Molecular Biology
neurophilosophy | October 6, 2007The Guardian reports that Craig Venter has created a synthetic chromosome:
[We] can reveal that a team of 20 top scientists assembled by Mr Venter, led by the Nobel laureate Hamilton Smith, has already constructed a synthetic chromosome, a feat of virtuoso bio-engineering never previously achieved. Using lab-made chemicals, they have painstakingly stitched together a chromosome that is 381 genes long and contains 580,000 base pairs of genetic code.
The DNA sequence is based on the bacterium Mycoplasma genitalium which the team pared down to the bare essentials needed to support life,…
evolgen | October 3, 2007Previous entries:
Part 1 - Introduction
Part 2 - The Backstory
This post is part of a series exploring the evolution of a duplicated gene in the genus Drosophila. Links to the previous posts are above. Part 3 of this series (Obtaining Sequences) can be found below.
Obtaining Sequences
In the previous post I described the aldolase gene family, which encode proteins involved in cellular respiration. There are two aldolase genes in the Drosophila melanogaster genome. If we want to study the evolution of these genes, we can obtain the sequences from the 12 Drosophila species that have had…
pharyngula | October 1, 2007
All of us mammals have pretty much the same set of genes, yet obviously there have to be some significant differences to differentiate a man from a mouse. What we currently think is a major source of morphological diversity is in the cis regulatory regions; that is, stretches of DNA outside the actual coding region of the gene that are responsible for switching the gene on and off. We might all have hair, but where we differ is when and where mice and men grow it on their bodies, and that is under the control of these regulatory elements.
A new paper by Fondon and Garner suggests that there…
pharyngula | October 1, 2007Casey Luskin has to be a bit of an embarrassment to the IDists…at least, he would be, if the IDists had anyone competent with whom to compare him. I tore down a previous example of Luskin's incompetence at genetics, and now he's gone and done it again. He complains about an article by Richard Dawkins that explains how gene duplication and divergence are processes that lead to the evolution of new information in the genome. Luskin, who I suspect has never taken a single biology class in his life, thinks he can rebut the story. He fails miserably in everything except revealing his own ignorance…
mark_antimony | September 30, 2007It's been quite busy last week. Despite the Neurobiology class didn't meet that week, my other classes kept my hands full. I blame it on two exams and a paper due during the week of Homecoming.
Since I don't have any new thoughts on Neurobiology, let's see what can be dug up from my Biochemistry class. For the lab, I wrote my paper of Desulforedoxen. Its job is reducing sulfates. You can look it up at JMol using "1DHG" as the code.
I found this protein very interesting. In class, we had learned about the driving forces for tertiary structure in proteins: H-bonding, hydrophobic/Vanderwal…
pharyngula | September 23, 2007
One concept that is sometimes used in developmental biology is the idea of the "master control gene" or "master switch" — a single gene whose expression is both necessary and sufficient to trigger activation of many other genes in a coordinated fashion, leading to the development of a specific tissue or organ. It's a handy concept on which to hang a discussion of transcription factors, but it may actually be of rather limited utility in the real world of molecular genetics: there don't seem to be a lot of examples of master control genes out there! Pax-6 is the obvious one, a gene that…
neurophilosophy | September 23, 2007
(Gene Genie logo created by by Ricardo Vidal)
Welcome to the 16th edition of Gene Genie, the carnival of genes and genetic diseases.
In this edition, genetics gets personal. The recent publication of Craig Venter's genome (and, before that, James Watson's) was big news. It ushered in the new era of personal genomics, to which a special section of this edition of Gene Genie is devoted.
So, without further ado, let's take a look at the entries for this edition.
Genes & genetic diseases
First off, we have several posts about cancer genes. BRCA1 is a tumour suppressor gene that…
sporte | September 19, 2007But I'm certain that you will find some interesting things.
Mendel's Garden will be ready for harvest, here on Sunday, October 7th, and I need your help.
You won't need to stay on the path, but I would like you to submit your best genetics & molecular biology articles by midnight, Friday October 5th.
Either send your articles to me: digitalbio at gmail dot com
or use the handy-dandy submission form.
With your help, Mendel's Garden is certain to bloom with earthly delights.
neurophilosophy | September 18, 2007At some point in the distant past, there was a dramatic increase in brain size in our hominid ancestors. From approximately 2 million years ago, to the present day, brain volume in the hominid lineage has increased by a factor of 3.5: the brain of Homo erectus had a volume of about 400 milliliters, while that of modern humans is roughly 1,400 ml.
The size of the human brain cannot be accounted for merely by an increase in body size, because Homo erectus was similar in size to modern humans, so the driving for this increase in brain size (or "encephalization") is still a topic of debate…
pharyngula | September 17, 2007
The Hox genes are a set of transcription factors that exhibit an unusual property: they provide a glimpse of one way that gene expression is translated into metazoan morphology. For the most part, the genome seems to be a welter of various genes scattered about almost randomly, with no order present in their arrangement on a chromosome — the order only becomes apparent in their expression through the process of development. The Hox genes, on the other hand, seem like an island of comprehensible structure. These are all genes that specify segment identity — whether a segment of the embryo…
grrlscientist | September 17, 2007tags: researchblogging.org, salmon, trout, spawning, molecular biology, cloning, conservation, endangered species
A trout germ cell is transplanted into the body cavity of a newly hatched salmon embryo. This is part of the process that allowed adult salmon to successfully spawn trout offspring.
Image: Science magazine
Have you ever heard of a trout with salmon for parents? Since when has one species given birth to another species? Well, ever since scientists began experimenting with salmon in the hope that they could genetically alter these fish by injecting sex cells from trout so the…
grrlscientist | September 13, 2007tags: blog carnivals, encephalon, cognition, learning
I am hosting the next issue of the blog carnival, Encephalon on Monday, 24 September. Of course, I want my efforts to be recognized as the best ever on behalf of this carnival so I am going to ask you all again to send me your submissions! Encephalon is THE carnival that focuses on blog writing about all aspects of neuroscience, from the molecular to the cognitive. So if you want your brainy words to be read by a larger and more diverse audience than you usually enjoy, be sure to get your articles, essays and poems to me by the 23rd of…
neurophilosophy | September 10, 2007
(Image credit: William Ormerod/ Unversity of Wisconsin-Madison)
A recent study into the biophysical properties of a highly reflective and self-organizing squid protein called reflectin will inform researchers about the process of "bottom-up" synthesis of nanoscale structures and could lead to the development of thin-film coatings for microstructured materials, bringing scientists one step closer to the development of an invisibility cloak.
Reflectin comes from the Hawaiian Bobtail squid, Euprymna scolopes, which is native to the Central Pacific ocean. E. scolopes leads a nocturnal…
neurophilosophy | September 3, 2007 The current issue of Chemical & Engineering News contains a series of articles by Sophie L. Rovner on memory:
Hold that thought is a comprehensive piece about what is known of the cellular and biochemical bases of memory formation.
Molecules for memory discusses the ethical issues regarding memory-enhancing drugs being developed by several pharmaceuticals companies.
The well-endowed mind considers what studies of knockout mice tell us about variations in human memory performance.
Memory at its worst looks at how highly emotional memories can lead to post-traumatic stress…
neurophilosophy | August 27, 2007
(Image: Roberto Sozzani)
Russian researchers affiliated with the Howard Hughes Medical Institute have developed a red fluorescent protein that is 7-10 times brighter than any other red fluorescent protein currently being used for imaging.
The protein, which has been named Katushka, is derived from a brilliant red sea anemone (Entacmaea quadricolor, the blue tip anemone, above) bought by one of the researchers from a pet shop in Moscow.
After acquiring the specimen, co-author Sergey Lukyanov took it to his laboratory, where he and his colleagues isolated the red protein. They…
pharyngula | August 24, 2007
Some of you may have never seen an arthropod embryo (or any embryo, for that matter). You're missing something: embryos are gorgeous and dynamic and just all around wonderful, so let's correct that lack. Here are two photographs of an insect and a spider embryo. The one on the left is a grasshopper, Schistocerca nitens at about a third of the way through development; the one on the right is Achaearanea tepidariorum. Both are lying on their backs, or dorsal side, with their legs wiggling up towards you.
There are differences in the photographic technique — one is an SEM, the other is a DAPI-…
neurophilosophy | August 24, 2007This year, several research groups have used bacterial proteins called channelrhodopsins to develop a technique with which light can be used to control the activity of nerve cells or the behaviour of small organisms.
For example, Ed Boyden's group at the MIT Media Lab used the method to activate or inhibit neurons on a millisecond-by-millsecond timescale, while Karl Deisseroth and his colleagues at Stanford have created an optical on/off switch that can control the movements of the nematode worm.
Devices employing such technologies could in theory be used in advanced neural prostheses for a…
evolgen | August 23, 2007The University of Michigan has put out a press release entitled:
Bits of 'junk' RNA aid master tumor-suppressor gene
With a title like that, how could I not blog the hell out of this bastard? I mean, they even put the scare quotes around "junk". Like that -- like I just did. Amazing!
The story is about three micro RNA genes (miRNAs) that interact with p53 -- the cancer gene -- and are not expressed properly in some lung cancer cells. Not only have these researchers cured cancer, Guido Bommer, the lead author, seems to think they've found the cure amidst piles of junk:
"In the 'junk' lies…
neurophilosophy | August 23, 2007 Obsessive compulsive disorder (OCD) is a psychiatric condition which is characterized by intrusive thoughts and ritualized and repetitive behaviours, such as excessive hand-washing, which are performed in order to neutralize the obsessions. OCD is one of a spectrum of disorders that includes Tourette's Syndrome, autism and bipolar disorder.
OCD affects approximately 2% of the population, and is listed by the World Health Organization as being amongst the top 10 most debilitating illnesses, in terms of decreased quality of life and loss of income. It is often treated - only mildly…
neurophilosophy | August 22, 2007A significant proportion of people with HIV/ AIDS develop neurological symptoms, such as impaired co-ordination, personality changes, deficits in learning and memory, and mania and depression.
HIV-associated dementia is difficult to treat; although highly active anti-retroviral therapy (HAART) has led to improved prognoses for patients, these drugs do not effectively penetrate the blood brain barrier. So, the brain can act as a "silent reservoir" for HIV, which can therefore cause lasting and irreparable damage.
Exactly how HIV causes dementia was unknown. But a new study by researchers…