Bobtail Squid and Their Shiny Friends: Cass' Rough Draft

Bobtail Squid and Their Shiny Friends: An In-Depth Look at Bioluminescent Vibrio fischeri

The Hawaiian Bobtail Squid (Euprymna scolopes), like many other ocean-dwelling species, relies on bioluminescence to protect itself from predators and hide from prey. It accomplishes this feat by colonizing a special organ with a species of bacteria called Vibrio fischeri, (the specific strain called ES114) which the squid can become bioluminescent under certain circumstances, all of which are met bythrough the light organ Repeat the muin topic of the sentence, difficult to understand". V. fischeri live throughout the world but are mainly found in temperate and tropical regions weird sentence, maybe to broad. Maybe mention a few main spots instead of starting out with the fact that they are found around the world. E. scolopes is born without its symbiote and must colonize its light organ within hours of birth to survive How does survival rely on the V. fisheri? Isn't it more of just an advantage?. V. fischeri aren’t luminescent in the open ocean, but become luminescent in the E. scolopes light organ. With these apparent obstacles, how does V. fischeri successfully colonize the light organ of E. scolopes? The answer is a complicated one. Why state a question here, is this the hypothesis, doesn't seem strong enough, too fluffy
With the advances of genome technology has allowed, scientists have been able to map genomes for an ever-increasing number of species, specifically including the strain of V. fischeri which forms a symbiotic relationship with E. scolopes, ES114. This mapping has allowed scientists to determine theSpecific genes which play an important role in the symbiosis HAVE ALSO BEEN IDENTIFIED (14). Scientists have also determined the morphology and anatomy of the light organ HAS ALSO BEEN DETERMINED in E. scolopes. This light organ takes up much of the space in the mantle cavity with bacteria only occurring in narrow channels throughout. In some of these channels, bacteria may only be a few cells thick. E. scolopes is born with all the necessary components of its light organ, but it takes numerous complex stages of development to reach its final state. Materials may be exchanged between V. fischeri and E. scolopes through the electron-rich vesicles which occur in the barrier between species. Light control is regulated by a reflector and the ink sac inside the mantle The flow of this paragraph is hard to follow. What is the main point? (10). ((Figure 2, source 10))

Bioluminescence has many advantages, AND IS FOUND IN A WIDE VARIETY OF HOSTS. especially in deep ocean waters. The list of OCEANIC creatures who take advantage of bioluminescence includes: bacteria, sponges, mollusks, annelids, arthropods, echinoderms, chordates., in addition to quite a few vertebrates. which may form a symbiosis with microscopic organisms to achieve bioluminescence. This list for oceanic bioluminescence is long compared to the terrestrial and freshwater lists. Terrestrial animals with bioluminescence include bacteria, fungi, snails, earthworms, and some arthropods. The limpet what is a limpet?is the only freshwater animal capable of producing bioluminescence.
Bioluminescence IS USEFUL IN ATTRACTING AND SEARCHING FOR PREY can help an animal find food by attracting prey or even by providing enough light for an animal to find food. In addition to finding prey, bioluminescence can CAMAFLOUGING an THE animal. avoid becoming prey. FOR EXAMPLE, The deep sea shrimp BLIND THEIR PREDATOR BY ejectsING light into the PREDATOR"S face of a predator to blind and distractING it ALLOWING —ITTHE SHRIMP TO ESCAPE. while the shrimp has a chance to get away. Another defense mechanism is to DISTRACT THE PREDATOR BY ejectING light in order to WHICH attract a bigger predator to eat whatever is preying on the animal. Bioluminescence in the Hawaiian bobtail squid protects it by disguising its shadow from predators swimming beneath it. The belly of the squid actually looks the same color as the water above and even changes throughout the day depending on the amount of light filteringED through the water. Bioluminescence IS ALSO USEFUL IN findING a mate. As seen in firefly mating rituals and confusing the loosejaw fish. where The light organ on the male’s chin is much larger than the female. Bioluminescence can be triggered in many ways. For the purpose of this paper, we will look at a particular bacterial symbiosis, but it can also be caused by different chemical compounds, depending on the organism the purpose can be thought of as the hypothesis, so is this the hypothesis. Why is this sited? is this the purpose of the cited journal? and even in the V. fisheri isn't it a chemical reaction that is responsible for biolumenesence? ** (20). Photolyase has been investigated in the V. fischeri strain which inhabits E. scolopes, but was found to have no benefit to the symbiotic relationship (19). **where did this come from. This paper reads like a string of little facts that have little continuity. I don't know why I need to know this when I don't even know what Photolyase is or how it is relevant here.
Boettcher and Ruby (IDENTIFIER?) have performed studies testing the light emission of V. fischeri outside the light organ of E. scolopes. They foundOBSERVED that while V. fischeri is luminescent inWHILE SYMBIOTIC within E. scolopes, HOWEVER THE BACTERIA does not produce the same effects outside the symbiosis even in the same concentration. weird The bioluminescent effect is triggered by an autoinducer which is distinctly different from other strains that are present in some fish symbioses. you introduced this term auto inducer with no explanation, needs some information to relate relevance. What does this have to do with concentration or luminecence The ES114 strain is visibly luminous immediately after removal from the light organ but this rapidly fades and cannot be reversed on any laboratory media.reversed? What reverse? Only by adding luciferase (an autoinducer) to the bacteria can researchers recreate luminescence outside an E. scolopes light organ (2). This shows that the V. fischeri and E. scolopes symbiosis is a very specific one. Weird sentence. Why does this show that there is a specific symbiosis? What do you mean by specific?

COLONIZATION OF THE E. SCOLOPES BY V.FISCHERI DEPEND ON SEVERAL GENETIC AND PHYSICAL FACTORS. Several factors affect the colonization of E. scolopes by V. fischeri, mostly the interplay between the genes and population dynamics of V. fischeri. Mucus secretion also plays a significant role. McCann et al. studied these population dynamics using both ES114 and a mutant strain called ESR1. They found that ESR1 is not able to compete with ES114 effectively during colonization. When exposing E. scolopes to V. fischeri under controlled conditions, scientists discovered an increase in cells the animal is exposed increases the chances of the light organ being colonized. Also, exposing E. scolopes to multiple strains of V. fischeri causes different results when in small and large inoculums. When in small inoculums, E. scolopes was only colonized with one of the three strains in the experiments but in large inoculums, E. scolopes was colonized by two or three strains (9). This shows the symbiotic relationship between E. scolopes and V. fischeri is very efficient. Why does this show efficiency? More = More, less = less. Is this efficiency? It seems like that is not the conclusion I would come to from that statement. I would think that all it tells me is that the squid is prone to be inhabited by one strain, but under the right conditions it is susceptible to multiple strains. Efficiency?
Different genes seem to play a part in the symbiosis between V. fischeri and E. scolopes. Genes encoding for plasmids and fluorescent proteins have been investigated to use in the study of V. fischeri in the light organ on E. scolopes and also in colonization. What? weird sentence. A study by Dunn et al. improves upon a plasmid, pES213, that the researchers had previously described and also looks at a red fluorescent protein (RFP) to work in tandem with green fluorescent protein (GFP) inside the light organ. Improvement for what purpose? Who/what gets the advantage? Using vectors Huh? what does this mean? in the study, the researchers found pES213 to be more stable than plasmids from E. coli and that encoding these plasmids with RFP and GFP showed no disadvantage in the colonization of the light organ. By marking these cells, scientists were able to determine that the donor and recipient cells are actually segregated in the light organ (3). The ability to mark cells will allow further studies about the dynamics of V. fischeri and E. scolopes symbiosis to be studied inside the light organ with no damage to either species.
The Toll/NF-B pathway appears to be present in E. scolopes, but it also shows unique characteristics. What is this pathway and why is it important? What is the function of the toll pathway? Many species exhibit several toll-like receptors (TLRs), but E. scolopes only exhibits one, which is unusual. The limitations of E. scolopes’ DNA doesn’t allow for Southern blots and other amplification, which could have led to the inability to identify any other TLRs. Weird sentence. What sort of limitations? And again is this limitation a limitation for WHAT/WHO…? ** Several elements which are essential to microbe-associated molecular pattern (MAMP)-induced initiation of the NF-B pathway were identified. This data gives evidence, albeit circumstantial, that the NF-B pathway is active during the initiation of symbiosis between V. fischeri and E. scolopes (5). It also shows while similar to other types of symbiosis, the one **THE ONE? WHAT? between V. fischeri and E. scolopes is very highly specialized and only keyed to each other. I have no idea of the reason for these pathways, and I get little sense that the author does either, it is difficult to follow and I don't understand its importance. Are these pathways just in species which have relationships with V. fisheri or what? There are big jumps from provided proof and conclusions drawn from the proof. needs more explaination.
Two systems are used in V. fischeri to detect the number of organisms and regulate early and late colonization factors in the light organ of E. scolopes. (FIRST LINE IS WORDY AND CONFUSING) First studied in 2000 by Visick and Skoufos, a gene called regulator of symbiotic colonization-sensor (rscS) and the lux gene were found to play an important role in colonization (17). The two genetic sequences are called ain and lux by Lupp and Ruby who corroborated that colonization cannot begin and persist without both genes functioning normally. The ainAIM sequence was found to be a requirement for normal initiation of colonization in the light organ of E. scolopes, but not the lux sequence. The lux sequence was found to come into play only after the ain system codes for it, and in ain system mutants it was found that the gene for motility of the V. fischeri cells is greatly reduced, causing a deficiency in colonization. Before luminescence can be regulated, the cell density in the light organ has to become greater than 1010 cells/ml and the lux sequence must be initiated (8).Why mention luminesence here, I thought the paragraph was on colonization…? These findings help us better understand how colonization of the E. scolopes light organ is accomplished by V. fischeri.How does it help to understand how colonization is accomplished? Isn't this talking about initiation and motility? But why would motility be important to colonization, after initiation? I don't understand what is going on here with these genes, they are important, I get that but for what purpose? What is the initiation? **
THE pila GENE, IDENTIFIED BY Stabb and Ruby, identified a gene which encodes for pili function and assembly. which they label pilA. TheyTHE pilA GENE determined that this gene plays a role in symbiote recognition of V. fischeri in the E. scolopes light organ during colonization. **great sentence, this is the why, recognition. you start the prargraph with it, tells the reader its importance first and then explains the rest. good job
Using two strains of V. fischeri, ES114 and a strain with mutated pilA genes, researchers found that a fully functioning pilA gene is very important in the colonization of E. scolopes, especially in mixed inoculums where there is competition between strains. Mutant pilA genes are selected against 106 fold in 15 years and would not survive in symbiosis with E. scolopes. This data shows the competition for infection comes when the V. fischeri are gaining entrance to the light organ instead of in the persistent infection of the light organ. Repeated tests appeared to show no competition after the initial colonization (16). This study shows how the outer appearance of a V. fischeri cell plays an important role in its recognition and acceptance by E. scolopes in order to form the symbiosis.
Mucus secretion plays a vital role in selecting for V. fischeri cells inside the light organ of E. scolopes. Yes this is a great introduction sentence In a study by Nyholm et al. it was determined that infection is limited by size of the particle? why particle here? instead of viability or type. It was discovered that during the initial stages of colonization, E. scolopes permits any particles which are 2 m in diameter to enter the crypts of the light organ but these particles are expelled before actual infection by V. fischeri. When E. scolopes are presented with gram negative or positive bacteria, a type of mucus is secreted which evacuates all particles in the light organ. After persistent infection by V. fischeri, mucus shedding is apparently suppressed; however mucus secretion is still present. After the initial mucus is expelled, V. fischeri is the only occupant of the light organ and the specificity between E. scolopes and V. fischeri increases as time goes on (13). Increasing specificity is an indication of how efficiently the symbiosis between these organisms actually works.
Another study by Nyholm and McFall-Ngai focuses on the mucosal membrane of E. scolopes during colonization and its interactions with V. fischeri. When V. fischeri has entered the light organ, there must be some mechanism by which it becomes exclusive. It has been previously noted that mucus is secreted and expelled by E. scolopes to eliminate bacteria and particles that are not V. fischeri, but how does this happen? It seems as though V. fischeri interacts differently with the mucus matrix of E. scolopes than other bacteria do. Vibrio fischeri is able to clump together more competitively than other non-specific bacteria and bind to the mucus matrix, possibly allowing it to withstand the expulsion of the mucus and unbound bacteria. This is not to say non-specific bacteria don’t clump together in the light organ, but V. fischeri appears to be better suited to this. It was also hypothesized that V. fischeri may alter the chemistry of the mucus in order to present a more adapted environment to their survival and not for non-specific bacteria (11). (THIS SECTION ON BIOLUMINESENCE CAN BE ORGANIZED TO KEEP IDEAS TOGETHER BECAUSE IT JUMPS FROM ONE IDEA TO ANOTHER BACK TO THE ORIGINAL)

Genetics again play an important role in the interactions between V. fischeri and E. scolopes after colonization of the light organ, as do lipopolysaccharides and mucus secretion. (I AM CONFUSED, DO GENETICS, LPS AND MUCUS SECRETION ALL PLAY AN IMPORTANT ROLE?) Two mutant type genes, SHOULD YOU IDENTIFIY THE GENES HERE? were investigatedIDENTIFIED by Adin et al. and were determined to be active outside the symbiosis between V. fischeri and E. scolopes. These genes, htrB and msbB,(UP ABOVE) BOTH GENES encode for lipid A secondary acyltransferases, and it was shown that mutant htrB1 modifies lipid A in such a way that is important to the initiation of colonization. Mutations to these genes caused a reduced motility in the V. fischeri but also caused an increase in luminescence of the light organ. They also appear to affect the permeability of the membranes which causes an increase in sensitivity to several compounds (1). This study contributes to the idea that there are many signals and complex interactions between V. fischeri and E. scolopes. (SHoUlD THIS BE IN THE FIRST PART OF THE PARAGRAPH AS SOME TYPE OF INTRO TO THE GENES?
The differential expression of genes between symbiotic and free-living strains of V. fischeri can illuminateHIGHTLIGHT the similarities and differences between the two environments in which they live, as investigated by Jones and Nishiguchi. Any V. fischeri which can colonize a light organ of E. scolopes are atHAVE a distinct advantage over their free-living relatives because of the nutrient-rich nature of the light organ, increased growth rates, and limited bacteriovory. This advantage must be seized by expressing the genes necessary for infection while V. fischeri are still living in open water. V. fischeri has been shown to participate in aerobic respiration while living in seawater, but has switched to anaerobic respiration when in the light organ, and researchers hypothesize that this is due to the large amounts of oxygen required for E. scolopes to bioluminesce, therefore removing oxygen from the light organ environment and only allowing anaerobic V. fischeri to persist (7). The results of this study show the importance of gene expression to V. fischeri both in seawater and in the light organ of E. scolopes.
Lipopolysaccharides (LPS) (MAYBE YOU SHOULD HAVE IDENTIFIED THE ABBREVIATION EARLIER IN THE PAPER WHEN YOU TALKED ABOUT THE LPS) have been shown by Foster, Apicella, and McFall-Ngai to cause apoptosis and, to a certain extent, morphogenesis of the cells in the light organ of E. scolopes. Two signals are believed to be responsible for this cell death, and LPS is only one. Lipid A is the likely component of LPS, which is encoded for by many genes. Researchers have found three pieces of evidence for lipid A; cell death was not caused only by V. fischeri, purified lipid A from other bacteria and V. fischeri both caused cell death in the light organ, and LPS with defective lipid A production did not produce the same cell death response when introduced to E. scolopes. SO MUCH INFORMATION IN THIS SMALL SPACE, COULD IT BE SEPERATED TO MAKE MORE SENSE. While any lipid A can cause the cell death within the light organ, the apoptosis is specific to V. fischeri because it is the only species of bacteria that is persistent within the light organ of E scolopes. It was discovered that the program of apoptosis was induced by LPS around nine hours after the initial exposure to LPS (4). This study shows that V. fischeri does have some effect on the light organ of E. scolopes. ((FIGURE 7, SOURCE 4))
E. scolopes to use bioluminescence as a way to hide from predators, there must be some control over the amount of light which is given off at a given time besides the control of the ink sac and reflectors. IN ADDITION TO CONTROLLING THE AMOUNT OF »»> In anotherACCORDING TO A study by Nyholm and McFall-Ngai, it was determined that light cues induce a venting of the contents of the light organ as a thick white paste. The relationship between eukaryotic cells in this paste and the V. fischeri cells appeared to be very close, with instances of V. fischeri attached to the outside of the E. scolopes cells. A good percentage of the cells exuded were viable as tested with stains and it is believed that this is part of the mechanism responsible for culturing live V. fischeri cells in seawater. In the natural environment, E. scolopes apparently vents its light organ at dawn and exudes 90% of the contents of the light organ, possibly in an effort to control the bacterial concentrations (12). This study gives a description of the contents of the light organ of E. scolopes and aides in accurately describing the microenvironment.

THE SYMBIOTIC RELATIONSHIP BETWEEN VIBRIO fISHERI AN EUPRYMnA IS USEFUL …….It may seem like the odds are stacked against Vibrio fischeri and Euprymna scolopes forming a symbiotic relationship, however this seems to not be the case. HOWEVER THERE ARE STILL QUESTIONS….(SOMETHING LIKE THAT) While scientists still don’t know the exact mechanism and reasons for this symbiosis, they do know some things about it. Studies have shown colonization to be very efficient, sometimes only taking a few cells to colonize the light organ. Advances have been made in marking V. fischeri so it can be better studied and understood while it is active in the light organ. This symbiosis appears to be very highly specialized and the appearance of the V. fischeri cells may play an important role in recognition by E. scolopes. The symbiosis appears to become increasingly specific to only accept V. fischeri cells into the light organ and allowing them to persist. It is believed that there are many complex signals and interactions between V. fischeri and E. scolopes and also that V. fischeri has some impacts on the cells in the light organ. Even though all the current research has helped us understand the relationship a little better, more research is needed to fully understand.
*The whole paper reeks of direct quotation, the author's voice is not consistent. The reader notices when direct quotes are being used. Need do spend some time developing concepts before writing and understanding the subjects before writing. The whole paper is choppy and lacks a good flow, but this does improve as the paper goes on. It would be a good idea trash the first half of the paper and rewrite. When writing it is common to take time to get into the "story" and find the voice of the paper, now just go back and start strong early. Tell the reader, don't suggest. The info is there just needs continuity and some work on relevance**

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