Challenging Assumptions About the Origin of Life. Before there was life on Earth, there were molecules. A primordial soup. At some point a few specialized molecules began replicating. This self-replication, scientists agree, kick-started a biochemical process that would lead to the first organisms. But exactly how that happened — how those molecules began replicating — has been one of science’s enduring mysteries. Now, research from UNC School of Medicine biochemist Charles Carter, PhD, appearing in the September 13 issue of the Journal of Biological Chemistry, offers an intriguing new view on how life began.
In the early 1980s, researchers found that ribozymes — RNA enzymes — act as catalysts. But for the hypothesis to be correct, ancient RNA catalysts would have had to copy multiple sets of RNA blueprints nearly as accurately as do modern-day enzymes. “The RNA world hypothesis is extremely unlikely,” said Carter. Moreover, there’s no proof that such ribozymes even existed billions of years ago. Astrobiology Magazine -- The Origin and Evolution of Life in the Universe. Postdoc: NorthCarolinaStateU.DrosophilaSystemsGenetics. Job: AuburnU.LabTech.Genomics. EvolDir. —Apple-Mail=_03B0D558-7596-4468-A45A-F085144F55E1 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii TEXAS, COLLEGE STATION.
Texas A&M University. The Department of Geography invites applications for a non-tenure track Visiting Assistant Professor in Geography with research and teaching interests in landscape genetics and spatial population genetics to begin 1 September 2014. The successful candidate will be required to teach two undergraduate classes per year in the Geography Department and the Environmental Studies Program at Texas A&M University. This position will be responsible for maintaining an active research agenda in coordination with the Biogeography Lab in the Department of Geography.
This will include writing proposals, helping with the analysis of genetic/genomic data, and interacting with graduate students. Minimum qualifications include a Ph.D. in Genetics, Bioeography, Landscape Ecology or related discipline. TEXAS, COLLEGE STATION. Most viewed on Haldane’s Sieve: August 2013. Course: GTPB_Portugal.RNAseq_exomes. EvolDir. Investigating the genetics of Bti resistance using mRNA tag sequencing: application on laboratory strains and natural populations of the dengue vector Aedes aegypti - Paris - 2013 - Evolutionary Applications. 'Near Optimal' Genetic Code.
Researchers have created a model that may explain the complexities of the origins of life. Their work, which appears in the Journal of the Royal Society Interface, offers new insights into how RNA signaling likely developed into the modern "genetic code. " "Our model shows that today's genetic code probably resulted from a combination of selective forces and random chance," explained Justin Jee, a doctoral student at NYU School of Medicine and the paper's lead author. The study's other co-authors included: Bud Mishra, who has appointments at NYU's Courant Institute of Mathematical Sciences and the Sackler Institute of Graduate Biomedical Sciences at NYU School of Medicine; Andrew Sundstrom of the Courant Institute; and Steven Massey, an assistant professor in the University of Puerto Rico's Department of Biology.
To address this question, the researchers created a model of genetic code evolution in which multiple "translating" RNAs and "genomic" RNAs competed for survival. Astrobiology Magazine -- The Origin and Evolution of Life in the Universe. Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model. Sequencing mRNA from Cryo-Sliced Drosophila Embryos to Determine Genome-Wide Spatial Patterns of Gene Expression.
Complex spatial and temporal patterns of gene expression underlie embryo differentiation, yet methods do not yet exist for the efficient genome-wide determination of spatial expression patterns during development. In situ imaging of transcripts and proteins is the gold-standard, but it is difficult and time consuming to apply to an entire genome, even when highly automated. Sequencing, in contrast, is fast and genome-wide, but is generally applied to homogenized tissues, thereby discarding spatial information.
To take advantage of the efficiency and comprehensiveness of sequencing while retaining spatial information, we cryosectioned individual blastoderm stage Drosophila melanogaster embryos along the anterior-posterior axis and developed methods to reliably sequence the mRNA isolated from each 25 µm slice. The spatial patterns of gene expression we infer closely match patterns previously determined by in situ hybridization and microscopy. Figures Copyright: © 2013 Combs, Eisen. Please review our new paper: Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression. It’s no secret to people who read this blog that I hate the way scientific publishing works today.
Most of my efforts in this domain have focused on removing barriers to the access and reuse of published papers. But there are other things that are broken with the way scientists communicate with each other, and chief amongst them is pre-publication peer review. I’ve written about this before, and won’t rehash the arguments here, save to say that I think we should publish first, and then review. But one could argue that I haven’t really practiced what I preach, as all of my lab’s papers have gone through peer review before they were published. No more. Some ground rules. OK. Peter A. Several years ago a postdoc in my lab, Susan Lott (now at UC Davis) developed methods to sequence the RNA’s from single Drosophila embryos. Anyway, we would love comments on either the method or the manuscript. RNA Affinities and the Origin of Life. The chemical components crucial to the start of life on Earth may have primed and protected each other in never-before-realized ways, according to new research led by University of Washington scientists.
It could mean a simpler scenario for how that first spark of life came about on the planet, according to Sarah Keller, UW professor of chemistry, and Roy Black, UW affiliate professor of bioengineering, co-authors of a paper published online July 29 in the Proceedings of the National Academy of Sciences. Scientists have long thought that life started when the right combination of bases and sugars produced self-replicating ribonucleic acid, or RNA, inside a rudimentary “cell” composed of fatty acids. Under the right conditions, fatty acids naturally form into bag-like structures similar to today’s cell membranes.
By concentrating more of the bases and sugar that are the building blocks of RNA, the system would have been primed for the next steps, reactions that led to RNA inside a bag. Astrobiology Magazine -- The Origin and Evolution of Life in the Universe. ANOVA-Like Differential Expression (ALDEx) Analysis for Mixed Population RNA-Seq. Results Most RNA-seq datasets contain many genes with zero read counts (e.g. [2], [19]–[21]) due to sparse sampling. The method described below explicitly accounts for the probability that genes with 0 read counts actually represent non-expressed genes as opposed to insufficient sequencing depth. Most statistical analyses of RNA-Seq data model the read counts obtained from the sequencer as having come from a Poisson-like process such that for gene the number of counts observed is a Poisson random variable from a process with rate .
Given for every gene in the sample. . Versus , where each quantity is estimated through technical replicates, have been used to argue that is over-dispersed. . , such over-dispersion implies that the are better modelled by a negative-binomial-like process [22]. Inferring proportions from counts The total number of reads we use the set of counts to infer its proportion within the sequenced sample. With . Where each to estimate and then using the set of . Is exactly zero. . ). RNA-Seq: A brief history - Seven Bridges Genomics. Seven Bridges Genomics | SBG Blog. Martian Clay Contains Chemicals Implicated in Origin of Life. Researchers from the University of Hawaii at Manoa NASA Astrobiology Institute (UHNAI) have discovered high concentrations of boron in a martian meteorite.
When present in its oxidized form (borate), boron may have played a key role in the formation of RNA, one of the building blocks for life. The work was published on June 6 in PLOS One. The Antarctic Search for Meteorites team found the Martian meteorite used in this study in Antarctica during its 2009-2010 field season. The minerals it contains, as well as its chemical composition, clearly show that it is of martian origin. Using the ion microprobe in the W. “Borates may have been important for the origin of life on Earth because they can stabilize ribose, a crucial component of RNA. RNA may have been the first molecule to store information and pass it on to the next generation, a mechanism crucial for evolution.
This work was born from the uniquely interdisciplinary environment of UHNAI. Origin of life researchers figure out how to build bigger RNAs. We'll probably never know exactly how life on Earth got its start. The conditions in which it began have long since been lost, and there are simply too many precursor molecules and potential environments that could have gotten the process going. Nevertheless, researchers hope to put together a pathway that's at least plausible, starting from simple molecules that were present on the early Earth and building up to an enclosed system with basic inheritance (from there, evolution can take over). A lot of progress has been made in understanding how a simple chemical, like hydrogen cyanide, can be built up through a series of reactions into a nucleotide, the basic building block of molecules like DNA and RNA. And we've learned quite a bit about how larger RNAs (more than 100 nucleotides long) can fold into complex structures that can catalyze reactions and undergo the chemical equivalent of Darwinian evolution.
Stanford creates biological transistors, the final step towards computers inside living cells. Bioengineers at Stanford University have created the first biological transistor made from genetic materials: DNA and RNA. Dubbed the “transcriptor,” this biological transistor is the final component required to build biological computers that operate inside living cells. We are now tantalizingly close to biological computers that can detect changes in a cell’s environment, store a record of that change in memory made of DNA, and then trigger some kind of response — say, commanding a cell to stop producing insulin, or to self-destruct if cancer is detected. Stanford’s transcriptor is essentially the biological analog of the digital transistor. Where transistors control the flow of electricity, transcriptors control the flow of RNA polymerase as it travels along a strand of DNA.
The transcriptors do this by using special combinations of enzymes (integrases) that control the RNA’s movement along the strand of DNA. You need more than just BIL gates to make a computer, though. A Laser Light Show in the Brain: What Optogenetics Means for Neuroscience. In 1992, Martin Chalfie made a spectacularly useful discovery, which I like to think of as perhaps the greatest use of cut-and-paste. Chalfie began with the fact that every gene has two parts: an encoding sequence that, using RNA as an intermediate, specifies a set of amino acids from which a cell can synthesize a protein, and a regulatory sequence that specifies, indirectly, when and where that protein should be built. By attaching the protein-coding end of a gene called GFP—a protein borrowed from a jellyfish that glows under a black light—to the regulatory region of other genes, Chalfie invented a new way in which scientists could harness nature’s toolkit to watch the actions of individual cells.
It became possible to induce a particular class of neurons to shine under black light in order to ferret out what sort of circuit they might participate in. The impact of this on understanding neuroscience is immense. Photograph by Charles Mazel/Corbis. Please review our new paper: Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression. 'Activating' RNA takes DNA on a loop through time and space. Long segments of RNA—encoded in our DNA but not translated into protein—are key to physically manipulating DNA in order to activate certain genes, say researchers at The Wistar Institute.
These non-coding RNA-activators (ncRNA-a) have a crucial role in turning genes on and off during early embryonic development, researchers say, and have also been connected with diseases, including some cancers, in adults. In an online article of the journal Nature, a team of scientists led by Wistar's Ramin Shiekhattar, Ph.D., detail the mechanism by which long non-coding RNA-activators promote gene expression.
They show how these RNA molecules help proteins in the cell to create a loop of DNA in order to open up genes for transcription. Their experiments have also described how particular ncRNA-a molecules are related to FG syndrome, a genetic disease linked to severe neurological and physical deficits. Rice-wheat-potatoes-interfere-with-gene-expression?utm_source=dlvr. Context of questionable relevance It was exactly one year ago today that I first uttered the phrase, “paleo is a logical framework applied to modern humans, not a historical reenactment.” That idea seemed pretty straightforward to me, and it was well-received to the point of being quoted in a real life book (you should buy it, but not just for that reason).
And sure, Robb and Andy misattributed it to somebody else in a podcast in the distant past, but I already forgave them for that. So here I am, still beating the drum of the paleo framework despite internal and external attempts to refute it, supersede it, minimize it, water it down, or exact (Exacto?) Its death by a thousand cuts. “This guy is irritatingly correct, time and time again, even when he has limited evidence.” – E. Even if I convince you that the individual arguments are flawed, the endeavor still wouldn’t tell you the paleo framework was correct or useful. The two relevant components of the basic paleo framework are: Is There a Jewish Gene? by Richard C. Lewontin. Legacy: A Genetic History of the Jewish People by Harry Ostrer Oxford University Press, 264 pp., $24.95 The Genealogical Science: The Search for Jewish Origins and the Politics of Epistemology by Nadia Abu El-Haj University of Chicago Press, 311 pp., $35.00 The question of ancestry has been of human concern in virtually all cultures and over all times of which we have any knowledge.
Surely pride or shame are appropriate sentiments for actions for which we ourselves are in some way responsible. My own skepticism notwithstanding, the belief is widespread that knowledge about the personal characteristics of ancestors who have never directly entered into our lives is relevant to our own formation. “Race” is a term of uncertain etymology and many meanings. In all these usages the implication is one of common ancestry tracing back ultimately to some relevant founding group, but obviously all such ancestries must incorporate members of other groups at various times in their histories. RDF: Scientists discover possible building blocks of ancient genetic systems in Earth's most primitive organisms.
Scientists believe that prior to the advent of DNA as Earth's primary genetic material, early forms of life used RNA to encode genetic instructions. What sort of genetic molecules did life rely on before RNA? The answer may be AEG, a small molecule that when linked into chains forms a hypothetical backbone for peptide nucleic acids, which have been hypothesized as the first genetic molecules. Synthetic AEG has been studied by the pharmaceutical industry as a possible gene silencer to stop or slow certain genetic diseases. The only problem with the theory is that up to now, AEG has been unknown in nature. A team of scientists from the United States and Sweden announced that they have discovered AEG within cyanobacteria which are believed to be some of the most primitive organisms on Earth. Eperlste : I'm pretty sure that most people... Eperlste : I'm pretty sure that most people... NESCent : Epigenetic changes accrued... NESCent : Epigenetic changes accrued...
Eperlste : Li: DNA copy number change... Eperlste: Li: DNA copy number change... Evoldir : Postdoc: RNA viral pathogen... Evoldir : Postdoc: RNA viral pathogen... AstrobiologyMag : Iron's Role in Early Life... AstrobiologyMag : Iron's Role in Early Life... Ethan Perlstein: Steitz reviewing the histo... Ethan Perlstein: Steitz is the doyenne of n... Ethan Perlstein: Joan Steitz (Yale/HHMI) ab... Tom Reinard: Strange cousins: Molecular... Evolution Review: Evolution Seen in Syntheti... EvolutionReview: Researchers make alternati... Astrobiology Mag: Valuch explains how heavil...