MedWorm provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest medical blog items that have been tagged with 'in vivo'. Sat, 03 Sep 2011 02:28:30 +0100 http://www.medworm.com/index.php?rid=5050575&cid=t_105302_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Fnew-contrast-agent-provides-better-in-vivo-imaging-of-bacteria%2F2011.07.22 A new contrast agent based on maltodextrin has been developed at Georgia Tech that can provide in vivo imaging of bacteria with a sensitivity two orders of magnitude greater than previously achieved. Unlike most previous methods, the new probes are able to enter bacterial cells by pretending to be food, while avoiding being ingested by the mammalian cells. From Georgia Tech: Maltodextrin-based imaging probes consist of a fluorescent dye linked to maltohexaose, which is a major source of glucose for bacteria. The probes deliver the contrast agent into bacteria through the organism’s maltodextrin transporter, which only exists in bacterial cells and not mammalian cells. In experiments using a rat model, the researchers found that (more…) *This blog post was originally publi... Better Health blogs http://www.medworm.com/rss/comments.php?id=5050575 Fri, 22 Jul 2011 12:00:13 +0100 5050575 http://www.medworm.com/index.php?rid=4768118&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2011%2F04%2F29%2Fjournal-club-classic-single-unit-physiology-in-barrel-cortex%2F This one is for the aficionados. Here is a little review of four classic single-unit physiology papers investigating the response properties and information flow from whisker through thalamus and into cortex.  It’s quite interesting comparing this data taken from sedated or anesthetized rats to my own in awake, behaving animals. That’s a story for another time and publication venue though Filed under: electrophysiology, in vivo Tagged: barrel cortex, single unit physiology (Source: Brain Windows) Brain Windows blogs http://www.medworm.com/rss/comments.php?id=4768118 Fri, 29 Apr 2011 20:10:38 +0100 4768118 http://www.medworm.com/index.php?rid=4522290&cid=t_105302_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2FlhQJJzD3j_8%2F Hired someone new and exciting? Promoted a rising star? Finally solved that hard-to-fill spot? Share the news with us and we’ll share with it others. That’s right. Send us your announcements and we’ll find a home for them. Don’t be shy. Everyone wants to know who is coming and going, especially with all the layoffs. Despite the downsizing, there is movement. Here are some of the latest changes. Recognize anyone? And here is our regular feature. Send us a photo and we will spotlight a different person each week. This time around, we note that Absorption Systems hired Stacy Pritt as director of preclinical laboratory operations. Previously, she was director and general manager of the biological test center at B. Braun Medical, oversaw regulatory compliance at Covance Research Product... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=4522290 Fri, 25 Feb 2011 13:06:21 +0100 4522290 http://www.medworm.com/index.php?rid=4482875&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2011%2F02%2F16%2Frapid-warping-of-two-photon-illumination-wavefronts%2F A short paper in Optics Express looks interesting.  In A high speed wavefront determination method based on spatial frequency modulations for focusing light through random scattering media, Meng Cui presents a method for rapidly determining the optimal wavefront to ‘cancel out’ the scattering when 785nm light passes through turbid media.  In his example, a glass diffuser was used, but the clear goal for this work is to replace the glass with a brain. To understand why this is so important for in vivo two-photon imaging, let’s review how 2-p imaging works. Light from a laser is focused to a point and swept across the field in a raster. The resulting fluorescence is of a different wavelength and can thus be filtered out from the excitation light. For each voxel, all the ... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=4482875 Wed, 16 Feb 2011 13:51:15 +0100 4482875 http://www.medworm.com/index.php?rid=4450389&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2011%2F02%2F08%2Fquick-picks-brainbow-flies%2F Nature methods published two papers which extend brainbow-like techniques of stochastic multicolored neuronal labeling into fruit flies.  Nature’s summary explains the two methods.   dBrainbow expression examples     The first technique, called dBrainbow, was developed by Julie Simpson, a neuroscientist at the Howard Hughes Medical Institute’s Janelia Farm Research Campus in Ashburn, Virginia, and her colleagues2. This method uses enzymes called recombinases to randomly delete some of the colour-producing genes from the string, leaving different genes next to the promoter regions in different cells. Individual cells are therefore uniquely coloured and so can be easily distinguished… The second technique, called Flybow, was developed by Salecker and ... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=4450389 Tue, 08 Feb 2011 15:05:00 +0100 4450389 http://www.medworm.com/index.php?rid=3973009&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2010%2F09%2F15%2Fupdate-diadem-final-results%2F The DIADEM automated neuronal reconstruction contest has finished.  Accurate, fast, and high-resolution automated neuron reconstruction is of vital importance to cracking the mystery of how neural circuits perform. Even with perfect knowledge of the firing patterns of every cell in a circuit, our understanding of how these patterns are produced and how the information is processed would be quite limited.  True understanding requires knowledge of the precise wiring diagram.  This prize is a good first step towards bringing awareness of this tricky problem to the world’s best computer scientists. $75,000 in prize money was to go to the group that was able to produce high-quality reconstructions of neuronal structures at least 20x faster than by-hand reconstructions.  In the finals... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=3973009 Wed, 15 Sep 2010 19:23:46 +0100 3973009 http://www.medworm.com/index.php?rid=3889174&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2010%2F08%2F20%2Fsoftware-update-ephus-scanimage-neuroptikon%2F Three excellent pieces of neuroscience software have been recently updated or freshly released.  I have used two of them, Ephus and ScanImage, on a daily basis as primary data collection tools. The third, Neuroptikon, is quite useful for post-hoc illustration of neural circuits. Ephus is a modular Matlab-based electrophysiology program that can control and record many channels of tools and data simultaneously.  Under control of a sophisticated internal looper or external trigger, you can initiate an ephys recording, trigger camera frames, adjust galvo positions, open/close shutters, trigger optical stimulation, punishments, rewards, etc.  It is a workhorse program for non-imaging related in vitro and in vivo electrophysiology experiments.  Ephus is named for the fabled baseball pitch,... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=3889174 Fri, 20 Aug 2010 23:51:53 +0100 3889174 http://www.medworm.com/index.php?rid=3848953&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2010%2F08%2F09%2Fcameleon-nanos-high-affinity-gecis%2F Takeharu Nagai’s lab has published in Nature Methods, Spontaneous network activity visualized by ultrasensitive Ca2+ indicators, yellow Cameleon-Nano, demonstrating a new set of calcium indicators based on yellow cameleon. Back when he was still Take-san, Take’s ability to churn out and manually screen hundreds of cameleon variants was impressive and inspiring. With high-throughput GECI pipelines now ramping up at Janelia, the idea of laboriously screening 200 variations on a theme (be it cameleons or GluSnFRs), seems a bit archaic. However, this paper is a good example of the progress that can still be made by understanding the needed sensor parameters and fiddling with the primary amino acid structure in a relatively low-throughput way. Take-sensei’s results are another... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=3848953 Tue, 10 Aug 2010 03:52:04 +0100 3848953 http://www.medworm.com/index.php?rid=3831467&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2010%2F08%2F06%2Fbackyard-brains-homebrew-ephys-rigs%2F News of a cool new toy comes from a colleague’s recent trip out to the MBL @ Woods Hole.  It is the perfect gift to spark the curiosity of a budding young (or old) neuroscientist. Backyard Brains makes the world’s best value electrophysiology rigs. The SpikerBox comes pre-assembled for $100 or build your own from a bunch of parts for $50. These rigs are surprisingly powerful. You can go out in the yard, catch a bug (or buy a cockroach), strap one on and start recording neuromuscular potentials. The box interfaces with gorgeous iPhone/iPad so you can hear, see and record the action potentials. They don’t make a big point of this, but you can also wire it up so that the piezo-speaker can drive an electrical stimulator of the cockroach’s leg. You can make the leg twi... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=3831467 Fri, 06 Aug 2010 15:01:44 +0100 3831467 http://www.medworm.com/index.php?rid=3411190&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2010%2F03%2F26%2Fupdate-bi-directional-optogenetic-control%2F The Deissseroth lab has released an updated version of their optical neuronal silencing gene Natronomonas halorhodopsin. In Molecular and Cellular Approaches for Diversifying and Extending Optogenetics, Gradinaru et al review current optogenetic methodology, and introduce eNpHR3.0-2A-ChR2, a genetic vector whose expression allows both action potential silencing and firing via illumination. This vector uses post-translational cleavage (via cis-acting hydrolase elements) of the 2A peptide to coexpress channelrhodopsin and halorohdopsin at high levels via a single promoter. The use of 2A provides a more balanced level of relative expression compared to the traditional strategy of using an IRES site, though differing degradation rates of the two proteins cause expression to not be truly st... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=3411190 Fri, 26 Mar 2010 19:57:55 +0100 3411190 http://www.medworm.com/index.php?rid=3362486&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fwww.molecularbrain.com%2Fcontent%2Fdownload%2Fsupplementary%2F1756-6606-3-5-s3.mov Atsushi Miyawaki’s lab has developed a series of neat tools for visualizing cell cycle progress. For zebrafish, the zFucci system consists of two fluorescent proteins, mKO2 and mAG, that are fused to Cdt1 and geminin genes.  Cell cycle- regulated proteolysis of these fusion proteins causes each cell to display orange fluorescence in G1 phase nuclei and green fluorescence in both the nucleus and cytoplasm of S/G2/M phase cells. Video of cell cycle transitions in culture. Click for the video. The last time I saw Atsushi give a talk, he showed an incredible time lapse video from the zebrafish cleavage stage that I haven’t been able to find online.  However, here is a video from later in development of the zebrafish that is still pretty remarkable. Development of a zebrafish visu... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=3362486 Sat, 13 Mar 2010 16:08:39 +0100 3362486 http://www.medworm.com/index.php?rid=3354459&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2010%2F03%2F10%2Fcnifers-of-acetylcholine%2F “If you find yourself needing to reread this paragraph, perhaps it’s not that well written. Or it may be that you are low on acetylcholine.” Acetylcholine (ACh) is a major modulator of brain activity in vivo and its release strongly influences attention. If we could visualize when and where ACh is released, we could more fully understand the large trial to trial variance found in many in vivo recordings of spike activity, and perhaps correlate that to attentional and behavioral states mediated by ACh transmission. Back in grad school, when I was desperately trying to figure out what biological question to answer with my GluSnFR glutamate sensor, I ended up in a meeting with Kleinfeld, his grad student Lee Schroder and Palmer Taylor. We plotted a strategy to make a FRET... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=3354459 Thu, 11 Mar 2010 05:53:24 +0100 3354459 http://www.medworm.com/index.php?rid=3331443&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2010%2F03%2F04%2Fjournal-scan-calcium-imaging-in-auditory-and-visual-cortex%2F A few papers on in vivo calcium imaging have just come out and are worth a careful read. The first two examine the fine organization of layer 2/3 of the mouse auditory cortex.  The canonical view of auditory cortex organization is that neurons are arranged in a tonotopic pattern, with a smooth gradient in auditory frequency tuning across the surface of the cortex.  Using two-photon imaging in anesthetized mice, the groups saw that, while there was an overall gradient, the tuning of neighboring neurons was highly variable.  These are similar results to what Sato et al and Kerr et al found in the whisker barrel cortex back in 2007.  Moral of the story : mapping brain organization by microstimulation or sparse sampling (as in the classic papers) can be very misleading. Functional organiza... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=3331443 Thu, 04 Mar 2010 15:18:48 +0100 3331443 http://www.medworm.com/index.php?rid=3318545&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2010%2F03%2F01%2Fcompressed-sensing-in-neuroscience%2F Wired has a nice lay-person write-up of the rapidly developing field of compressed sensing. This is a technique that allows accurate reconstructions of highly undersampled sparse datasets. This field really took off in 2004 when Emmanuel J. Candès discovered that a tomography phantom image could be reconstructed exactly even with data deemed insufficient by the Nyquist-Shannon criterion. It is probably the hottest topic in imaging theory today. Modified Shepp-Logan phantom with enhanced contrast for visual perception. According to this review, Compressed Sensing MRI, its successful application requires three conditions to be met : Transform Sparsity: The desired image must have a sparse representation in a known transform domain (i.e., it must be compressible by transform coding), I... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=3318545 Mon, 01 Mar 2010 15:03:53 +0100 3318545 http://www.medworm.com/index.php?rid=3283703&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2010%2F02%2F18%2Fjournal-club-in-vivo-inhibition-dynamics%2F Inhibition has a powerful role shaping the network dynamics of the cortex, but most studies of inhibitory circuitry are done in brain slice or anesthetized animals. In Membrane potential dynamics of GABAergic neurons in barrel cortex of behaving mice, Gentet et al use two-photon imaging to guide dual, whole-cell patch clamp of inhibitory and excitatory neurons in the mouse barrel cortex.  These mice are head fixed, but awake and naturally whisking.  The authors can then see how the membrane dynamics of both subthreshold and suprathreshold voltages are correlated across pairs of cells.  Differences between the correlations for excitatory and inhibitory neurons shed light on how cortical circuitry processes sensory information in natural brain states. For Journal Club #5, Mac Hooks, a pos... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=3283703 Thu, 18 Feb 2010 15:18:14 +0100 3283703 http://www.medworm.com/index.php?rid=3172065&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2010%2F01%2F13%2Fadaptive-optics-for-in-vivo-microscopy%2F Imaging fluorescence in an intact, living brain is difficult due to absorption and scattering of excitation and emission light.  Two photon microscopy uses excitation light in the narrow optical window (700-950nm) where water and hemoglobin do not significantly absorb, which allows structure determination and functional imaging down to depths of ~600nm from the surface of the brain.  However, scattering of the excitation light still occurs at these wavelengths, which distorts the excitation volume and causes a rapidly increasing fluorescent background at greater depths. The vasculature was labeled by injecting flourescein dextran into the circulatory stream. The light source was a regenerative amplifier. ‘‘0 mm’’ corresponds to the top of the brain. Left, XZ projection. Right, ex... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=3172065 Wed, 13 Jan 2010 16:56:06 +0100 3172065 http://www.medworm.com/index.php?rid=2977425&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2009%2F11%2F09%2Fthree-cheers-for-gcamp%2F Three papers are out online in Nature Methods that show big improvements in calcium imaging with genetically encoded sensors.  They are are based on the fluorescence intensity indicator, GCaMP.   GCaMP, first developed by Junichi Nakai, consists of a GFP that has been circularly permuted so that the N and C termini are fused and new termini are made in the middle of the protein.  Fused to one terminus is calmodulin and the other is a peptide, M13, that calmodulin (CaM) binds to in the presence of calcium. The name is supposed to look like GFP with a CaM inserted into it, G-CaM-P.  Normally the GFP is dim, as there is a hole from the outside of its barrel into the chromophore.  Upon binding calcium, this hole is plugged and fluorescence increases. The first paper, A genetically encod... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=2977425 Mon, 09 Nov 2009 23:54:11 +0100 2977425 http://www.medworm.com/index.php?rid=2894641&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2009%2F10%2F14%2Fplaying-quake-with-a-real-mouse%2F Most people play Quake with a computer mouse, but researchers in David Tank’s lab at Princeton have done it with a living mouse, AND they are recording the intracellular activity of individual neurons of the mouse during the gaming session. As reported in Intracellular dynamics of hippocampal place cells during virtual navigation, the virtual reality environment of the video game was sufficiently realistic to generate place cell activity in the mouse’s hippocampus.  Now where did I see that cheese power-up? Place cells modulate their activity dependent on the location the mouse is at. They have mostly been identified with extracellular recordings in freely moving mice. Extracellular recording only permits the detection of the rates of action potential firing, rather then the... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=2894641 Wed, 14 Oct 2009 18:21:32 +0100 2894641 http://www.medworm.com/index.php?rid=2857491&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2009%2F10%2F02%2Fautomated-roi-analysis-for-calcium-imaging%2F One of the most time consuming and frustrating tasks associated with fluorescence imaging in the brain is picking out your regions of interest.  Which pixels do you include in as part of the cell and which are part of the surrounding neuropil?  Often, the answer is not obvious, and even with painstaking selections you can make errors.  Eran Mukamel et. al, from Mark Schnitzer’s lab just published this Neurotechnique Automated Analysis of Cellular Signals from Large-Scale Calcium Imaging Data that aims to simplify and improve the results of ROI selection.  The authors used a multistage approach to identify and quantify the calcium-dependent fluorescence changes of imaged neurons. First, they used principal component analysis to identify the components of the image that were likel... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=2857491 Fri, 02 Oct 2009 23:04:54 +0100 2857491 http://www.medworm.com/index.php?rid=2398984&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2009%2F05%2F08%2Fjournal-scan-transynaptic-tracing-fly-olfaction-fast-super-resolution-localization-of-perception%2F Here’s a group of four recent papers that are worth checking out but I don’t have the time to cover.  The first provides a set of tools for neuronal circuit tracing. The second pushes super-resolution imaging into fast, live-cell imaging.  The third, by a friend from graduate school, uses G-CaMP to make strong claims about olfactory coding in fruit flies. The last reports remarkable data pointing to the distributed nature of conscious perception in humans, which would have been a great data set to reference in my recent talk on free will. Genetically timed, activity-sensor and rainbow transsynaptic viral tools  We developed retrograde, transsynaptic pseudorabies viruses (PRVs) with genetically encoded activity sensors that optically report the activity of connected neurons a... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=2398984 Fri, 08 May 2009 20:39:44 +0100 2398984 http://www.medworm.com/index.php?rid=2398985&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2009%2F05%2F08%2Finfrared-fluorescent-proteins%2F Hunting for new fluorescent proteins in the coral reefs of the Caribbean and Australia is a task that a lucky few researchers have managed to get funding for. Scuba diving in some of the world’s most beautiful places; it’s not a bad gig, if you can get it.  Most fluorescent protein scientists are confined to a lab, mutating existing fluorescent proteins from jellyfish and coral. Shifting their excitation and emission spectra has allowed multiple fluorescent proteins to be used as molecular highlighters at the same time, since their colors are distinct from each other. Some members of this palette are shown in Brain Windows top image bar.  After over a decade of research, the spectrum is pretty well covered.  Except for one area…  The infrared. The near-infrared band i... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=2398985 Fri, 08 May 2009 19:33:12 +0100 2398985 http://www.medworm.com/index.php?rid=2380960&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2009%2F04%2F29%2Fdeisseroth-is-on-fire%2F Is there any biology lab hotter that Karl Deisseroth’s right now?  In the last TWO WEEKS he’s authored 3 Nature papers Parvalbumin neurons and gamma rhythms enhance cortical circuit performance Driving fast-spiking cells induces gamma rhythm and controls sensory responses Temporally precise in vivo control of intracellular signalling 2 Science papers Phasic Firing in Dopaminergic Neurons Is Sufficient for Behavioral Conditioning Optical Deconstruction of Parkinsonian Neural Circuitry and a PLOS One for icing. Manipulation of an innate escape response in Drosophila: photoexcitation of acj6 neurons induces the escape response He’s the Xander Cage of neuroscience, having just triggered an avalanche, he manages to move quickly enough to stay ahead as his pursuers get ... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=2380960 Wed, 29 Apr 2009 21:58:54 +0100 2380960 http://www.medworm.com/index.php?rid=2182654&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2009%2F02%2F11%2Fsymposium-a-revolution-in-fluorescence-imaging%2F This coming Tuesday and Wednesday (Feb 17th & 18th) at UCSD, there will be a symposium honoring Roger Tsien, featuring presentations from 32 former and current members of the Tsien Lab. The topics are quite diverse, concentrated in genetically-encoded indicators, but also featuring fluorescent cell penetrating peptides for cancer therapy, photophore ligases for imaging synaptic development, and even a radical new design for the internal combustion engine. The quality of speakers and subjects looks to be outstanding.  Here is a complete schedule.  You may notice that at 11:15 AM on Tuesday in Price Center East Ballroom, I will be presenting recent progress we have made in the development of genetically-encoded calcium indicators and their application to in vivo imaging.  Don’t... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=2182654 Thu, 12 Feb 2009 04:45:42 +0100 2182654 http://www.medworm.com/index.php?rid=2092629&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2009%2F01%2F09%2Fbrainstorm-1-the-calcium-memory-sensor%2F As mentioned in the previous post, this is the first installment of BrainStorm, a section of ideas I have under development, but don’t have the time to physically work on.  This section will contain organically developed ideas, organized by project.  Reader feedback is encouraged. How can we identify the group of neurons that encode a particular thought?   I don’t want to simply see correlations of in activity of a few scattered neurons with a given thought, but identify the entire neuronal ensemble.  Which neurons are active at a precise moment in a task?  How are they wired together? Which are the drivers of activity? Existing technology is inadequate to identify the entire neural ensemble that encodes a thought. Immediate early gene expression  patterns have not been s... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=2092629 Fri, 09 Jan 2009 19:06:39 +0100 2092629 http://www.medworm.com/index.php?rid=1990881&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F11%2F25%2Fmice-aren%25e2%2580%2599t-that-blind%2F Just saw a cool informal talk from Andreas Burkhalter about the mouse visual cortex.  He has a fascinating paper, Area Map of Mouse Visual Cortex, in the Journal of Comparative Neurology, in which he identifies not just three or four areas of mouse visual cortex, but twelve! Each area has a complete map of the entire visual field.  He combines triplet injections of Di-I, Di-O and BDA as fiducial markers with a label for callosal connections. He fixes the tissue in a manner that allows the unrolling and flattening of the entire mouse cortex. This allows him to segment and show the orientation of each field in a single cortical layer in the same slice. Different layers give different patterns of projection. Given the richness of the data obtained, I’m surprised that more systems neuros... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1990881 Tue, 25 Nov 2008 20:28:41 +0100 1990881 http://www.medworm.com/index.php?rid=1975206&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F11%2F20%2Fsome-interesting-posters-sfn%2F Here’s a few posters that caught my eye at SfN.  Click the titles for the full abstract Optimizing two-photon activation of channelrhodopsin-2 for stimulation at cellular resolution J. P. RICKGAUER1,2, D. W. TANK1,2;  Spiral pattern of 2-photon excitation can drive neurons to spike.  A low NA objective helps. Need to do piezo-based Z-scanning if you use high NA, don’t with low NA. In vivo two-photon imaging 1 mm deep into cortical brain tissue with novel microprism probe  *T. H. CHIA, M. J. LEVENE;  A cute method to image 1mm into cortex with 2-photon imaging. They used 2-6 month old mice. The just took a triangular prism whose hypotenuse was silvered and stuck it in the cortex. Then they internally reflected the beam off the prism and fired it sideways into cortex. Got g... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1975206 Fri, 21 Nov 2008 03:27:11 +0100 1975206 http://www.medworm.com/index.php?rid=1773566&cid=t_105302_136_f&fid=37846&url=http%3A%2F%2Fhealthinfoispower.wordpress.com%2F2008%2F09%2F07%2Fmk-0457-alone-and-in-combination-with-docetaxel-inhibits-ovarian-cancer-growth-in-vivo%2F …[T]he [M.D. Anderson Cancer Center & Baylor College of Medicine] researchers concluded that [Aurora kinase] AK inhibition [produced by MK-0457] significantly reduces ovarian cancer tumor burden and cell proliferation, and increases tumor cell apoptosis in preclinical ovarian cancer mouse models. The researchers noted that the role of Aurora kinase inhibition in ovarian cancer merits further [...] (Source: Libby's H*O*P*E*) Libby's H*O*P*E* blogs http://www.medworm.com/rss/comments.php?id=1773566 Mon, 08 Sep 2008 00:49:39 +0100 1773566 http://www.medworm.com/index.php?rid=1642713&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F07%2F21%2Fthe-great-geci-shootout%2F Dierk Reiff’s lab has done another head-to-head in vivo showdown between various GECIs and a synthetic dye. Their paper, Fluorescence changes of genetic calcium indicators and OGB-1 correlated with neural activity and calcium in vivo and in vitro, is very interesting and deserves a full write-up. I will present a detailed analysis of the paper in a future update.  For now, check the abstract. Recent advance in the design of genetically encoded calcium indicators (GECIs) has further increased their potential fordirect measurements of activity in intact neural circuits. However, a quantitative analysis of their fluorescence changes (F) in vivo and the relationship to the underlying neural activity and changes in intracellular calcium concentration ([Ca2+]i) has not been given... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1642713 Mon, 21 Jul 2008 19:25:52 +0100 1642713 http://www.medworm.com/index.php?rid=1596486&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F07%2F08%2Fvoltage-sensitive-imaging-powering-up%2F I’m starting to come around on voltage imaging. I haven’t been a fan of it for a number of reasons. The response sizes suck.  Classic dyes and genetically encoded systems get a few percent fluorescence change at best.  The response speeds suck. Measuring continuous current injections from -100mV to +150mV is not very interesting.  Action potentials are interesting.  But they are fast. Toxicity. The dyes kill neurons, or strongly perturb their electrical properties. OK, voltage-sensitive imaging isn’t totally useless, for example see Carl Petersen’s recent paper on Spatiotemporal Dynamics of Cortical Sensorimotor Integration in Behaving Mice (2007). But if the above problems could be solved, then voltage sensitive imaging would be a strong competitor to calciu... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1596486 Tue, 08 Jul 2008 22:29:44 +0100 1596486 http://www.medworm.com/index.php?rid=1560925&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F07%2F01%2Fslick-labeling-and-new-fps%2F There is a nice writeup of the single-neuron labeling with inducible Cre-mediated knockout (SLICK) paper from Guoping Feng’s lab over at the Alzheimer’s Research forum. The method simultaneously knocks out a gene in a small number of cells, while highlighting the knocked-out cells with a cytosolic fluorescent protein. In a comment to the Schizophrenia Research Forum, Joseph Gogos points out a similar technique his lab published last year in Current Biology. Also in the writeup is coverage of the new fluorescent protein variants from the Tsien Lab.  These include mOrange2 made by Nathan Shaner, which is a much more photostable version of mOrange. This should immediately replace mOrange in most constructs.  Also of note is TagRFP-T from Michael Lin and his trusty undergraduat... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1560925 Tue, 01 Jul 2008 19:40:08 +0100 1560925 http://www.medworm.com/index.php?rid=1556392&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F06%2F30%2Fgiving-synapses-a-born-on-labelinthe%2F Memories are thought to be encoded by the patterns of synaptic connections in the brain. Learning can either delete or change the strength of existing synapses, or add new synapses. Following a learning process, how can we tell which synapses were added to encode this new memory?   One strategy is to make a timelapse movie of the synapses.  In mice, this can be accomplished by installing a cortical window on the skull, and imaging the changes in structure of GFP labelled neurons. However, this is technically demanding, only works with sparsely labeled neurons, and accesses only a small subset of the neurons which may be involved in the learning process.   Ideally, one could have a tag which can discriminate between synapses existing before learning takes place, and new ones generated ... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1556392 Mon, 30 Jun 2008 17:25:43 +0100 1556392 http://www.medworm.com/index.php?rid=1531367&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F06%2F19%2Fmore-than-a-honey-machine%2F Just saw an interesting seminar on honeybees and the algorithims they use to fly, land and communicate. No brain imaging, just interesting behavior from a brain the size of a piece of cous-cous. Mandyam Srinivasan -  Queensland Brain Institute How flexible is learning in insects?  Can they apply rules they learn to novel situations?  Can they generalize? Bees have a compound eye. 9000 ommatidia to observe the world.  3 primary colors. 2 eyes are very close, so stereo vision is quite difficult using triangulation.  To get 3d they use an active mechanism.  Move, then see what happens to the image on the retina. When traveling in straight line, distant objects will track slowly across retina.  Rotation screws up optic flow. How do we train bees?  Can do it in your backyard.  Miria... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1531367 Thu, 19 Jun 2008 21:39:18 +0100 1531367 http://www.medworm.com/index.php?rid=1261670&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F02%2F27%2Fblog-roundup-sted%2F Here’s a quick overview of some posts that got my attention in the last month… Neurodudes has a brief writeup of video-rate superresolution imaging from Stefan Hell’s group. I don’t have access to Science Express PDF’s through our institutional subscription (how much must they be charging for that?), making a full writeup impossible. But you can at least check out the abstract and supporting info here. Video-Rate Far-Field Optical Nanoscopy Dissects Synaptic Vesicle Movement (Westphal et al.). The optical resolution isn’t quite as good as PALM or STORM, but the speed of acquisition is fantastic, permitting its use on dynamic living processes. Eric Thomson from Neurochannels has posted a detailed Journal Club style review at Nature Network of the paper Sp... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1261670 Wed, 27 Feb 2008 18:22:10 +0100 1261670 http://www.medworm.com/index.php?rid=1246643&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F02%2F20%2Fjournal-club-content%2F I’m going to try adding an additional type of content. Notes from journal clubs I attend. These will be more of a quick data dump format than a strict write-up, and topics will be broader than the specific field of brain imaging. The text formatting will be normal text = presented material, italics = audience interjections, bold = presenter responses. Journal Club entries can be accessed specifically by the top navigation bar. Hopefully this can expand our audience and perhaps promote additional discussion. The first Journal Club discussion is here : Sparse representation of sounds in the unanesthetized auditory cortex. Hromádka T, Deweese MR, Zador AM. How do neuronal populations in the auditory cortex represent acoustic stimuli? Although sound-evoked neural responses in the anesth... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1246643 Wed, 20 Feb 2008 23:32:40 +0100 1246643 http://www.medworm.com/index.php?rid=1240219&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2008%2F02%2F18%2Fpulse-shaping-for-2-photon-signal-enhancement%2F Gains in signal to noise ratios of organic dyes and genetically encoded indicators often come in modest steps following screening of large numbers of compounds or clones. Improvements are usually specific to individual chromophores, leading to the pigeonholing of development efforts on a small handful of indicators that have already undergone systemic optimization (i.e. cameleons, G-CaMP and troponin-based GECIs). Indicator photobleaching imposes strict limits on the amount of information which can be extracted by optical indicators. Improvement of specific indicators and their constituents is a worthy and necessary goal, but more generalizable improvements can be made by changing the nature of the illumination source. A series of papers from a variety of groups has shown that careful mani... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1240219 Tue, 19 Feb 2008 06:11:59 +0100 1240219 http://www.medworm.com/index.php?rid=1001041&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2007%2F11%2F02%2Fbrainbow-mice-are-out%2F Jeff Lichtman’s Brainbow mouse paper is out! Not that I really need to report that news, as it is, of course, on the cover of Nature. Jean Livet comes up with some really clever genetic strategies involving incompatible, overlapping Lox sites to generate random, combinatorial patterns of multiple fluorescent proteins inside the cell. Around 90 different shades can be discerned by spectral deconvolution. Besides making pretty covers, why is this so cool? Well, this technique provides a method for generating high resolution maps of the brain. With a single fluorescent tag, the processes of neighboring cells blur together and became impossible to trace unambiguously. With brainbow, many neighboring axons are clearly resolvable. This is the perfect genetic tool to use for a large-scale,... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=1001041 Fri, 02 Nov 2007 19:46:05 +0100 1001041 http://www.medworm.com/index.php?rid=865685&cid=t_105302_155_f&fid=35947&url=http%3A%2F%2Ftissuepathology.typepad.com%2Fweblog%2F2007%2F09%2Ften-minute-canc.html Purdue researchers are developing a microfluidics device that can identify cancer cells during a routine visit to the doctor. By Katherine Bourzac Researchers at the University of Texas are developing a microfluidics device that detects oral-cancer cells in 10 minutes and is simple and cheap enough for use in the dentist's office. The device could be adapted to test for other cancers, including cervical cancer. It works well on cancer cells grown in the lab and is currently being tested on biopsies from oral-cancer patients. Many oral cancers are painless or, in their early stages, resemble dental disease, so patients and doctors may overlook them, says Carter Van Waes, chief of head and neck surgery at the National Institute on Deafness and Other Communication Disorders. The National ... Digital Pathology Blog blogs http://www.medworm.com/rss/comments.php?id=865685 Wed, 12 Sep 2007 13:31:00 +0100 865685 http://www.medworm.com/index.php?rid=856917&cid=t_105302_155_f&fid=35947&url=http%3A%2F%2Ftissuepathology.typepad.com%2Fweblog%2F2007%2F09%2Fvirtual-histolo.html On a recent search of PubMed for "virtual histology"  I was surprised how many articles were found dealing with "virtual histology" in cardiology.  Investigators trying to quantify histopathologic changes in-vivo beyond what can be done with conventional cardiac catherization currently.  The below abstract and editorial appeared in Heart in May.  Published online 13 May 2007 (omitted numbered references): Abstract As a luminogram, coronary angiography provides a good overview of the coronary artery tree. Using quantitative coronary measurements, the degree of coronary obstruction can be determined. The limitation of coronary angiography is that it does not provide information on the arterial wall structure and therefore cannot assess the ex... Digital Pathology Blog blogs http://www.medworm.com/rss/comments.php?id=856917 Mon, 10 Sep 2007 13:10:00 +0100 856917 http://www.medworm.com/index.php?rid=816806&cid=t_105302_155_f&fid=35947&url=http%3A%2F%2Ftissuepathology.typepad.com%2Fweblog%2F2007%2F08%2Freal-time-elast.html in men scheduled for radical prostatectomy, according to a report in the July BJU International. "Elastography is a contrast-media-free technique, which allows for detection of suspicious areas in the outer gland," Dr. Leo Pallwein from Medical University Innsbruck, Austria told Reuters Health. "It has the potential to become a reliable screening tool in men with elevated PSA." Dr. Pallwein and colleagues assessed the value of elastography for detecting prostate cancer in 15 men scheduled for radical prostatectomy. Elastography detected 28 of 35 cancer foci (80% sensitivity), the authors report, but missed 7 foci, most of them in the inner gland or in the basal area of the outer gland. The only four sites with false-positive findings were obtained in the first five... Digital Pathology Blog blogs http://www.medworm.com/rss/comments.php?id=816806 Wed, 22 Aug 2007 13:45:00 +0100 816806 http://www.medworm.com/index.php?rid=499497&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2007%2F03%2F24%2F19%2F Novel Methods to Dissect Neural Circuits - Saturday afternoon Dmitri Chklovskii, Janelia Farm Reconstruction of neuronal wiring diagram from automated serial EM. Must be able to track identity of segments between slices, determine synapses and the cells they belong to. Wiring diagram draft was done in c. elegans (~7000 synapses, 279 neurons) in 1986, Mitra’s student finished it in 2006. How do we do it? Automated alignment of serial sections by translation, slight rotation and elastic stretching. Automated segmentation of color coding, makes a draft that must be reviewed by human editor. State of art is 10x faster than manual tracing, reconstructed complete 10×10x10um^3 volume two man-months. 1000 synapses, 1000 axons, 100 dendrites. Biological results : If there are an equal # of s... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=499497 Sat, 24 Mar 2007 22:01:29 +0100 499497 http://www.medworm.com/index.php?rid=499499&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2007%2F03%2F24%2Fcshl-meeting-session-iv%2F Evening Session - Optical Measures of Neuronal Excitation And Signaling Rainer Friedrich - Measuring spatio-temporal activity patterns by temporally deconvolved 2-photon calcium imaging Bulk loading of olfactory cortex with AM Ca dyes. Calcium signal is much slower than action potentials because the signal is a convolution of Ca trace with binary spikes. Deconvolution of the raw Ca signal with a canonical Ca response derives the firing rate. Reconstruction of population activity pattern improves only a little bit with letting tau or spike amplitude vary. This technique requires low noise. Published in nature methods. Application in olfactory bulb of zebrafish. Factor analysis of spatially clustered activity in OB maps regions of activity to amino acid properties (aromatic, long-chain, basi... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=499499 Sat, 24 Mar 2007 19:30:02 +0100 499499 http://www.medworm.com/index.php?rid=497786&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2007%2F03%2F23%2Fcshl-imaging-neurons-meeting-session-i%2F Wow! A very busy start to the conference on Imaging Neurons and Neural Activity at Cold Spring Harbor Labs. I arrived at 6:30pm Thursday. Since then, I have seen 30 talks with copious note-taking, seen too many posters, given 1 talk, seen Ohio State win, and had lots of informal science talk over some beers. Not a lot of sleep though! There is literally no time to refine my notes, but to be timely with my posts I will be posting raw notes that will be updated and refined over the course of the next week or two. Session I - Novel photoactivation and tagging methods Optical Probes Louis J. DeFelice, Vanderbilt - Neuronal transporters for monoamines analyzed with fluorescent substrates and fluorescently labeled transporters. The goal – take a small molecule orally and get spatially specific... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=497786 Sat, 24 Mar 2007 00:49:45 +0100 497786 http://www.medworm.com/index.php?rid=487427&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2007%2F03%2F19%2Fin-vivo-electroporation-of-calcium-dyes%2F Hot on the heels of the recent report on optimized in vivo imaging of calcium using genetically-encoded calcium indicators, Nagayama et al. report a novel neurotechnique for calcium imaging with dyes in vivo. See also Helmchen and Nevian’s preview. Previously, there were three major methods of imaging intracellular calcium dynamics in vivo. Single cell loading of calcium dye through a patch or sharp electrode This method results in high dye concentrations and vivid contrast. However, this limits the imaging to single cells and it can be difficult to hold the cell for sufficient time to fully fill the cell with dye. Bulk loading of AM-ester forms of organic calcium dyes by perfusion This produces a stain which includes many cells, both neurons and astrocytes. Although this is effe... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=487427 Tue, 20 Mar 2007 02:43:48 +0100 487427 http://www.medworm.com/index.php?rid=487429&cid=t_105302_122_f&fid=35068&url=http%3A%2F%2Fbrainwindows.wordpress.com%2F2007%2F03%2F08%2Fgecis-take-another-step-forward%2F In conclusion, the new FCIP mouse line provides important improvements for the analysis of Ca2+ signaling in the intact brain. These include (i) a homogeneous and bright staining of the entire cytosol of individual neurons down to secondary and tertiary dendrites, (ii) the full functionality of the sensor protein allowing measurement of small suprathreshold depolarizations consisting of as few as 2–3 action potentials, (iii) the linear response properties of CerTN-L15 within a physiologically relevant activity range, and (iv) the possibility of in vivo Ca2+ imaging with single-cell and even subcellular resolution. In other words, they are getting close, but they aren’t quite there yet. It might be surprising that they can see 2APs fairly easily but cannot reliably discern 1AP. This... Brain Windows blogs http://www.medworm.com/rss/comments.php?id=487429 Thu, 08 Mar 2007 23:11:16 +0100 487429