77 Matching Annotations
  1. Jul 2018
  2. Apr 2018
    1. Visick KL, Ruby EG, (2006) Vibrio fischeri and its host: It takes two to tango. Current Opinion in Microbiology 9:632–638.

      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.

    2. Nyholm SV, McFall-Ngai MJ, (2004) The winnowing: Establishing the squid-vibrio symbiosis. Nature Reviews Microbiology 2:632–642.

      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.

    3. Foster RG, Soni BG, (1998) Extraretinal photoreceptors and their regulation of temporal physiology. Reviews of Reproduction 3:145–150.

      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.

    4. An evolutionary route to such novelty is the assembly of existing components in new combinations or contexts, a process that has been called genetic or evolutionary “tinkering”

      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?

    5. autogenic

      Produced by the organism.

    6. In the squid light organ, the photoreceptive tissues also may function to perceive environmental light, providing the animal with a mechanism to compare this exogenous light with symbiont light emission.

      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.

    7. confocal

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

    8. using primers specific to the cDNA encoding each of these proteins, we performed RT-PCR on 7 tissues of the adult host, including those that are and those that are not dedicated to light modulation

      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.

    9. To determine whether they also co-localize in light-organ tissues, we applied 2 independent analyses of these 3 components: localization of message by PCR and of protein by immunocytochemistry.

      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.

    10. we analyzed the light organs both of animals that had been colonized by the symbiont at hatching and of those that had not been colonized

      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?

    11. ORFs

      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.

    12. mutant V. fischeri strains defective in light emission (lux mutants) have demonstrated that symbiont luminescence somehow participates in the transformation of the organ from its juvenile morphology

      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.

    13. tissues surrounding the eye and those dorsal to the symbiont-containing crypts share the expression of a family of proteins, the reflectins

      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.

    14. symbiont

      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

    15. vesicles

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

    16. The complexity of such photoreceptors can vary from diffusely distributed photoreceptive cells, characteristic of dermal light sense, to complex organs in discrete locations on an animal's body

      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.

    17. Opsin proteins typically mediate the associated phototransduction, although often through isoforms distinct from those produced in the retina (1⇓–3).

      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).

  3. Mar 2018
    1. In bacterial light organs, the animal host must control not only light emission but also the symbiont populations. This management of the symbionts by the host is essential to maintain symbiont number and to sanction cheaters (i.e., dark mutants that might arise and compromise the function of the organ)

      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.

    2. True JR, Carroll SB, (2002) Gene co-option in physiological and morphological evolution. Annu Rev Cell Dev Biol 18:53–80.

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

    3. Visick KL, McFall-Ngai MJ, (2000) An exclusive contract: Specificity in the Vibrio fischeri-Euprymna scolopes partnership. J Bacteriol 182:1779–1787

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

    4. Nealson KH, Hastings JW, (1979) Bacterial bioluminescence: Its control and ecological significance. Microbiol Rev 43:496–518.

      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.

    5. Visick KL, Foster JF, Doino J, McFall-Ngai M, Ruby EG, (2000) Vibrio fischeri lux genes play an important role in colonization and development of the host light organ. J Bacteriol 182:4578–4586.

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

    6. Crookes WJ, et al., (2004) Reflectins: The unusual proteins of squid reflective tissues. Science 303:235–238.

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

    7. Young RE, Roper CFE, Walters JF, (1979) Eyes and extraocular photoreceptors in midwater cephalopods and fishes: Their roles in detecting downwelling light for counterillumination. Mar Biol (Berlin) 51:371–380.

      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.

    8. Young RE, Roper CF, (1976) Bioluminescent countershading in midwater animals: Evidence from living squid. Science 191:1046–1048.

      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.

    9. Terakita A, (2005) The opsins. Genome Biology 6:213.

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

    10. fluorochromes

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

    11. rhodamine phalloidin

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

    12. he peptide was a mixture of phosphorylated and unphosphorylated serine in position #357, so that antibodies might be generated to both the activated and non-activated forms of the molecule

      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.

    13. 14-mer

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

    14. phyML

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

    15. Using the cDNA sequences, we first used NCBI BLASTX analyses to identify the closest matches to the derived amino acid sequences

      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

    16. no-RT control

      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.

    17. RACE primers (Table S2) were constructed from the EST sequences identified as having similarity to a transcript of interest.

      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.

    18. a finding of hyperpolarization mediated by r-opsin would be unprecedented.

      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.

    19. Genes associated with hyperpolarizing ciliary phototransduction also are present in the light organ, and their sequence characteristics predict that they could be capable of driving the associated activities in ciliary phototransduction, but no ciliary opsin was detected.

      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.

    20. Whereas the opsin expressed in the light organ is of the rhabdomeric type, and all key components of the rhabdomeric cascade are present in the light organ, the ERG spectra demonstrate hyperpolarization of the photoreceptor cell membranes.

      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.

    21. Retinal tissues of E. scolopes were used as a positive control for the cross reactivity of these antibodies in regions known to produce these proteins

      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.

    22. we used antibodies raised against cephalopod opsin, arrestin, and rhodopsin kinase (25, 26) to localize the protein in host tissues.

      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.

    23. dioptrics

      Tissues that are able to bend light.

    24. arrestin message could be detected only in the eye and light organ, rhodopsin and rhodopsin kinase messages were present also in the optic lobe of the brain, and rhodopsin kinase was detectable at low levels in other tissues.

      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.

    25. Components of visual transduction cascades, including opsin, arrestin, and rhodopsin kinase, co-localize in the retina, because they function in concert during phototransduction

      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.

    26. the provision of the proteins of phototransduction cascades is constitutive, i.e., that it is independent of the presence of symbiont luminescence.

      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.

    27. characteristic rhabdomeric depolarization was observed in the electroretinographic spectra of the eyes, whereas the light-organ tissue responded with hyperpolarization

      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.

    28. we performed electroretinograms (ERGs) (21, 22), which extracellularly record photoreceptor membrane potential, of both eyes and light organs of juvenile E. scolopes.

      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.

    29. Also present were genes with similarities to those encoding proteins typically associated with ciliary photoreceptor cells,

      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.

    30. In 5 instances (i.e., in the case of rhodopsin, arrestin, rhodopsin kinase, G alpha i, and G protein beta subunit 1), the same isoform seems to occur in both eye and light organ tissues.

      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.

    31. predicted proteins are highly similar to the phototransduction constituents that are associated with rhabdomeric photoreception

      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.

    32. motif

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

    33. To ensure that these cDNAs were host derived, we also examined the symbiont genome for similar sequences,

      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.

    34. We identified 11 such cDNAs (Fig. 2; Table S1), including the gene encoding the visual pigment opsin itself, as well as molecules involved in subsequent activation and deactivation of the cascades.

      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.

    35. Recent studies of the transcriptome of the light organ of E. scolopes revealed the expression of several genes that encode proteins with sequence similarity to components of visual transduction cascades

      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.

    36. mediates


    37. The morphology of the light organ, as well as behavioral studies, have suggested that the animal uses the light in counterillumination

      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).

    38. previous studies of the anatomy and biochemistry of the light-organ lens and reflector demonstrated dramatic biochemical convergences with those of eyes

      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.

    39. diverticula

      Pouches or bulges in tissues.

    40. iris

      Structure that controls the amount of light entering the eye.

    41. tapetum

      A layer of reflective tissue between the choroid and retina.

    42. choroid

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

    43. tissues that modulate the intensity and direction of symbiont light emission

      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.

    44. system for the analysis of tissues that interact with light and as a natural model of symbiosis

      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.


    45. the PSVs in certain bioluminescent squid species have been implicated in the perception and control of light emission, particularly in counterillumination

      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.

    46. nuchal organ

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

    47. Extraocular photoreceptors are widespread across the animal kingdom.

      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/

    48. extraocular photoreceptors

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

    49. visual transduction cascades

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

    50. immunocytochemistry

      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.

    51. Electroretinograms

      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.

  4. Feb 2018
    1. antagonistic signals

      Signals that conflict or interfere with one another.

    2. membrane potential

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

    3. epithelium-lined crypts

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

  5. Dec 2017
    1. parietal

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

    2. refractive index

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

    3. ventrally

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

    4. Transcriptome

      All of the mRNA transcripts in a cell.

    5. bioluminescent

      Biologically produced light.