New Webvision Chapter: Evolution of Phototransduction, Vertebrate Photoreceptors and Retina


After much work by a number of our contributors, not the least of whom is the author of this particular effort, we have a spectacular new addition to Webvision:  A section on the Evolution of Phototransduction, Vertebrate Photoreceptors and Retina by Trevor D. Lamb.  Be sure to check it out and let us know what you think in the comments.

Continue reading “New Webvision Chapter: Evolution of Phototransduction, Vertebrate Photoreceptors and Retina”

Interesting paper: Characterization Of Neurite Outgrowth And Ectopic Synaptogenesis In Response To Photoreceptor Dysfunction

Gene heat map

Authors Stylianos Michalakis, Karin Schäferhoff, Isabella Spiwoks-Becker, Nawal Zabouri, Susanne Koch, Fred Koch, Michael Bonin, Martin Biel, and Silke Haverkamp have a new paper out that looks at the earliest gene microarray analysis results associated with neurite outgrowth in the degenerate retina.  The title is a overly broad, but the results focusing on gene expression changes in the A3B1 mouse retina (a CNGA3/CNGB1 double-knockout) are intriguing, particularly their proposal that Tp53, Smad and Stat3 signaling contribute to synaptic plasticity at least. Continue reading “Interesting paper: Characterization Of Neurite Outgrowth And Ectopic Synaptogenesis In Response To Photoreceptor Dysfunction”

Building Retinal Connectomes

Connectomics image

There has been quite a bit of discussion of connectomes in the last while with President Obama’s new BRAIN initiative.  It is important to consider some of the requirements of obtaining a true synapse level wiring map in the brain as many are articulating from this initiative.  While there are new technologies that will be required to undertake this initiative for mapping the entire brain, the NIH NEI has been funding an ongoing project to study retinal circuitry which guides the community in how to approach a true synapse level map of the nervous system.

An example of this work  in Current Opinion in Neurobiology titled Building Retinal Connectomes is a review that illustrates the importance of having a complete network graph of connectivities in the retina and by extension other neural systems.  Complete network graphs are what will be required to understand how retinal systems (and any neural system) is constructed.  Even though the retinal community understands how retinas are wired in broad strokes, the precise, fine details are critical and elucidating them requires a new level of complete annotation derived from advances in light and ultrastructural imaging, data management, navigation and validation.

Authors are Robert E. Marc, Bryan W. Jones, J. Scott Lauritzen, Carl B. Watt and James R. Anderson.


What Do Whales See?


This beautiful article in The Atlantic by Alexis Madrigal talks about the eyes of cetaceans or whales and has some beautiful imagery from photographer Bryant Austin.  More importantly, the article asks: “So, what does the world look like to a whale?” which is a fundamental question in comparative anatomy.

The really unusual thing about this article is that vision science gets very little coverage in the popular press and this particular article discusses some of the science of vision including retinal science, after interviews with Leo Peichl who studies comparative anatomy of the mammalian retina at Max Planck.  I’ve long admired Leo’s work and am pleased to see it covered in The Atlantic along with work by Sonke Johnsen, Michael Land and Dan-Eric Nilsson, particularly by one of my favorite writers, Alexis Madrigal.


Image of Ella the whale’s eye from Bryant Austin.

Interesting Paper: Precedence Of The Eye Region In Neural Processing Of Faces


Just seeing an eye… and only the eye is enough to establish the first components of neural facial recognition.  In this interesting paper by Elias B. Issa and James J. DiCarlo, the authors found using a combination of functional magnetic resonance imaging (fMRI) that the first stage in the primate visual/face processing circuitry is tuned to regions in images containing eyes.  Even a single eye is enough to trigger recognition pathways.

fMRI and electrophysiological recording work in facial processing has established that the facial processing network possesses six areas that are extensively interconnected and the anatomical analysis suggests a nested, hierarchical layout where signals progressing through the system become more established.  This of course begs for a true connectomics analysis which will be difficult at the large scale, but tractable at the mesoscale.  It turns out that this is an interesting computational problem as identification of isolated components of images that connate larger meaning is difficult.  Discovering how neural systems unravel this will have substantial importance to diverse applications.

Continue reading “Interesting Paper: Precedence Of The Eye Region In Neural Processing Of Faces”

Interesting Paper: Looking Inside A Trilobite Eye


Trilobites were one of the most successful marine arthropods that lived from the Early Cambrian throughout the Devonian, finally going extinct in the Permian ages, a run of over 270 million years.  They are well represented in the fossil record and even the earliest forms had complex compound eyes much like modern arthropods.  These eyes had elongated lenses composed of calcite that modeling has revealed to provide excellent optical properties with good depth of field and little to no spherical aberration.  These lenses brought light to photoreceptor cells at the base of the lens, but we’ve never before had an understanding of what that structure or anatomy looked like.

The problem of course with the fossil record is that very little internal structure remains in fossilized specimens.  However, a very cool new study that examines trilobite eyes through X-ray tomography by Brigitte Schoenemann and Euan N. K. Clarkson reveals how these cells looked, down, perhaps to the cellular level.  Followup work with μct-scanning and synchrotron radiation analysis reveals that the sensory structures (like rod or cone outer segments) are arranged in flower petal like structures around a central, diamond shaped photoreceptor cell body with pigment granules packed in-between.  Its kind of like a modern limulus eye (image here).

It will be interesting to see if they can image other species of trilobite to get an evolutionary look at how eyes and perhaps primitive retinas developed over 500 million years ago.


Image Credit:  Bryan William Jones, Ph.D.

Interesting papers: Light and vision in the deep-sea benthos

Vision in fishes and crustaceans is a fascinating and understudied area.  In past decades, there were far more studies on the visual systems of sea-dwelling creatures, but with the push towards applied or translational research, the number of reports in these species have dropped off, much to our detriment as one never knows where the applications of basic research will pay off.

At the same time, the whole study of bioluminescence and vision is an interesting examination of how organisms use bioluminescence for mating, warning or aposematismcrypsis or counter-illumination and predation.  It is explicitly a visual phenomenon and as such, has informed a variety of investigations into biomedical, commercial and military applications. Continue reading “Interesting papers: Light and vision in the deep-sea benthos”

Photonic Crystal Light Collectors In Fish Retina Improve Vision In Turbid Water

Elephantnose retina

Fish have some of the most amazing retinas in the animal kingdom.  Like other fish species that live in environments with little to no light, the elephantnose fish (Gnathonemus petersii) use electrical fields to navigate through dark and murky waters.  However, unlike some of those species, the elephantnose fish has not lost its eyes through evolution and uses vision for some functions.

This paper published in Science back in May, 2012 by authors Moritz Kreysing, Roland Pusch, Dorothee Haverkate, Meik Landsberger, Jacob Engelmann, Janina Ruiter, Carlos Mora-Ferrer, Elke Ulbricht, Jens Grosche, Kristian Franze, Stefan Streif, Sarah Schumacher, Felix Makarov, Johannes Kacza, Jochen Guck, Hartwig Wolburg, James K. Bowmaker, Gerhard von der Emde, Stefan Schuster, Hans-Joachim Wagner, Andreas Reichenbach, and Mike Francke shows that the elephantnose fish has absolutely unique and interesting structures that optimize light capture ability and make them insensitive to spatial noise.  Also in the mesopic range they match the rod and cone opsin sensitivity curves allowing the use of both rods and cones throughout large ranges of light intensities, but importantly, arrange the cone photoreceptors in functional assemblies that act as photonic reflectors, creating lightwells in a sense that optimize photon capture.  The rod photoreceptors meanwhile are positioned *behind* the photonic lightwells or reflectors.  The result is that the photonic lightwells or reflectors become wavelength sensitive light intensifiers that functionally match the dynamic range of both rods and cones while boosting sensitivity in the red wavelengths that are the first wavelengths filtered out by water.  The thinking is that this allows the elephantnose fish to easily see large predators in murky or turbid environments.


Interesting: The Spatial Organization Of Cholinergic Mosaics In The Adult Mouse Retina

Cholinergic Strettoi

This Short Communication published in the European Journal of Neuroscience back in 2000 by Lucia Galli-Resta, Elena Novelli, Maila Volpini and Enrica Strettoi was a paper I did not know existed.  That said, I ran into it the other day looking for some reference material and found it to be quite useful.  This communication represents an analysis of the cholinergic amacrine cell mosaics in the C57Bl6/J murine retina.  It served as a useful baseline for cell positioning, and cell mosaicing in both cholinergic arrays of the retina and is a nice analysis that should serve as a reference point for future genetic analysis studies in normal and pathological retinal tissues.  Enrica Strettoi’s laboratory has been carefully exploring the functional organization of the retina for some time now in the normal and pathological states and its always a joy to discover her work in the literature, even if it is 13 years old.


Notable Paper: On Cone Bipolar Cell Axonal Synapses In The OFF Inner Plexiform Layer Of The Rabbit Retina

JCN cover 2013

This paper in the Journal of Comparative Neurology by  J. Scott Lauritzen, James R. Anderson, Bryan W. Jones, Carl B. Watt, Shoeb Mohammed, John V. Hoang and Robert E. Marc is another effort out of the Marc Laboratory For Connectomics that continues to define complete neural circuits to completeness.

This paper is another elucidation of data from the first Rabbit Retinal Connectome volume (RC1) that reveals that the division between the ON and the OFF inner plexiform layer (IPL) is not structurally absolute. ON cone bipolar cells make noncanonical axonal synapses onto specific targets and receive amacrine cell synapses in the nominal OFF layer, creating novel motifs, including inhibitory crossover networks. Automated transmission electron microscopic imaging, molecular tagging, tracing, and rendering of ∼400 bipolar cells reveals axonal ribbons in 36% of ON cone bipolar cells, throughout the OFF IPL. The targets include γ-aminobutyrate (GABA)-positive amacrine cells (γACs), glycine-positive amacrine cells (GACs), and ganglion cells. Most ON cone bipolar cell axonal contacts target GACs driven by OFF cone bipolar cells, forming new architectures for generating ON–OFF amacrine cells. Many of these ON–OFF GACs target ON cone bipolar cell axons, ON γACs, and/or ON–OFF ganglion cells, representing widespread mechanisms for OFF to ON crossover inhibition. Other targets include OFF γACs presynaptic to OFF bipolar cells, forming γAC-mediated crossover motifs. ON cone bipolar cell axonal ribbons drive bistratified ON–OFF ganglion cells in the OFF layer and provide ON drive to polarity-appropriate targets such as bistratified diving ganglion cells (bsdGCs). The targeting precision of ON cone bipolar cell axonal synapses shows that this drive incidence is necessarily a joint distribution of cone bipolar cell axonal frequency and target cell trajectories through a given volume of the OFF layer. Such joint distribution sampling is likely common when targets are sparser than sources and when sources are coupled, as are ON cone bipolar cells.

Figure Above: The first Rabbit Retinal Connectome volume (RC1), constructed via automated transmission electron microscopy (ATEM) and computational molecular phenotyping (CMP), spans the mid-inner nuclear layer (INL) at section 001 to the ganglion cell layer (GCL) at section 371, shown in a mirror image below. RC1 is a short cylinder ≈ 250 μm in diameter and ≈ 30 μm high containing 341 ATEM sections and 11 intercalated CMP sections. The cylinder is capped at top and bottom with 10-section CMP series allowing molecular segmentation of cells, and an activity marker, 1-amino-4-guanidobutane (AGB), to mark cells differentially stimulated via glutamatergic synapses. ATEM section 001 is a horizontal plane section through the INL visualized with GABA.glycine.glutamate → transparency mapping and a dark gold alpha channel (ANDed taurine + glutamine channels). ATEM section 371 is a horizontal plane section through the GCL visualized with GABA.AGB.glutamate → transparency mapping.

Activation of Survival Pathways In The Degenerating Retina of rd10 Mice

Survival rd10

An interesting article was published  in Experimental Eye Research by Marijana Samardzija, Hedwig Wariwoda, Cornelia Imsand, Philipp Huber, Severin R. Heynen, Andrea Gubler and Christian Grimm that examines survival pathways that are induced in the retinas of rd10 mice.  Dynamics of retinal degeneration in the rd10 mouse was also examined including an analysis of retinal vasculature and kinetics.  The study is fairly comprehensive including crude anatomical approaches, biochemistry, real-time PCR, Western blotting and immunofluorescence.  They recapitulate some of the studies that have examined development of the rd10 mouse up to pnd15, but then explored the phases of initial retinal degeneration and explored survival mechanisms and pathways (Lif, Edn2, Fgf2, Mt1, Mt2, p-JAK2, CASP1 and GFAP) in the cells that remain.  It would have been interesting to follow these results at later stages of degeneration.  The authors mention remodeling, but only in passing which was too bad as there are some really interesting aspects of cell survival there.  Regardless, its an interesting paper worthy of having a look at.


Interesting Article: Cellular Resolution Panretinal Imaging of Optogenetic Probes Using a Simple Funduscope

An interesting paper by Adi Schejter, Limor Tsur, Nairouz Farah, Inna Reutsky-Gefen, Yishay Falick, and Shy Shoham published an interesting paper that shows in vivo fluorescent images with cellular resolution using optogenetic probes expressed in retinal ganglion cells by adapting a simple endoscope as a low cost fundoscopic imaging system.

The authors were able to resolve really nice, high quality images that reveal the entire retina, showing ganglion cells as well as the ganglion cell fibers expressing a channelrhodopsin2-e YFP construct.

Thanks to friend of Webvision, Steve Fliesler for sending this along.


Amazing Anamorphic Illusions

This illusion has been making the rounds on the Internet lately and we here at Webvision thought we’d share it with this crowd.  These anamorphic illusions are reminiscent of some of the sidewalk chalk paintings that have become popular recently that rely on highly distorted or skewed representations (Ponzo Illusion) of objects or situations that rely on interpretation of perspective to create the illusion.

The Brusspup Youtube Channel has recently posted a number of actually really wonderful illusions, large and small and is worth a few minutes of your time.

Interesting Article: On the Perception, Production And Function Of Blue Colouration In Animals

Kate D. L. Umbers has published an interesting manuscript, titled “On the perception, production and function of blue colouration in animals”.  Its available for free at the Journal of Zoology here and covers those studies that have proposed a function for blue coloration in the animal kingdom, taking a multi-disciplinary approach before taking you on a discussion of “blue”.  What initially grabbed my attention was Table 1. A non-exhaustive list of visual pigments of various taxa showing the wavelengths at which their opsins are maximally sensitive.  After that, it was easy to get sucked into the discussion of production of blue, pigmentary and structural blues as well as the crux of the paper which is the functions of blue.

As an aside, if you ever get a chance to see Robert Marc’s lecture on color, do it.  Its magnificent.  His discussion of the color blue from the physics to the neurobiology is truly wonderful.