Genomics

In “Kinky genes: Biophysics of DNA affects how it works” (New Scientist, 08 July 2011), MacGregor Campbell reports DNA is typically a long double-helical strand that can expose its sequences of base pairs. These are translated by RNA and particles called ribosomes into proteins, which do the cell’s work. When not in use, DNA wraps around structural proteins called histones to form compact chromosomes. This wrapping is poorly understood, but one thing we do know is that it plays a key role in gene expression. Histones have up to 1000 times greater attraction for some DNA subsequences than others, but why this should be was a mystery.

From “Chromosomes’ Big Picture: Similarities Found in Genomes Across Multiple Species; Platypus Still out of Place” (ScienceDaily, July 11, 2011), we learn: “Basically what this all means is that if the chromosome number of a species can be given, the relative sizes of all the chromosomes can instantly be known,” Yu said. “Also, if you tell me the genome size in the chromosome base pair, I can tell you the base pair length of each chromosome.”According to Yu, the most surprising finding is the extremely consistent distribution pattern of the chromosomes, a result from comparing the full sets of chromosomes — called genomes — of the 68 random eukaryotes. The team found that nearly every genome perfectly formed an S-curve Read More ›

From “Environs Prompt Advantageous Gene Mutations as Plants Grow; Changes Passed to Progeny” (ScienceDaily, July 5, 2011) we learn:

If a person were to climb a towering redwood and take a sample from the top and a sample from the bottom of the tree, a comparison would show that the two DNA samples are different.Christopher A. Cullis, chair of biology at Case Western Reserve University, explains that this is the basis of his controversial research findings. Read More ›

“Genome Duplication Encourages Rapid Adaptation of Plants” (ScienceDaily, May 4, 2011) While nearly all animals have two sets of chromosomes — one set inherited from the maternal parent and the other inherited from the paternal parent — many plants are polyploids, meaning they have four or more chromosome sets. “Some botanists have wondered if polyploids have novel features that allow them to survive environmental change or colonize new habitats,” says Assistant Professor Justin Ramsey. “But this idea had not been rigorously tested.” Forcing duplication on wild plants (instead of the centuries old practice of forcing it on tame ones) produced quick results, as it does in tame ones: Ramsey compared the performance of the transplanted yarrows and found that the Read More ›

Of course, it was put there by a Canadian poet.

Recently we learned that “An original piece of “living poetry” has been created in a lab in Canada.” Christian Bok encoded some of his verse into a DNA strip and got it inserted into an E.coli bacterium:

Dr Bok used cryptography to embed his poem into the genetics of the bacterium, devising a chemical alphabet in which each letter is represented by a specific triplet of nucleotides. So, for example, the nucleotide sequence “ATA” codes for the letter “y” and GTG stands for the letter “n”.

– Rachael Buchanan, “Poet writes verse in bug’s genes and receives reply”, BBC News (28 April 2011).

Better: Read More ›

From the Max Planck Institute, we learn (April 21, 2011): Despite being closely related to the lyre-leaved rock cress, the thale cress has a considerably smaller genomeIt would appear reasonable to assume that two closely related plant species would have similar genetic blueprints. However, scientists from the Max Planck Institute for Developmental Biology in Tübingen, working in cooperation with an international research team have now decoded, for the first time, the entire genome of the lyre-leaved rock cress (Arabidopsis lyrata), a close relative of the thale cress (Arabidopsis thaliana), the model plant used by geneticists. They discovered that the genome of the lyre-leaved rock cress is fifty percent bigger than that of the thale cress. Moreover, these changes arose over Read More ›

From “No Two of Us Are Alike — Even Identical Twins: Pinpointing Genetic Determinants of Schizophrenia”, (ScienceDaily, March 28, 2011) we learn

Singh looked at about one million markers of identical twins (and their two parents) where only one twin had schizophrenia. “The most informative feature of schizophrenia is that it sometimes runs in the family. So, for example, the risk of developing schizophrenia is much higher if your brother, sister, mother or father have the disease,” says Singh, noting in the general population about one percent have schizophrenia. “We started with the belief that monozygotic twins are genetically identical, so if one member of identical twins has schizophrenia, then the risk for the other twin should be 100 percent, if it’s all due to genes. However, studies over the years have shown that the risk of the disease in both twins is only 50 percent.” That means either the twins are genetically not identical or the familial disease involves non-genetic (random) effects. 

Singh and his team have now demonstrated that the monozygotic twins are not genetically identical.

The part I find curious is, Read More ›

In this article in The Scientist, “Imprinting Diversity”, Cristina Luiggi interviews Joachim Messing about ways in which genomic imprinting may be a strong driver of diversity: Sexual reproduction yields offspring with two copies of the same gene, one from each parent; but in an epigenetic phenomenon known as genomic imprinting, only one copy of certain genes is turned on or off, depending on which parent contributed it. Imprinted genes are stamped by patterns of DNA methylation or histone modification during gamete formation, and their activation or inactivation is then passed on to offspring. Previously, approximately 100 genes were thought to be imprinted in mammals. But Rutgers University molecular biologist and F1000 Member Joachim Messing, discusses a recent paper that found Read More ›

A friend put me onto a “neat” summation of the “Hox paradox” in Bioscience last year: “Taken together, these findings presented researchers with a paradox. On one hand, the basic machinery underlying early development, such as the Hox genes, is widely conserved among divergent phyla. But at the same time, these genes also underlie the development of distinct morphologies between more closely related species. The resolution of this “Hox paradox” is that the general role of many genes in patterning the embryo has been preserved, but the precise pattern of their expression or their influence on later events of development have both changed. These modifications are possible only through changes in regulatory interactions, whether mediated through changes in protein or Read More ›

From ScienceDaily (Feb. 18, 2011) this news, “Promise of Genomics Research Needs a Realistic View, Experts Urge”

Unrealistic expectations about genomic medicine have created a “bubble” that needs deflating before it puts the field’s long term benefits at risk, four policy experts write in the current issue of the journal Science.

Ten years after the deciphering of the human genetic code was accompanied by over-hyped promises of medical breakthroughs, it may be time to reevaluate funding priorities to better understand how to change behaviors and reap the health benefits that would result.

You mean, the dead shall not rise again in this life?

And,practically speaking,

After all, while advances are being made in personalized medicine through the tools of pharmacogenetics, “the most powerful predictor of drug efficacy is whether a patient takes the drug.”

In my own country, tens of thousands end up in the emerg every year due to beggaring around with powerful prescribed meds.

Reality check: If it’s powerful enough to help you, when taken right, it’s …

In many diseases a large number of genes play a role, making meaningful predictions difficult both for individuals and in public health.

To say nothing of all the other factors, like environment and age of first onset. Now this zinger: Read More ›

Or sea slugs? Like, humans had 100, 000 genes, which proved we were a big-brained ape, then 30, 000, a bit more than a worm. Oh but wait, the fern has 250,000 genes and someone who has never kept a fern can be confident that they’re mostly junk. Now, ten years on, here’s the kind of thing we hear: Since the human genome was sequenced, we know more about our own history, and the lines between us and other species have blurred, Cole-Turner said. A comparison with the Neanderthal genome revealed that Neanderthals likely mated with our ancestors, since between 1 percent and 4 percent of some modern humans’ DNA came from Neanderthals. Even the genome from the first amphibian Read More ›

SCIENCE: “Now THAT’s a genome. A rare Japanese flower named Paris japonica sports an astonishing 149 billion base pairs, making it 50 times the size of a human genome—and the largest genome ever found. Until now, the biggest genome belonged to the marbled lungfish, whose 130 billion base pairs weighed in at an impressive 132.83 picograms. (A picogram is one-trillionth of a gram). The genome of the new record-holder, revealed in a paper in the Botanical Journal of the Linnean Society, would be taller than Big Ben if stretched out end to end. (The smallest genome known among organisms with nuclei is that of a mammalian parasite known as Encephalitozoon intestinalis, with a relatively paltry 2.25 million base pairs). The Read More ›

Cornell Geneticist John Sanford argued that Darwinism is wrong because the rate of genetic deterioration is so high that natural selection could not arrest it. If natural selection cannot arrest genetic deterioration, how then could it be the mechanism for evolutionary improvement? Sanford predicted through his research that human genome is deteriorating. This was a daring scientific prediction, and now Michael Lynch of the elite National Academy published on the topic for his inaugural paper. The NAS has now made the paper available to the public free of charge. Read it, and weep, literally: Rate, Molecular Spectrum, and Consequences of Human Mutation Unfortunately, it has become increasingly clear that most of the mutation load is associated with mutations with very Read More ›