the RNA was in the area of the transport machinery on the mitochondrial surface, then a second transport sequence was required to direct the RNA into the targeted organelle. With these two modifications, a wide range of RNAs were targeted to and imported into the mitochondria, where they worked to repair defects in mitochondrial respiration and energy production in two different cell line models of human mitochondrial disease.
    • Nitchakan Chaiprukmalakan
      Nitchakan Chaiprukmalakan on 03 Apr 12
       
      This article shows the importance of the RNAs in making proteins for the mitochondria to work efficiently.  The article summarizes a method in repairing the mitochondria that is still being worked on.
  • wasin kusakabe on 01 Apr 12
     
    Mutations in the mitochondrial genome inflicts diseases
adisa narula

The Top 10 Everything of 2009 - TIME - 1 views

www.time.com/...945379_1944416_1944420,00.html

dna genetics disease epigenetic

shared by adisa narula on 01 Apr 12 - No Cached
  • adisa narula on 01 Apr 12
     
    The decoding of the human genome nearly a decade ago fueled expectations that an understanding of all human hereditary influences was within sight. But the connections between genes and, say, disease turned out to be far more complicated than imagined.
Kaoko Miyazaki

lincRNA: A recently discovered RNA organizes stem cell differentiation - 0 views

scitechstory.com/...izes-stem-cell-differentiation

RNA lincRNA

shared by Kaoko Miyazaki on 11 Apr 12 - No Cached
  • Kaoko Miyazaki on 11 Apr 12
     
    Organizing how proteins assemble in embryonic cells and taking control over/deciding whether a stem cells stays pluripotent or not are only two of the main functions of the recently discovered lincRNAs. These new discoveries of lincRNAs and ongoing experiments only help researches such as Mitchell Guttman from the Broad Institute widen up the study of genetics and the human genome to a new field.
Nitchakan Chaiprukmalakan

How a single gene mutation leads to uncontrolled obesity - 0 views

www.sciencedaily.com/...120318143904.htm

shared by Nitchakan Chaiprukmalakan on 13 Apr 12 - No Cached
  • Researchers at Georgetown University Medical Center have revealed how a mutation in a single gene is responsible for the inability of neurons to effectively pass along appetite suppressing signals from the body to the right place in the brain.
  • The research team specifically found that a mutation in the brain-derived neurotrophic factor (Bdnf) gene in mice does not allow brain neurons to effectively pass leptin and insulin chemical signals through the brain. In humans, these hormones, which are released in the body after a person eats, are designed to "tell" the body to stop eating. But if the signals fail to reach correct locations in the hypothalamus, the area in the brain that signals satiety, eating continues.
  • He has found that the gene produces a growth factor that controls communication between neurons.
  • ...5 more annotations...
  • The Bdnf gene generates one short transcript and one long transcript. He discovered that when the long-form Bdnf transcript is absent, the growth factor BDNF is only synthesized in the cell body of a neuron but not in its dendrites. The neuron then produces too many immature synapses, resulting in deficits in learning and memory in mice. Xu also found that the mice with the same Bdnf mutation grew to be severely obese
  • large-scale genome-wide association studies showed Bdnf gene variants are, in fact, linked to obesity.
  • both leptin and insulin stimulate synthesis of BDNF in neuronal dendrites in order to move their chemical message from one neuron to another through synapses. The intent is to keep the leptin and insulin chemical signals moving along the neuronal highway to the correct brain locations, where the hormones will turn on a program that suppresses appetite.
  • "If there is a problem with the Bdnf gene, neurons can't talk to each other, and the leptin and insulin signals are ineffective, and appetite is not modified
  • One possible strategy would be to produce additional long-form Bdnf transcript using adeno-associated virus-based gene therapy, Xu says. But although this kind of gene therapy has proven to be safe, it is difficult to deliver across the brain blood barrier,
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