Protein responsible for converting light to a chemical signal that allows us to see.

Review of the factors that support horizontal acquisition of symbionts from the environment, using the Euprymna scolopes and Vibrio fischeri model. Horizontal acquisition occurs when symbionts are transferred from one host species to another.

This paper is from the symbiont perspective.

Review of the factors that support horizontal acquisition of symbionts from the environment, using the Euprymna scolopes and Vibrio fischeri model. Horizontal acquisition occurs when symbionts are transferred from one host species to another.

This paper is from the host perspective.

Extraocular photoreceptors were generally thought to be primarily involved in the regulation of daily and seasonal cycles. Their other functions were unknown.

This review paper outlines the variety of extraocular photoreceptors present in nonmammalian organisms and their importance in regulating time-related physiological processes.

Evolutionary 'tinkering' is responsible for novel adaptations throughout the tree of life from fish to apes.

Read more in Science Daily: Distantly related fish find same evolutionary solution to dark water

And Cosmos: How did our brains get so big?

Produced by the organism.

The finding that the light organ possesses the same proteins that are found in photoreceptors of the eye may mean that the light organ has the ability to sense light from both the environment and from the bacterial symbionts.

The ability to compare the two light sources would potentially allow the squid to control the light produced by the bacteria in order to match the light in the environment.

Technique that allows high-definition viewing of microscopic samples in 3D.

Using reverse transcription polymerase chain reaction (RT-PCR), the authors amplified sequences for the genes coding for opsin, arrestin, and rhodopsin kinase (RK). Transcripts were extracted from the tissues of the light organ, eye, gills, mantle, tentacle, and arm.

The authors used two methods to discover if opsin, arrestin, and rhodopsin kinase also occur in the light organ.

In the first method (message expression), the authors looked for the molecular signals of these proteins in tissues from the light organ, eye, gills, mantle, tentacle, and arm.

In the second method (immunocytochemistry), the authors looked for evidence of protein production in the tissues of the light organ using confocal microscopy.

Bacterial symbionts play an important role in the in the morphogenesis (progression from one developmental stage to the next) of the light organ in the Hawaiian bobtail squid.

Read more in Science: Mysteries in Development- How Do Microbes Shape Animal Development?

Open Reading Frames (ORFs) are sequences of DNA that are not transcribed. They can be used to search for transcripts that code for specific proteins of interest.

The lux genes in Vibrio fischeri code for the proteins that produce bioluminescence.

Visick et al. (2000) created three mutant lux genes that were unable to produce bioluminescence. The mutant strains of V. fischeri carrying the modified genes were used to test whether bioluminescence was a key factor in development from juvenile to adult.

Crookes et al. (2004) determined that the composition of reflective tissue found in the tissues of E. scolopes was different from the composition of reflective tissue commonly found in other animal tissues.

In most animals, the reflective tissue is composed of thin layers of purine crystals, which are able to bend light (i.e., they have a high refractive index). The reflective tissue in E. scolopes is composed of a group of proteins high in methionine, tyrosine, arginine, and tryptophan.

An organism that lives in close association with a "host" organism.

The relationship may be positive for both the host and the symbiont (mutualistic), positive for the symbiont and neutral for the host (commensal), or positive for the symbiont and negative for the host (parasitic).

Symbiosis: It's Complicated

Membrane-bound "bubbles" that shuttle proteins to different locations in a cell.

In many organisms, the ability to sense light is especially important for allowing organisms to sync to the various rhythms of light in the environment, e.g., daily, monthly, or yearly rhythms.

This has allowed for the diversity of structures other than the eye that can sense light. Researchers are still working to learn more about about these structures.

Opsins are a group of proteins that are sensitive to light. There are many different forms of opsin, and they are involved in both visual and nonvisual systems throughout the animal kingdom.

Some opsins bind to retinal (a chemical involved in animal vision) and undergo a change in their structure when subjected to light.

This change in conformation is the signal that initiates the series (cascade) of proteins in the retina responsible for the ability to see (this process is called phototransduction).

Bacteria in the light organ continue to grow and multiply. If the numbers get too high, the bacteria could potentially switch from being beneficial to being harmful.

Additionally, if bacteria develop mutations that cause them to stop producing luminescence, the mutants will use resources without providing benefit to the squid.

Consequently, the squid must have a way to control the number of bacteria that colonize the light organ. They do this by ejecting 75% or more of the bacteria in the light organ each day.

The authors review how new functions can evolve when existing genes gain new functions.

Visick and Mc-Fall-Ngai review the contributions of Vibrio fischeri to the development of the light organ as Euprymna scolopes matures.

Review of bioluminescence in bacteria. Examines the possible role bioluminescence plays for the bacteria as well as some of the organisms that have symbiotic relationships with these bacteria.

Study showing that E. scolopes is only able to undergo normal development if V. fischeri possesses the ability to produce luminescence.

Study that looked at the reflective tissues of the light organ and established their similarity to the reflective tissues found in the eye.

Early study providing evidence that, in addition to signals coming from the eyes, extraocular photoreceptors also provide signals that contribute to the ability of some species of squid to be able to adjust the amount of light they produce to match the downwelling light in the environment.

Early study detailing physical evidence that some species of squid are able to adjust the amount of light they produce to match the ambient light in the environment, a process called counterillumination.

Review paper outlining the seven subfamilies of opsins, their functions, and possible phylogenetic relationships.

Fluorescent molecule that binds to an antibody, allowing researchers to see if a protein is present and, if so, where it is.

Red fluorescent dye (or fluorochrome) used to visualize cellular components such as actin.

Proteins in the phototransduction cascade can be in either an "on" (activated) or "off" (inactivated) state. The authors created antibodies to bind to either state to ensure that they would be able to detect the protein regardless of what form it was in.

Short sequence of a protein, 14 amino acid residues in length.

A software program used to determine how related two species, genes, etc. are.

Basic Local Alignment Search Tool (BLASTX) is a search algorithm developed by the National Center for Biotechnology Information (NCBI)

For more information about BLASTX, go to: NCBI: BLAST

A negative control containing all the reagents of the PCR reaction, except the reverse-transcriptase. This kind of control is used to ensure that the reagent mixture is not contaminated.

Primers are short, single-stranded sequences of DNA used to amplify RNA sequences of interest using polymerase chain reaction (PCR). Amplifying a sequence means exponentially increasing the number of copies.

The studies done to date suggest that any given type of opsin is involved in only one phototransduction pathway.

This means that if the r-opsin present in E. scolopes is able to initiate both rhabdomeric and ciliary cascades, this would be the first instance of an opsin functioning in more than one pathway.

In addition to the presence of genes involved in ciliary phototransduction, both rhabdomeric and ciliary opsin are present in diverse invertebrates.

Consequently, it is possible that c-opsin could be present in E. scolopes, even though it was not detected.

The molecular and immunochemistry data provide strong evidence that rhabdomeric phototransduction is present in the light organ. However, the electroretinogram data suggest that both rhabdomeric and ciliary pathways are present, even though no ciliary opsin was found.

A positive control is used to verify that your experiment is working the way you want.

In this study, the authors tested their immunocytochemical test by using it on tissues that they already knew contained the three proteins.

The authors created antibodies against the three proteins so they could detect them in specific tissues using immunocytochemistry.

They incubated squid eyes and light organs with the antibodies and stained with secondary antibodies that were tagged with a fluorescent molecule.

The stained eyes and light-organs were mounted on microscope slides and viewed with a confocal microscope. A fluorescent signal identified the presence of the proteins.

Tissues that are able to bend light.

Arrestin and rhodopsin were found only in tissues responsible for modulation of light, i.e., the eye and light organ. Rhodopsin kinase was found in these tissues and at low levels in other tissues.

Work by Hargrave and McDowel (1992) and by Ridge et al. (2003) on phototransduction in the retina established that these three proteins are part of the G-protein-coupled pathway required in order for phototransduction to occur.

The authors tested the light organ tissues from animals without Vibrio (hatchlings) and from those with Vibrio (juveniles) to determine if the Vibrio are necessary to trigger the phototransduction cascades.

The authors found phototransduction proteins in the hatchlings, suggesting that the presence of Vibrio is not necessary for phototransduction to occur.

The rhabdomeric form of opsin (r-opsin) is involved in the visual systems of invertebrates. When r-opsin is excited (a stimulus is applied), the expected response in an electroretinogram is depolarization.

Only r-opsin was found in the light organ of E. scolopes. Because of this, the authors were surprised when they excited tissue in the light organ and it hyperpolarized. Hyperpolarization is usually associated with c-opsin, the form of opsin found in vertebrates.

Electroretinograms (ERGs) measure the change in voltage across cells when exposed to a light stimulus. The authors compared the response of photoreceptive tissues in both the eyes and light organs of juvenile Euprymna.

Electrical signals of rhabdomeric photoreceptors typically respond by depolarizing, that is, becoming more negative.

Electrical signals of ciliary photoreceptors typically respond by hyperpolarizing, that is becoming less negative.

Ciliary photoreception is generally associated with vision in vertebrates and is characterized by different phototransduction proteins than those involved in rhabdomeric phototransduction.

This finding suggests that the light organs have several pathways that may allow for sensing light.

Five key proteins that are required for the perception of light in the eyes of Euprymna were also found in the light organ. This suggests that the light organ also contains the biochemical pathways necessary to sense light.

Rhabdomeric photoreception is generally associated with vision in insects and molluscs and is characterized by specific phototransduction proteins. The authors identified the proteins they expected to find in E. scolopes.

Recurring patterns of a sequence of DNA or amino acids. For example, opsins contain seven transmembrane helices.

If proteins associated with the visual transduction cascade were found in both Euprymna (host) and Vibrio (symbiont), the results would be very challenging to interpret. Because of this, the authors made sure the sequences were only from Euprymna.

The authors looked for evidence that the light organ produces proteins similar to those found in the eye that could generate a phototransduction cascade.

The authors identified 11 sequences that code for proteins similar to those responsible for phototransduction in the eye.

Chun et al. (2006) generated 11 cDNA libraries from the light organ of the bobtail squid.

Developmentally important time periods were chosen for analysis in order to provide a tool that would allow researchers to ask questions about how the bobtail squid responds to colonization by Vibrio fischeri.

Initiates.

Jones and Nishiguchi (2004) were the first to test the hypothesis that Hawaiian bobtail squid use bioluminescence for counterillumination (a strategy for camouflage). They measured changes in bacterial luminescence that matched changes in down-welling light (light coming from above).

Montgomery & McFall-Ngai (1992) and others discovered that proteins in the lens of the light organ of E. scolopes were similar to the proteins commonly found in the lenses of some mammal and cephalopod eyes.

Pouches or bulges in tissues.

Structure that controls the amount of light entering the eye.

A layer of reflective tissue between the choroid and retina.

Layer of tissue beneath the retina that supplies nutrients and oxygen to the retina.

The authors determined that light organs have tissues that are similar to the eye: a lens that is able to focus light, reflective tissue that is able to reflect light, and an iris that can control the amount of light entering or leaving the light organ.

The Euprymna scolopes-Vibrio fischeri symbiosis is a system with a single host and single symbiont, making it a great system to study how bacterial symbionts are acquired.

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The structures that control the amount of light emitted to produce counter-shading (PSVs) are different from the structures that produce the light.

Counter-shading refers to the fact that parts of animals that are exposed to light are usually lighter in color than those parts that are not exposed to light.

A group of photoreceptive cells that form a simple photoreceptive organ in some species of cephalopods (the class that includes squid and octopuses).

Extraocular photoreceptors range from simple to complex and are essential for many functions, including circadian entrainment (syncing of internal biological clock to environmental signals such as light and dark) and phototaxis (movement toward light, such as what is seen in many plants).

Read more in Scientific American: https://www.scientificamerican.com/article/seeing-without-eyes1/

Cells located somewhere other than the eye that are able to convert photons of light into chemical signal.

Sequences or series of proteins responsible for generating the signals involved in vision.

A technique that uses secondary antibodies bound to a fluorescent chemical to identify the presence of specific proteins.

The secondary antibodies bind to primary antibodies, which identify the protein of interest. The presence of the protein of interest can be detected by looking at the cells under a fluorescent microscope.

A test that measures how retinal cells respond to a light stimulus. Electroretinography is usually used to diagnose problems in the human eye, but it also has other uses.

Signals that conflict or interfere with one another.

The voltage generated by the difference in the concentrations of ions on either side of a membrane.

"Pouches" within the light organ that are lined with columnar-shaped cells, where the Vibrio attach.

A simple organ associated with the pineal gland in some animals and responsible for regulating circadian cycles.

Unitless measure of how much light bends when passing through a substance.

On the "bottom" surface, or siphon side of the squid.

All of the mRNA transcripts in a cell.

Biologically produced light.