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Sasicha Manupipatpong

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

  • 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
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  • 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
       
      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
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    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
Sasicha Manupipatpong

Identical DNA codes discovered in different plant species - 2 views

  • 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
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  • 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
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    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).
wasin kusakabe

Athletic frogs have faster-changing genomes - 0 views

    • wasin kusakabe
       
      Physical activities can change the DNA sequence which can be passed on to later generations. However this has only been tested on frogs and may not apply to mammals like us.
  • athletic frogs tended to have faster-changing genomes.
  • Stretches of DNA accumulate changes over time
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  • Physically fit frogs have faster-changing genomes
  • During exercise, the circulatory system provides blood and oxygen to the tissues that are needed most
  • When physical activity has stopped, the rush of blood and oxygen when circulation is restored to those tissues produces a burst of free radicals that can cause wear and tear on DNA, eventually causing genetic changes that -- if they affect the DNA of cells that make eggs or sperm -- can be passed to future generations.
Nitchakan Chaiprukmalakan

Missing Lincs - Science News - 6 views

    • Nitchakan Chaiprukmalakan
       
      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.
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  • 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.
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    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.
nidthamsirisup

Mysterious Noncoding DNA: 'Junk' or Genetic Power Player? | PBS NewsHour - 0 views

  • Genes represent only a tiny fraction -- 1 percent -- of our overall genetic material. Then there's the other 99 percent of our DNA -- the stuff that doesn't make protein
  • Researchers have found that some of this noncoding DNA is in fact essential to how our genes function and plays a role in how we look, how we act and the diseases that afflict us.
  • Embedded in this 99 percent is DNA responsible for the mechanics of gene behavior: regulatory DNA. Greg Wray of Duke University's Institute for Genome Sciences and Policy describes the regulatory DNA as the software for our genes, a set of instructions that tells the genome how to use the traditional coding genes.
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  • "It's like a recipe book," Wray said. "It tells you how to make the meal. You need to know the amounts. You need to know the order. The noncoding DNA tells you how much to make, when to make it and under what circumstances."
  • common diseases are probably more influenced by regulatory differences, Harismendy said. These include Type 2 diabetes, Crohn's disease, Alzheimer's Disease and a variety of cancers, including breast, colon, ovarian, prostate and lung.
  • According to Wray, research has shown that diseases like bipolar syndrome and clinical depression may be associated with noncoding mutations that determine whether the brain is producing too much or not enough of a particular neurotransmitter. One noncoding mutation gives a person almost complete protection against the nasty malaria parasite, plasmodium vivax.
  • Another piece of noncoding DNA regulates the enzyme responsible for lactose tolerance, the ability to digest milk. Research by Wray and other scientists has shown that in four populations where dairy consumption is a vital part of the diet, new mutations have appeared that essentially keep the gene that produces the lactase enzyme from switching off.
  • And recent research done by evolutionary biologists suggests that differences in regulatory DNA may represent a major part of what separates us from chimpanzees.
Paige Prescott

Human Genome Project Science - 7 views

  • 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.
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    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

  • 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
       
      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.
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    Mutations in the mitochondrial genome inflicts diseases
orasa sukmark

Making a Friendlier Mosquito - Biology Online - 1 views

  • Genetically modified mosquitoes that cannot transmit malaria are one hope for battling the disease that still kills over one million people a year. But that plan faces some serious snags, according to UC Davis researchers who are suggesting an alternative strategy.
  • nsmit malaria are one hope for battling the disease that still kills over one million people a year. But that plan face
  • Genetically modified mosquitoes that cannot transmit malaria are one hope for battling the disease that still kills over one million people a year.
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  • enetically modified mosquitoes that cannot transmit malaria are one hope for battling the disease that still kills over one million people a year. But that plan faces some serious snags, according to UC Davis researchers who are suggesting an alternative strategy
  • releasing into the wild mosquitoes genetically engineered to resist malaria
  • If the resistant mosquitoes breed and spread their genes through the population, malaria transmission should be shut down.
  • the malaria resistance genes available are not very effective
  • , there's no way to reliably push the genes through the population.
  • Transposons are essentially DNA parasites that snip themselves in or out of the genome under the right circumstances. Scientists can add a new gene into a transposon and use it to carry that DNA into the insect genome. But it's in the interest of that transposon to just get rid of the extra DNA,
  • a transposon that gives an advantage to mosquitoes that already carry genes to block malaria, so that those genes spread through the population by natural selection.
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    scientists have found a way to reduce mosquitoes that can transmit malaria. 
chanon chiarnpattanodom

Cancer epigenetics takes center stage - 1 views

    • chanon chiarnpattanodom
       
      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
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  • 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,
Kaoko Miyazaki

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

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    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.
Kantham Hongdusit

Inducible gene expression from the plastid genome by a synthetic riboswitch - 0 views

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    Riboswitches, natural RNA sensors that mediate the control of gene expression by beinding with metabolites, are engineered via a simulation to meet the requirements of translational regulation in organelles. These new riboswitches are able facilitate the expression of chloroplast genes
Nickyz P.

It's Alive! Artificial Life Springs From Manmade DNA : Discovery News - 0 views

  • "This is the first synthetic cell that's been made," said Venter. "We call it synthetic because the cell is totally derived from a synthetic chromosome, made with four bottles of chemicals on a chemical synthesizer, starting with information in a computer."
  • Venter and his colleagues created a special code, similar to Morse code, to "write" within the DNA itself. Instead of dots and dashes, they used the sequence of four DNA nucleotides, thymine (T), guanine (G), cytosine (C), and adenine (A), as a code for any letter, number or punctuation mark. Using the code, the team included the names of the study co-authors, a website, and even several philosophical quotes, complete with punctuation.
Nitchakan Chaiprukmalakan

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

  • 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.
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  • 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,
Sea Maskulrath

The Ice Age Elephant - Mammuthus primigenius | Scitech | The Earth Times - 0 views

  • preserved remains of a shaggy monster that lived in Siberia at -40°C 10,000 years ago have been uncovered;
  • The frozen and p
  • Only microscopic amounts of DNA are left on the skeletons, including all the bacteria that lived on the animals. No usable DNA is therefore often found in bone, but mammoth hair is plentiful. Shampooed and bleached and digested, the hair, even at 18,000 years old, can have 90% of the DNA left. The genome shows 4 different "races" of this species. Research has also shown the recreated blood of mammoth. It doesn't decrease its oxygen capacity at the low temperatures the mammoth had to endure. That increased oxygen-offloading ability was one of the essential physiological changes evolved especially for this species, just like the Yuka kidney.
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  • reserved remains of a shaggy monster that lived in Siberia at -40°C 10,000 years ago have been uncovered;
  • Cloning the mammoth has been an aim of Japanese scientists for several years. They discovered almost intact bone marrow from a thigh bone in Yakutsk and hope to use a female elephant for what is obviously more than a simple experiment within the next 5 years.
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    The return of the giant, not a long wait :) 
adisa narula

The Top 10 Everything of 2009 - TIME - 1 views

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    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.
Sasicha Manupipatpong

New genes linked to brain size, intelligence - 2 views

  • genes that increase your risk for a single disease that your children can inherit
  • factors that cause tissue atrophy and reduce brain size, which is a biological marker for hereditary disorders
  • schizophrenia, bipolar disorder, depression, Alzheimer’s disease and dementia
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  • sample large enough to reveal clear patterns in genetic variation and show how these changes physically alter the brain
  • smaller brains
  • gene variants that deplete brain tissue beyond normal in a healthy person
  • unearth new genetic variants in people who have bigger brains as well as differences in regions critical to learning and memory
  • screened the genomes of people suffering from a specific brain disease and combed their DNA to uncover a common variant.
  • consistent relationship between subtle shifts in the genetic code and diminished memory centers
  • variations in their DNA that help boost or lower their brains’ susceptibility to a vast range of diseases
  • People also can take preventive steps through exercise, diet and mental stimulation to erase the effects of a bad gene
  • Once we identify the gene, we can target it with a drug to reduce the risk of disease
  • genes that explain individual differences in intelligence
  • gene called HMGA2 affected brain size as well as a person’s intelligence
  • People whose HMGA2 gene held a letter “C” instead of “T” on that location of the gene possessed larger brains and scored more highly on standardized IQ tests
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    Specific genes have been identified which affect brain size and intelligence--a difference of one nucleotide in the DNA sequence could determine how well you score on a standardized IQ test.
Sasicha Manupipatpong

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

  • 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)
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  • 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
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    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".
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