like a mouse fibroblast cell expressing HP1alpha,
or the sexless sprawl of Kirby eaten by
wild birds playing orgasmic ping pong.
i reached out my arms, palms open.
i said, what do you want of me?
I said, you can have it all.
an impeach-o-meter + the consequence of qubits = aphotic breathing.
he said he didnt predict that what i was going to say would be important so he listened to me as he read the Times. but how can he know before i speak that what i am saying is a thing of import. how would anyone do that?
I have drunk the stars. In addition to analysis.
meant for it to be
and i failed.
Im thinking about bongos and how they’re not ashamed to party.
Expression of combinations of three different fluorescent proteins in a mouse brain produced ten different colored neurons. Individual neurons in a mouse brain appear in different colors in a fluorescence microscope. This “Brainbow” method enables many distinct cells within a brain circuit to be viewed at one time.
The transformation of a fertilised egg into a tiny living embryo
ranks among nature’s most impressive feats. Now scientists have
replicated this critical step towards a new life for the first time,
growing an artificial mouse embryo from stem cells in the lab.
The cells, grown outside the body in a blob of gel, were shown to
morph into primitive embryos that perfectly replicated the internal
structures that emerge during normal development in the womb.
The scientists let the artificial embryos develop in culture for
seven days – about one third of the way through the mouse pregnancy. By
this point the cells had organised into two anatomical sections that
would normally go on to form the placenta and the embryonic mouse.
The mouse embryo breakthrough is not designed to grow mice or babies
outside the womb, but to open a new window on the embryo’s development
just prior to implantation.
Photograph: Redmond Durrell / Alamy/Alamy
Examples of experimental models of human cancer and their use. Modelling human cancer in other organisms allows us to observe and monitor the effect of therapies against the cancer before actually administering it to patients. This is best done in animal models as their biology is most similar to humans’. Non-animal, eukaryotic models are still useful for studying oncogenic processes in pathways that are conserved between the model and humans.
Classical transgenic mice use a tissue-specific promoter to drive the expression of an gene. The aim is to express the gene only in a particular tissue, and see if it causes tumours to form. It should also identify driver and passenger mutations. The downfall of this strategy is that oncogenes usually acts to de-differentiate the cell, so that would switch off the promoter that is driving its expression, resulting in a self-inhibitory feedback loop. Classical knockout mice have one or both copies of a gene knocked out in the germline, so all cells have the knockout. This is good for studying sporadic versus familial loss of heterozygosity events, but there is no control over where and when that gene is deactivated.
Inducible systems include the tet on and tet off systems, where tetracycline/doxycyline results in the induction (tet on) or inhibition (tet off) of the transcription of a gene. In tet on, doxycyline binds a transactivator that drives transcription; in its absence, there is no transcription. In tet off, the transactivator binds the locus without doxycycline; in its presence, the transactivator dissociates from the gene.
Cre-lox systems work by recombining DNA across lox sites. Any sequences occurring in between the lox sites are said to be “floxed”, and is removed upon Cre presence.
The ER-Tam system is a switchable system that works on the protein level. Proteins fused with the estrogen recetor (ER) are not functional unless tamoxifen is present. Tamoxifen can be removed to make the protein nonfunctional again.
in vivo models
Mouse models are widely used due to their evolutionary and genetic similarity to humans. Differences do exist, such as telomere length and mutation rate. They can be the recipient of xenografts and their cancers largely resemble human cancers.
Flies and yeast do not get cancer, but instead serve as models for oncogenic pathways. They can be subject to genetic and chemical screens to identify putative driver mutations causing pathway deregulation, and to identify drugs that can combat such mutations.
Cell cultures are generally not useful for monitoring tumours, because tumours are complex organs made of many cell types, and culture conditions usually maximise prolferation. Organoid culture allows growth of organs in 3D from a patient biopsy. This can be subjected to functional assays, drug screens, and genome editing for truly personalised therapy that is specific to the patient. However, this shares a common downfall with cell culture in that there is no contribution from the tumour microenvironment in a culture.
Sharpless, N.E.; DePinho, R.A. 2006. “The mighty mouse: genetically engineered mouse models in cancer drug development.” Nature Reviews Drug Discovery5 (9):741-754.
Vidal, M.; Cagan, R.L. 2006. “Drosophila models for cancer research.” Current Opinion in Genetics & Development16:10-16.
Xu, H.; Tomaszewski, J.M.; McKay, M.J. 2011. “Can corruption of chromosome cohesion create a conduit to cancer?” Nature Reviews Cancer11 (3):199-210.
WHAT IS IT? The hippocampus is found deep in the brains of many mammals, including humans. It’s named for its seahorse shape (in Greek, hippokampos literally means “horse sea monster”).
WHY IS IT IMPORTANT? It helps us form memories and navigate space. It contains special cells called “place cells” that create a mental map of our environment. The hippocampus is also one of the first structures to suffer in patients with Alzheimer’s disease, which is characterized by memory loss. The number of patients with Alzheimer’s is predicted to triple by 2050.
WHERE DO WE GO FROM HERE? Scientists at Harvard Medical School were recently able to re-create Alzheimer’s disease from human cells in a culture dish. This will “revolutionize drug discovery in terms of speed, costs and [disease relevance],” according to a senior co-author on the study.
Image by Chris Henstridge/MTA-KOKI/Nikon Small World.
Unlike the brain and spinal cord that are housed in protective bone, peripheral nerves connect regions of the body to the central nervous system like telephone cables. Peripheral nerves relay movement information from the brain to the muscles, for example, or sensory information from the skin to the brain. Remarkably, and also different from the brain and spinal cord, peripheral nerves have a tremendous capacity to regenerate when injured. Severed peripheral nerves grow about 1 mm per day (about an inch per month) until the two severed ends reconnect and innervate a once paralyzed muscle.
Image by Zhong Hua, Johns Hopkins University School of Medicine.
A study of mice found that the drug can trigger out-of-control “autophagy”, a process by which cells digest themselves.
When it is properly regulated, autophagy provides a valuable cleanup service – getting rid of unwanted debris that is dissolved away by enzymes within cell “pockets”.
Dr Prasun Guha, from Johns Hopkins University School of Medicine in the US, who led the research published in the journal Proceedings of the National Academy of Sciences, said: “A cell is like a household that is constantly generating trash. Autophagy is the housekeeper that takes out the trash – it’s usually a good thing. But cocaine makes the housekeeper throw away really important things, like mitochondria, which produce energy for the cell.”
The scientists carried out postmortems that showed clear signs of autophagy-induced cell death in the brains of mice given high doses of cocaine. They also found evidence of autophagy in the brain cells of mice whose mothers received the drug while pregnant.
The scientists showed that an experimental drug called CGP3466B was able to protect mouse nerve cells from cocaine death due to autophagy. Since the drug has already been tested in clinical trials to treat Parkinson’s and motor neurone disease, it is known to be safe in humans. But much more research is needed to find out whether the drug can prevent the harmful effects of cocaine in people, said the team.
Co-author Dr Maged Harraz said: “Since cocaine works exclusively to modulate autophagy versus other cell death programs, there’s a better chance that we can develop new targeted therapeutics to suppress its toxicity.”
Image: There were clear signs of autophagy-induced cell death in the brains of mice given high doses of cocaine. Credit: OJO Images/Alamy
N6-methyladenine: A Newly Discovered Epigenetic Modification
The majority of cellular functions are carried out by proteins encoded by specific genes present in cellular DNA. Genes are first transcribed to RNA which is then translated to proteins. The regulation of this process is important for maintaining correct cellular function. One of the ways that cells regulate gene expression is by epigenetic modifications to chromatin. The term “epigenetics” refers to reversible chemical modifications of DNA and histone proteins (DNA in the nucleus of eukaryotes is wrapped around histones) that affect the transcriptional status of genes. A number of histone modifications such as methylation and acetylation of lysine residues have already been discovered and characterized. Until recently; however, methylation of the 5 position of cytosine was the only known epigenetic DNA modification (A). Methylation of cytosine by DNA methyltransferases is associated with transcriptional silencing, while the removal of these methyl groups by TET enzymes is associated with transcriptional re-activation (B and C). In addition to controlling gene silencing, cytosine methylation also silences retrotransposons, a class of mobile genetic elements. If left unregulated, transposons can insert themselves into important regions of the genome and lead to mutagenesis.
Recently, N6-methyladenine, a new epigenetic modification, was discovered in mammalian cells. N6-mA had previously been discovered in prokaryotes and simple eukaryotes and was shown to function as a transcriptional activator. By contrast, a recent report published in Nature, has shown that N6-mA functions as a transcriptional silencer in mammalian cells, specifically in mouse embryonic stem cells. N6-mA primarily acts to silence the LINE-1 family of retrotransposons during early embryogenesis, which prevents genomic instability. The authors identified N6-mA by using a modified single molecule DNA sequencing technique. DNA bound to a specific modified histone protein was immunoprecipitated using an antibody against a specific histone modification (H2A.X), sequenced, and analyzed by mass spectrometry (D). This identified and determined the position of N6-mA. The authors then generated knockouts of the enzyme Alkbh1, which they believed may function as a demethylase for N6-mA. When Alkbh1 was absent from cells, they found an increase in the levels of N6-mA, showing that Alkbh1 functions as an N6-mA demethylase in vivo. This is important because epigenetic modifications are reversible. Genes can be turned off by methylation and then turned back on by removing the methyl group, so determining the enzyme responsible for the removal of N6-mA supports its role as an epigenetic modification.
My work in the lab is starting to pick-up in pace! I was feeling very overwhelmed these past few weeks because I’m so new to this area of research and I just had no idea what I was doing. I’m still not super confident in all the steps and procedures for everything but I at least understand why I’m doing certain things!
The project I’m working on contains 3 components: a viral synthesis, general testing with a mouse cancer line cells, and the actual study on hippocampal neurons. It’s a lot but I’m excited about seeing it all come together!
Watching thoughts — and addiction — form in the brain
More than a hundred years ago, Ivan Pavlov conducted what would become
one of the most famous and influential psychology studies — he
conditioned dogs to salivate at the ringing of a bell. Now, scientists
are able to see in real time what happens in the brains of live animals
during this classic experiment with a new technique. Ultimately, the
approach could lead to a greater understanding of how we learn, and
develop and break addictions.
In a mouse brain, cell-based detectors called CNiFERs change their fluorescence when neurons release dopamine. Credit: Slesinger & Kleinfeld labs)
Scientists presented their work at the 252nd
National Meeting & Exposition of the American Chemical Society
The study presented is part of the event: “Kavli symposium on
chemical neurotransmission: What are we thinking?” It includes a line-up
of global research and thought leaders at the multi-disciplinary
interfaces of the Brain Research through Advancing Innovative
Neurotechnologies (BRAIN) Initiative with a focus on chemists’
contributions. The effort was launched in 2013 by the Obama
Administration to enable researchers to study how brain cells interact
to form circuits.
“We developed cell-based detectors called CNiFERs that can be
implanted in a mouse brain and sense the release of specific
neurotransmitters in real time,” says Paul A. Slesinger, Ph.D., who used
this tool to revisit Pavlov’s experiment. Neurotransmitters are the
chemicals that transmit messages from one neuron to another.
CNiFERs stands for “cell-based neurotransmitter fluorescent
engineered reporters.” These detectors emit light that is readable with a
two-photon microscope and are the first optical biosensors to
distinguish between the nearly identical neurotransmitters dopamine and
norepinephrine. These signaling molecules are associated respectively
with pleasure and alertness.
Slesinger, of the Icahn School of Medicine at Mount Sinai in New
York, collaborated on the project with David Kleinfeld, Ph.D., at the
University of California at San Diego. Their team conditioned mice by
playing a tone and then, after a short delay, rewarding them with sugar.
After several days, the researchers could play the tone, and the mice
would start licking in anticipation of the sugar.
“We were able to measure the timing of dopamine surges during the
learning process,” Slesinger says. “That’s when we could see the
dopamine signal was measured initially right after the reward. Then
after days of training, we started to detect dopamine after the tone but
before the reward was presented.”
Slesinger and colleagues will also share new results on the first
biosensors that can detect a subset of neurotransmitters called
neuropeptides. Ultimately, Slesinger says they’d like to use this
sensing technique to directly measure these neuromodulators, which
affect the rate of neuron firing, in real time.
One of the most common genetic defects in human deafness is the disappearance of an important family of proteins: the claudins. Claudins are the most critical component of tight junctions (shown here in blue), the place where two adjacent cells meet. Imagine a tight circle of people linking arms to protect what’s inside; tight junctions are what protect a tissue from unwanted molecules or cells trying to pass through. When mice cannot make claudin, the tight junctions in the cochlea (the spiral-shaped portion of the inner ear) are disrupted, robbing them of their hearing sensitivity.
Image by Dr. Alexander Gow and Cherie Southwood, Wayne State University.
Goat testicles in men, human organs in pigs: the past and future of xenotransplantation
In 2003, a South Korean company called Maria Biotech announced its newest success: it had created mouse embryos with human cells in them. The idea is that the mice could be born with human cells in all their tissues, and this would make them more accurate animal models for research. The problem came when a reporter asked whether there would truly be human cells in every tissue. Read more
Do you have any advice for anyone looking to start a polyphasic sleep cycle? What was your adjustment period like? Is it hard to keep the routine?
I was wondering when someone would come asking about this!
For those not aware, polyphasic sleep means sleeping multiple times during one 24-hour period. Doing so generally lets people spend less time sleeping overall. Here are a few examples of polyphasic schedules:
The most extreme form of polyphasic sleep, Uberman, is comprised of six 20-minute naps, totaling only 2 hours of sleep every day. I currently sleep on an Everyman schedule—I take three 20-minute naps every day and a 3 hour core sleep. This is my old monophasic schedule compared to the Everyman one I use now: