Molecular Biology
sb admin | December 17, 2008Larry Moran points to a couple of posts critical of microarrays (The Problem with Microarrays):
Why microarray study conclusions are so often wrong
Three reasons to distrust microarray results
Microarrays are small chips that are covered with short stretches of single stranded DNA. People hybridize DNA from some source to the microarray, which lights up if the DNA hybridizes to the probes on the array.
Most biologists are familiar with microarrays being used to measure gene expression. In this case, transcribed DNA is hybridized to the array, and the intensity of the signal is used as a…
evolgen | December 17, 2008Larry Moran points to a couple of posts critical of microarrays (The Problem with Microarrays):
Why microarray study conclusions are so often wrong
Three reasons to distrust microarray results
Microarrays are small chips that are covered with short stretches of single stranded DNA. People hybridize DNA from some source to the microarray, which lights up if the DNA hybridizes to the probes on the array.
Most biologists are familiar with microarrays being used to measure gene expression. In this case, transcribed DNA is hybridized to the array, and the intensity of the signal is used as a…
neurophilosophy | November 19, 2008
This beautiful image of the brain of a 5-day-old zebrafish larva, which was created by Albert Pan of Harvard University, has just won 4th place in the 2008 Olympus BioScapes Digital Imaging competition. (See a larger version here.)
It was created using the Brainbow technique, a genetic method for labelling neurons, with which individual cells can be made to express a random combination of fluorescent proteins. An image of a mouse brainstem labelled using the same method was awarded 1st prize in last year's competition.
sb admin | November 16, 2008
Population biologists often want to infer the demographic history of the species they study. This includes identifying population subdivision, expansion, and bottlenecks. Genetic data sampled from multiple individuals can often be applied to study population structure. When phylogenetic methods are used to link evolutionary relationships to geography, the approaches fall under the guise of phylogeography.
The past decade has seen the rise in popularity of a particular phylogeographical approach for intra-specific data: nested clade analysis (Templeton et al. 1995; Templeton 2004). Many of…
neurophilosophy | November 3, 2008Learning and memory are widely thought to involve long-term potentiation (LTP), a form of synaptic plasticity in which a neuron's response to the chemical signals it receives is enhanced. This leads to a strengthening of the neuronal circuit, so that the memory encoded in the circuit can persist for long periods of time.
One of the mechanisms by which this synaptic strengthening occurs is an increase in the density of receptors in the membrane of the neuron receiving the signals. This process, which involves trafficking of receptors within cells, is implicated not only in learning and…
neurophilosophy | October 8, 2008In his 1941 book Man on His Nature, the Nobel Prize-winning physiologist Sir Charles Sherrington described the brain as "an enchanted loom where millions of flashing shuttles weave a dissolving pattern." Little could he have known that within 50 years neuroscientists would have at their disposal techniques for visualizing this pattern.
These techniques are collectively known as calcium imaging. Developed in the 1980s, they use synthetic chemical dyes or genetic constructs whose spectral properties change when they bind calcium ions, leading to a change in fluoresence which can be detected…
grrlscientist | October 7, 2008tags: dopamine, behavior, evolution, rewarding affiliative behaviors, brain reward pathways, songbirds, birdsong, zebra finch, Poephila guttata, neurobiology
A pair of wild Zebra (Chestnut-eared) Finches, Poephila guttata.
Image: Adelaide Zebra Finch Society [larger view].
People have been known to "sing for joy" and we often experience happiness when others sing for us. Additionally, birdsong has often brought joy to those who have listened, but what about the birds themselves? Do birds experience "happiness" when they hear birdsong, or when they sing for others? According to newly…
neurophilosophy | October 7, 2008The transmissible spongiform encephalopathies (TSEs), which include variant Creutzfeldt-Jakob Disease in humans, "Mad Cow" Disease in cattle and scrapie in sheep, are progressive and fatal neurodegenerative disorders characterized by the accumulation within nerve cells of an abnormally folded and insoluble form of the prion protein.
The infectious agent which causes these diseases is generally believed to be the prion protein itself. According to Stanley Prusiner's prion hypothesis, abnormal prion molecules act as a "seed" upon their entry into a cell, causing the normal cellular form of the…
edyong | October 7, 2008
It is the instinct of every mother to protect their children as they grow up, shielding them from the dangers of the outside world. Right from birth, life can be a difficult experience. Within a few hours, the child is sent from a safe, warm, constantly-nourished cocoon into a bright, noisy and threatening world. This stressful transition poses a serious threat to the newborn's vulnerable and still-developing mind. But new research has shown that even in these first vital hours, mothers are already inadvertently protecting their children - by shutting down their brain cells.
In…
edyong | October 1, 2008
The world is currently home to 6.5 billion people and over the next 50 years, this number is set to grow by 50%. With this massive planetary overcrowding, Band Aid's plea to feed the world seems increasingly unlikely. Current food crops seem unequal to the task, but scientists at Texas University may have developed a solution, a secret ace up our sleeves - cotton.
Cotton is famed for its use in clothes-making and has been grown for this purpose for over seven millennia. We do not think of it as a potential source of food, and for good reason. The seeds of the cotton plant are rife with…
neurophilosophy | September 24, 2008
The September issue of Scientific American contains an excellent and lengthy article about a state-of-the-art technique called optogenetics, by molecular physiologist Gero Miesenböck, who has been instrumental in its development.
As its name suggests, optogenetics is a combination of optics and genetic engineering. It is a powerful new method for investigating the function of neuronal circuits, based a number of light-sensitive proteins which have recently been isolated from various micro-organisms.
By fusing their genes to promoters which control where they will be activated, researchers…
grrlscientist | September 18, 2008tags: ratite, tinamous, evolution, biogeography, phylogenomics, convergence, flightlessness, Paleognath, homoplasy, vicariance
White-throated Tinamou, Tinamus guttatus.
Image: Wikipedia.
New research suggests the ostriches, emus, rheas and other flightless birds known as ratites have lost the ability to fly many times, rather than just once, as long thought. Further, the ratites appear to form a group with the tinamous, a group of birds that can fly, while the ostriches are set apart as the "sister group" -- the closest relatives.
Birds are divided into two groups based on jawbone…
grrlscientist | September 12, 2008tags: Bovine spongiform encephalopathy, BSE, mad cow disease, Creutzfeldt-Jakob Disease, CJD, pathogenic mutation, prion protein gene
Image: Orphaned.
Mad Cow Disease, technically known as Bovine Spongiform Encephalopathy (BSE), is one of a group of transmissible diseases that destroy brain tissue, collectively known as Transmissible Spongiform Encephalopathies (TSEs). TSEs are an unknown agent(s) that act by damaging the structure of brain proteins known as "prions" (PREE ons). In turn, these damaged prion proteins damage other normal prions and together, they build up to collectively…
sporte | August 21, 2008One of the things that drives me crazy on occasion is nomenclature. Well, maybe not just nomenclature, it's really the continual changes in the nomenclature, and the time it takes for those changes to ripple through various databases and get reconciled with other kinds of information. And the realization that sometimes this reconciliation may never happen.
One of the projects that I've been working on during the past couple of years has involved developing educational materials that use bioinformatics tools to look at the isozymes that metabolize alcohol. As part of this project, I've been…
neurophilosophy | August 11, 2008
National Library of Medicine / Hot Medical News
This silent film clip shows several victims of a disease called kuru. They are - or rather were - members of the South Fore, a tribe of approximately 8,000 people who inhabit the Okapa subdistrict of the Eastern Highlands Province of Papua New Guinea. In the 1950s and '60s, a kuru epidemic swept through the South Fore, claiming the lives of more than 1,000 members of the tribe. Later it was established that the disease was transmitted by the tribe's practice of ritualistic mortuary cannibalism.
The word kuru means "shaking death" in the Fore…
neurophilosophy | August 8, 2008The classic Nobel Prize-winning studies of David Hubel and Torsten Weisel showed how the proper maturation of the developing visual cortex is critically dependent upon visual information received from the eyes. In what would today be considered highly unethical experiments, Hubel and Weisel sewed shut one eye of newborn kittens. They found that this monocular deprivation had dramatic effects on the visual part of the brain: the columns of cortical tissue that normally receive inputs from the closed eye failed to develop, while those that receive inputs from the other eye were significantly…
grrlscientist | August 6, 2008tags: virology, mimivirus, sputnik, virophage, microbiology, molecular biology
Now here's an astonishing discovery that's hot off the presses: a virus that infects other viruses! This amazing finding is being published tomorrow in the top-tier peer-reviewed journal, Nature.
I don't know about you, but when I was in school, I was taught that viruses could only infect other living cells, and further, I was taught that viruses are not living cells. So, logically, one could conclude that viruses cannot infect other viruses. But a new discovery by a group of scientists in France reveals…
grrlscientist | August 6, 2008tags: researchblogging.org, premature hair graying, autosomal dominant trait, genetics, horses, hair color, syntaxin-17, melanocortin-1 receptor, cis-acting regulatory mutation, melanoma, evolution
This horse is in the process of losing its pigment.
It will end up being all white by the time it is eight years old.
Image: Horse Wallpaper [larger view].
Even though I have always been a fan of black horses, my heart did leap at the sight of the noble Shadowfax racing towards Gandalf in response to his call in the Lord of the Rings. White horses have symbolized purity throughout most ages…
edyong | August 4, 2008For the first time, scientists have developed drugs that mimics the effects of endurance exercise. With the aid of two chemicals, Vihang Narkar, Ronald Evans and colleagues from the Salk Institute managed to turn regular lab rodents into furry Paula Radcliffes - mighty mice that were capable of running further and for longer than their peers. One of the drugs only worked in combination with exercise, but the other managed to boost stamina without it.
Using drugs to boost performance isn't a new development. Steroids can help body-builders to build their bodies, while giving athletes an extra…
pharyngula | August 1, 2008Every time I mention this developmentally significant molecule, Sonic hedgehog, I get a volley of questions about whether it is really called that, what it does, and why it keeps cropping up in articles about everything from snake fangs to mouse penises to whale fins to worm brains. The time seems appropriate to give a brief introduction to the hedgehog family of signaling molecules.
First, a brief overview of what Sonic hedgehog, or shh, is, which will also give you an idea about why it keeps coming up in these development papers. We often compare the genome to a toolbox — a collection of…