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Nitchakan Chaiprukmalakan

Proteins and quantum transition: Instant shape-shifting - 0 views

scitechstory.com/...nsition-instant-shape-shifting

shared by Nitchakan Chaiprukmalakan on 13 Apr 12 - No Cached
  • The genetic code in DNA provides the template to manufacture protein into all the cells of an organism.
  • Proteins are made by stringing together amino acids. For general purposes there are twenty amino acids in protein and they can be put together in endless combinations, some in short chains (yeast averages 466 amino acids), some long chains (titins have nearly 27,000 amino acids) and everything in-between. The pattern of amino acids determines much of the functionality of the protein.
  • Proteins are three-dimensional puzzle pieces. They are generally very complicated in shape. Even a small protein of only 100 amino acids can theoretically have 10^100 (ten to the hundredth power) different configurations.
  • ...7 more annotations...
  • most protein reconfigurations occur in nanoseconds
  • In research on proteins, it was assumed (given their chemical composition) proteins would uniformly fold as they cool down and unfold as they heat up. (Think of a balloon expanding and shrinking with the temperature of the air inside.) The experiments didn’t bear this out; the rate of folding or unfolding according to temperature change was unequal (asymmetric) and uneven (nonlinear).
  • In recent biochemistry a great deal of work is done with ‘tagging’ or ‘marking’ molecules with fluorescent and phosphorescent materials. It’s well known that fluorescence and phosphorescence are phenomena closely related to protein folding and they can only be understood in terms of quantum transition between molecules.
  • With a quantum transition, the protein could change configuration by ‘jumping’ – skipping all the transition steps – to the final configuration. They call this quantum folding and they developed a mathematical model that shows how the folding, which is virtually instantaneous, would react to change in temperature.
  • Their quantum transition model matched the folding curves for 15 different proteins and also provides an explanation for the different rates of folding and unfolding among these proteins.
  • Luo and Lu’s paper is short, a mere 16 pdf pages, and the model is unpretentious mathematically. (Luo has several other related papers on arXiv.) It comes from unknown researchers in an unknown corner of the academic world, and it’s published on the open-source arXiv system. The lack of pedigree means that it will take more time than usual for scientists around the world to learn of it, examine it, and possibly test it.
    • Nitchakan Chaiprukmalakan
      Nitchakan Chaiprukmalakan on 13 Apr 12
       
      This is not accepted as a true fact yet and has to be proven.
nidthamsirisup

Study suggests why some animals live longer - 1 views

www.physorg.com/...2012-03-animals-longer.html

animals dna project genetics

shared by nidthamsirisup on 02 Apr 12 - No Cached
    • nidthamsirisup
      nidthamsirisup on 02 Apr 12
       
      A new method to detect proteins associated with longevity which helps further our understanding into why some animals live longer than others.
  • The study, led by Dr. Joao Pedro Magalhaes and postgraduate student, Yang Li, is the first to show evolutionary patterns in biological repair systems in long-lived animals and could, in the future, be used to help develop anti-ageing interventions by identifying proteins in long-lived species that better respond to, for example, DNA damage
  • these species have optimised pathways that repair molecular damage, compared to shorter-lived animals, such as mice
  • ...4 more annotations...
  • found a similar pattern in proteins associated with metabolism, cholesterol and pathways involved in the recycling of proteins
  • Proteins associated with the degradation of damaged proteins, a process that has been connected to ageing, were also linked with the evolution of longevity in mammals.
  • If we can identify the proteins that allow some species to live longer than others we could use this knowledge to improve human health and slow the ageing process.
  • “We developed a method to detect proteins whose molecular evolution correlates with longevity of a species. The proteins we detected changed in a particular pattern, suggesting that evolution of these proteins was not by accident, but rather by design to cope with the biological processes impacted by ageing, such as DNA damage. The results suggest that long-lived animals were able to optimise bodily repair which will help them fend off the ageing process.”
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
  • 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
  • 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."
  • demonstrates how organisms have evolved in a different manner to achieve better adaptations and to have optimum protein translation efficiency
  • 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.
Nitchakan Chaiprukmalakan

New study: Tracking proteins that repair DNA - 0 views

scitechstory.com/...cking-proteins-that-repair-dna

shared by Nitchakan Chaiprukmalakan on 13 Apr 12 - No Cached
  • DNA damage could be caused by many things including toxins, radiation, or a failure in molecular chemistry. If it happens in one cell, the damage may do nothing, or at worse cause the cell to die. If damage occurs in a reproductive cell (a zygote) it can be an inherited mutation; the consequences of which can go on for generations
  • The DNA repair workers are (so far as we know) protein molecules.
  • Under microscopic observations it was seen that the UvrA protein randomly jumps from one DNA molecule to the next, staying about 7 seconds before moving on. However, when UvrA formed a complex with two UvrB molecules (UvrAB), the search became more sophisticated and slower. The complex would slide along the DNA strand for as long as 40 seconds before moving to another molecule. Sometimes it was observed that the UvrAB motion would ‘pause,’ apparently checking for structural abnormalities that might indicate DNA damage.
  • ...1 more annotation...
  • It’s assumed the protein complex is analyzing, but the mechanism of analysis is unknown. It’s also unknown if the UvrAB complex (or similar complex) actually does the repair, or if it signals for some other protein complex(es) to make the repair.
nidthamsirisup

Stem Cell Treatment Spurs Cartilage Growth - Science News - 0 views

www.sciencenews.org/...eatment_spurs_cartilage_growth

proteins DNA disease gene

shared by nidthamsirisup on 15 Apr 12 - No Cached
  • A small molecule dubbed kartogenin encourages stem cells to take on the characteristics of cells that make cartilage, a new study shows
  • And treatment with kartogenin allowed many mice with arthritis-like cartilage damage in a knee to regain the ability to use the joint without pain.
  • Kartogenin steers the stem cells to wake up and take on cartilage-making duties. This is an essential step in the cartilage repair that falls behind in people with osteoarthritis, the most common kind of arthritis, which develops from injury or long-term joint use.
  • ...2 more annotations...
  • The molecule turned on genes that make cartilage components called aggrecan and type II collagen. Tests of mice with cartilage damage similar to osteoarthritis showed that kartogenin injections lowered levels of a protein called cartilage oligomeric matrix protein. People with osteoarthritis have an excess of the protein, which is considered a marker of disease severity.
  • kartogenin inhibits a protein called filamin A in the mesenchymal stem cells
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,
  • ...4 more annotations...
  • 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
chanon chiarnpattanodom

Chimeric green fluorescent protein-aequorin as bioluminescent Ca2+ reporters at the sin... - 1 views

www.pnas.org/...7260.full

shared by chanon chiarnpattanodom on 16 Apr 12 - No Cached
    • chanon chiarnpattanodom
      chanon chiarnpattanodom on 16 Apr 12
       
      Experiment on Ca2+ reaction with a protein aequorin. Aequorin can be found in jellyfish, when in contact with Ca2+ will emit light. Using the gene that contributes to this protein, make a similar protein emitting another wavelength of light.
Sasicha Manupipatpong

Gene switches do more than flip 'on' or 'off': Can exhibit much more complex binding be... - 1 views

www.sciencedaily.com/...120411131911.htm

genes switch on off more complex

shared by Sasicha Manupipatpong on 16 Apr 12 - No Cached
  • right genes for the job are turned on only in the specific cells where they are needed
  • molecular "clutch" that converts treadmilling to a stable bound state, moving the transcription process forward to completion to turn the gene on
  • act like a switch; they are either "on" (bound to DNA) or "off" (not bound)
  • ...12 more annotations...
  • can exhibit much more complex binding behavior
  • transcription factors' binding process is dynamic and involves more than just being bound or unbound
  • In addition to a stable binding state (on or off)
  • "treadmilling," where no forward transcription process is occurring
  • indicator of whether a gene was turned on or off
  • measure and calculate how long a protein is associated with all of the different genes it regulates
  • proteins that bind in the stable state are associated with high levels of gene transcription
  • if we can regulate the transition between treadmilling and stable binding, we can regulate the outcome in terms of gene expression
  • genetic medicine -- a new way to regulate the 'switches' that turn gene expression associated with disease on or off.
  • measured how long it took the competitor transcription factor to replace the resident protein and used this data to calculate the residence time at each location in the genome
  • specific proteins called "transcription factors" that control which genes are turned on or off in cells by binding to nearby DNA
  • new insights on how cells respond to developmental cues and how they adapt to changing environmental conditions
  • Sasicha Manupipatpong on 16 Apr 12
     
    Genes have been discovered to be more complex than we previously thought--rather than having only on and off states, there is an intermediate state called "treadmilling".
Nitchakan Chaiprukmalakan

Hoogsteen base pairs: An alternate structure in DNA - 0 views

scitechstory.com/...-an-alternate-structure-in-dna

shared by Nitchakan Chaiprukmalakan on 13 Apr 12 - No Cached
  • This discovery, made by a team of researchers from the University of Michigan (USA) and the University of California, Irvine (USA) and published in the journal Nature January 26, 2011 [Transient Hoogsteen base pairs in canonical duplex DNA] involves a new capability of nuclear magnetic resonance (NMR) machines and something most people have never heard of (including me): Hoogsteen base pairs.
  • It was discovered by the biologist Karst Hoogsteen in 1963. In effect, the Hoogsteen base pair is a ‘normal’ Watson-Crick base pair (usually A-T) flipped-over like an upside-down step on a ladder.
  • It changes the geometry and allows for truly exotic formations such as a triple helix or even quadruplex structures.
  • ...4 more annotations...
  • Hoogsteen base pairs were known to exist primarily in RNA and had been observed in DNA only when there was damage to the DNA structure, or something else like a protein or drug was bound to it.
  • In RNA the Hoogsteen base pairs have been studied fairly extensively. They are considered an “excited state” and are useful to observe unusual protein binding. In DNA the Hoogsteen base pairing, which by the way has two forms, normal and reverse, was considered an anomaly.
  • It was discovered that normal DNA undergoes these shifts about 1% of the time and they last only milliseconds.
  • “Together, these data suggest that there are multiple layers of information stored in the genetic code.” Because critical interactions between DNA and proteins are thought to be directed by both the sequence of bases and the flexing of the DNA molecule, these excited states represent a whole new level of information contained in the genetic code.
Mickey Tsai

Parkinson's disease sufferer Sheila Roy can write for the first time in 15 years thanks... - 0 views

www.dailymail.co.uk/...s-thanks-new-gene-therapy.html

gene therapy disease

shared by Mickey Tsai on 15 Apr 12 - No Cached
  • one of only 15 people worldwide to undergo the radical treatment, which involves inserting corrective genes into the brain
  • The genes provide the coded instructions for proteins needed to make dopamine, a brain chemical essential for proper control of movement.
  • Lack of dopamine leads to the symptoms of tremor, stiffness and poor balance associated with Parkinson’s.
  • ...3 more annotations...
  • Mrs Roy is taking part in an early-stage study of the ProSavin therapy
  • Following her treatment Sheila Roy has been able to carry out tasks like writing, something she has been unable to do for 15 years
  • Gene therapies hold great promise for people with Parkinson’s in the future, as they could mean an end to the daily regime of drugs that most people with the condition currently face.
  • Mickey Tsai on 15 Apr 12
     
    A woman with Parkinson's was able to write for the first time in 15 years because of gene therapy. Parkinson's includes symptoms such as tremors, loss of balance which makes it impossible to do even simple tasks. Doctors injected a modified virus carrying the genes to the motor centre of her brain which provide coded instructions for proteins needed to make dopamine. Lack of dopamine leads of the symptoms associated with Parkinson's. This is part of the ProSavin therapy developed by Oxford BioMedica. Gene therapies hold a lot of hope for people with Parkinson's that could end the daily routine of drugs that most of them go through.
Rafael Chen

New Plant Mutation Produces Tap Root With Large Amounts Of Oil, Proteins, And Starch - 1 views

www.sciencedaily.com/...970707211536.htm

shared by Rafael Chen on 15 Apr 12 - No Cached
  • The discovery could lead to genetically engineered plants that store commercially useful substances in an enlarged root
  • The pickle mutation mimics what happens in seeds, which typically are the major structures accumulating and storing proteins and oil
  • In this mutation the cells destined to become primary root cells retain the character of embryonic cells
  • ...2 more annotations...
  • They fail to make the switch from embryonic to adult
  • The mutation has its greatest effect when gibberellin is not present during the first 24 hours of growth
  • Rafael Chen on 15 Apr 12
     
    A mutation in plants that makes the tap root accumulate large amounts of oils, proteins, and starch was discovered by scientist, this could lead to genetically engineered plants that store commercially useful substances in an enlarged root.
Pop karnchanapimonkul

The Ballooning Brain: Defective Genes May Explain Uncontrolled Brain Growth in Autism: ... - 0 views

www.scientificamerican.com/article.cfm

brain genes autism

shared by Pop karnchanapimonkul on 13 Apr 12 - No Cached
  • linked atypical gene activity to excessive growth in the autistic brain
  • autistic brain sprouts an excess of neurons and continues to balloon during the first five years of life, as all those extra neurons grow larger and form connections.
  • start to lose neural connections, faster than typical brains
  • ...11 more annotations...
  • 67 percent more neurons in their prefrontal cortex (PFC) than typical children
  • executive functions"—high-level thinking, such as planning ahead, inhibiting impulses and directing attention.
  • In brain tissue from both autistic children and autistic adults, genes coding for proteins that identify and repair mistakes in DNA were expressed at unusually low levels. Additionally, all autistic brains demonstrated unusual activity levels for genes that determine when neurons grow and die and how newborn neurons migrate during early development
  • Some genes involved in immune responses, cell-to-cell communication and tissue repair, however, were expressed at unusual levels in adult autistic brains, but not in autistic children's brains
  • autistic child develops in the womb, something—an inherited mutation or an environmental factor like a virus, toxin or hormone—muffles the expression of genes coding for proteins that usually fix mistakes in sequences of DNA
  • Errors accumulate.
  • The genetic systems controlling the growth of new neurons go haywire, and brain cells divide much more frequently than usual, accounting for the excess neurons found in the PFC of autistic children.
  • autistic brain grow physically larger and form more connections than in a typical child's brain.
  • immune system reacts against the brain's overzealous growth,
  • Not all researchers, however, accept
  • If scientists definitively link autism to a characteristic sequence of changes in gene expression and unusual neural growth, then it becomes possible to target and reverse any one of the thousands of steps in that sequence.
  • Pop karnchanapimonkul on 13 Apr 12
     
    Article about how genetic expression may be the cause for autism.
Paige Prescott

DNA The Code of Life | The Language of Life | deCODEme - 4 views

www.decodeme.com/genetic-code

dna

shared by Paige Prescott on 25 Mar 12 - No Cached
  • Genes are especially important segments of DNA that directly influence one or more traits. They are relatively small segments of chromosomes, where the sequence of DNA nucleotides encodes a recipe for making a protein. Small differences in the sequence of DNA nucleotides of a particular gene can lead to differences in the structure and behavior of the proteins they encode. It is these differences, in turn, that account for the variable characteristics of the people around you.
  • Paige Prescott on 25 Mar 12
     
    deCodeMe is a private company that sells DNA technology
chanon chiarnpattanodom

Cancer epigenetics takes center stage - 1 views

www.pnas.org/...392.full

shared by chanon chiarnpattanodom on 16 Apr 12 - No Cached
    • chanon chiarnpattanodom
      chanon chiarnpattanodom on 16 Apr 12
       
      DNA methylation is a chemical process where a methyl group is added on either the cytosine ring or the adenine ring, used in "higher leveled" organisms. Important in cell differentiation since methylation will cause cells to "remember" and remain differenciated instead of expressing other genes. 
  • Epigenetics is defined as modifications of the genome, heritable during cell division, that do not involve a change in the DNA sequence.
  • Epigenetic alterations in cancer include global hypomethylation
  • ...18 more annotations...
  • the promoters of housekeeping genes that are generally protected from methylation.
  • may lead to aberrant silencing of tumor suppressor genes
  • discovered loss of imprinting (LOI) in cancer
  • Genomic imprinting, the subject of the report by Nakagawa et al. (2), is an epigenetic modification of a specific parental allele of a gene, or the chromosome on which it resides, in the gamete or zygote, leading to differential expression of the two alleles of the gene in somatic cells of the offspring.
  • we found that LOI can occur in the normal colonic mucosa of colorectal cancer patients with LOI in their tumors
  • This LOI was linked to cases showing microsatellite instability (MSI) in the tumors
  • However, these patients do not have mutations in mismatch repair genes
  • One potential cause of MSI in these sporadic cancers is hypermethylation and epigenetic silencing of the hMLH1 mismatch repair gene
  • Nakagawa et al. (2) now confirm the original study of Cui et al. that LOI occurs in both tumor and normal tissue of patients
  • The present study (2) also offers an intriguing mechanistic hypothesis to explain the relationship between H19 DMR methylation and LOI in these patients
  • Nevertheless, the study calls attention to this remarkable highly conserved multifunctional protein,
  • The potential link to CTCF suggested by this study also calls our attention to the link among DNA methylation, epigenetics, and chromatin.
  • A clue to the link between MSI and epigenetics may be provided by another sometimes overlooked common thread in epigenetics, namely DNA replication
  • repeat-induced gene silencing is thought to be propagated through hemimethylated intermediates during DNA replication
  • The studies of Cui et al. (11), Nishihara et al. (20), and Nakagawa et al. (2) suggest a new and provocative view of the timing of epigenetic changes in cancer.
  • Studies of transgenic mice with constitutive biallelic expression of IGF2, comparable to LOI, show reduced apoptosis and increased tumor formation
  • I conclude by noting that the distinction between cancer genetics and epigenetics has blurred considerably in recent years
  • Many conventional “genetic” mechanisms directly affect proteins that regulate chromatin,
avikan

New Hope Of a Cure For H.I.V. - NYTimes.com - 0 views

query.nytimes.com/...fullpage.html

shared by avikan on 11 Apr 12 - No Cached
  • So people with H.I.V. now must take drugs every day for life, which some researchers say is not a sustainable solution for tens of millions of infected people.
  • CCR5,
  • This is what was done with the Trenton patient. Some of the man's white blood cells were removed from his body and treated with a gene therapy developed by Sangamo BioSciences. The therapy induced the cells to produce proteins called zinc-finger nucleases that can disrupt the CCR5 gene.
  • ...5 more annotations...
    • avikan
      avikan on 11 Apr 12
       
      Millions of people worldwide are currently affected by HIV and many have died from AIDS. Scientists have been trying for many years to find a cure for the epidemic, but now many are trying to find a way to prevent the passing on of the virus for future generations. Although no definite treatment has been discovered yet, recent findings have shown promising results for the future. 
    • avikan
      avikan on 11 Apr 12
       
      With the fast developing biological technologies we are seeing today, scientists hope's are growing stronger.  Maybe one of us one day will be a part of the phenomenon, in search of a way to help the millions affected by the epidemic  
    • avikan
      avikan on 11 Apr 12
       
      CD4 cells initiate the body's response to infections.
    • avikan
      avikan on 11 Apr 12
       
      Many forms of HIV, initially use CCR5 to enter and infect host cells. A few individuals carry a mutation known as CCR5 delta 32 in the CCR5 gene, protecting them against these strains of HIV.
    • avikan
      avikan on 11 Apr 12
       
      For over 30 years scientists have been trying to find a cure for the HIV/AIDs epidemic and so far have been unsuccessful 
    • avikan
      avikan on 11 Apr 12
       
      Incase some of us forgot, AIDs stands for Acquired immune deficiency syndrome, a disease in which there is a severe loss of the body's cellular immunity. And HIV stands for Human immunodeficiency virus, a virus that causes AIDs
Kaoko Miyazaki

The Rinn Lab - 0 views

www.rinnlab.com/research.html

RNA

shared by Kaoko Miyazaki on 11 Apr 12 - No Cached
  • Kaoko Miyazaki on 11 Apr 12
     
    John Rinn (RNA researcher at Harvard Medical School) continues on his ongoing research about Long Intergenic Noncoding RNA's (lincRNAs). lincRNAs used to be overlooked and classified as 'waste' products, but today it is seen as the contractors that create the DNA's coding sequence needed for the organism's structure. In simpler terms, lincRNAs are responsible for putting molecular materials in places they are supposed to be - as though following a rough draft to make a final master piece. Because lincRNAs have so many functions, if step goes wrong, it could cause potential harm to the organism such as creating a tumor. But because of their many functions like guiding the interactions of protein DNA to name one, John Rinn and other current scientists hypothesize that lincRNAs are what differentiates us from other organisms and makes us, us.
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.
wasin kusakabe

Direct transfer of plant genes from chloroplasts into the cell nucleus: Gene function p... - 0 views

www.sciencedaily.com/...120413121916.htm

Genes Chloroplasts Cell Nucleus DNA

shared by wasin kusakabe on 14 Apr 12 - No Cached
  • Chloroplasts, the plant cell's green solar power generators, were once living beings in their own right.
  • This changed about one billion years ago, when they were swallowed up but not digested by larger cells.
  • either direct transport in the form of DNA fragments from the chloroplasts to the nucleus or transport in the form of mRNA, which is then transcribed back into DNA.
  • ...5 more annotations...
  • Genes consist of several modules, separated by non-coding DNA regions (introns).
  • It was found that the transfer takes place without the involvement of RNA and that the DNA apparently jumps directly from the cell's chloroplasts into its nucleus.
  • t is thought that the introns even help the splicing enzymes by folding themselves into stable RNA structures, thus directing the enzymes to the right locations.
  • Since the introns obstruct protein synthesis, they need to be removed from the mRNA, a procedure described as splicing.
    • wasin kusakabe
      wasin kusakabe on 14 Apr 12
       
      The Chloroplasts was an different entity before they were swallowed up by larger cells to corporate with each other.
  • wasin kusakabe on 14 Apr 12
     
    The differences between the genes in the chloroplasts and the genes in the nucleus being researched.
Paige Prescott

Old Cancer Drugs Offer New Tricks - Science News - 0 views

www.sciencenews.org/..._cancer_drugs_offer_new_tricks

cancer epigenetics

shared by Paige Prescott on 14 Apr 12 - No Cached
  • Drugs that alter some chemical tags on DNA make cancer cells behave more like normal cells
  • And the drugs seem to make cancer cells more susceptible to chemotherapy and attacks from the immune system.
  • drugs called azacitidine and decitabine, when used in low doses, change gene activity in leukemia and breast cancer cells in the lab. If DNA is a cell’s hard drive, then chemical tags attached to the DNA or DNA-packaging proteins called histones serve as software packages to tell the hard drive how to function. This type of chemical programming is called epigenetics.
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