This paper focuses on the member of the Mollusca phyla, Crassostrea gigas. It goes into depth on how the genome of the oyster reveals how it has been able heat chock protein 70 and apoptosis inhibitors contribute to the organisms ability to survive in very stressful environmental conditions. this contributes to the GIGA project because the genome had to have been coded and that can go towards the GIGA coalition.

"Whole-genome assembly is now used routinely to obtain high-quality draft sequence." This supports the main idea of which GIGA stands for. A database for easy access to high- quality sequences of a certain organism.

This paper speaks of how parasitisms has developed in worms. Scientist have been able to figure this information out using the genome of 3 different tapeworms. They also identify treatments to ride humans of these parasites. This aids with the GIGA project because uses the genetic code of invertebrates, which can be a part of the GIGA database.

This paper is on ring phylum Annelid. With the information in this study Animal body plan evolution can be more defined which can help researchers better understand the evolution of metazoans. It mentions on how other organisms who were classified under different phyla should actually fall under Annelid. Showing how this paper can help researchers narrow down the evolution of these creatures consisting of invertebrates.

This study focuses on the Placozoan Trichoplax genome in order to understand the organisms that fall under this category. It focuses in where they stand in categories of animals as one of the first emerging animals. It can be used to study how the first animals ever looked on this earth and their DNA can present a lot more information that can still be found out.

This has to do with how arthropods are more closely related to aquatic invertebrates than other terrestrial invertebrates. This shows how evolution of invertebrates were different then originally thought and with the help of data from this study other scientist can know this and use it for themselves.

This paper focuses on how to two taxa are actually very similar to one another. This all contributes to the database for flatworms and the taxa they pertain to.

This study focuses on how the Human Genome Project has lead humanity to leap into the future and gain a ton of knowledge. This is more of an example of how the GIGA project can be of use. It goes into detail of what we have learned since the HGP was completed. This is more of a reflection of the possibilities the GIGA project can have for marine invertebrate genome.

This is an article that is justifying the reasons for mapping a genome and how it can be useful in advancing knowledge, research, and technology.

Focuses on the genome size of an early branching phylum. This is all scarce information so this study is important into better understanding the entire phylum which is pretty wide spread. This is perfect example of what GIGA is trying to prevent. They want to create a global database of information of marine invertebrates especially due to the lack of information on these creatures.

This project is essentially a genomic mapping project of the the microbes that live within humans. Another example of how databases are useful, which supports the reasoning for creating the GIGA project.

This is a perfect example of how creating a database of a genome can enhance the spread of information and the use of certain standards and information in order go further into research of the tick genome. Shows how the GIGA initiative can be of use.

This is an older paper, published establishing a new phylum Cycliophora. This contributes to database on new discoveries on marine invertebrates. it foes into depth on the larva of the organism and what makes it different form other invertebrates.

This article focuses on the ENCODE project and goes to explain its functions and what it can lead to. It focuses on learning and understanding the functional regions of the human DNA, but it makes you think that if this can work for humans why can it not work for any other species? This shows incentive to the GIGA coalition and what it can mean for researchers in the marine invertebrate field.

This paper focuses on how Tunicates are the closest living relatives to vertebrates. This study can assist from en evolutionary standpoint to picture a transition from an invertebrate to vertebrate creatures. This pertains to paper at hand because it will contribute to the database for GIGA.

This article focuses on the evolution of body plans of invertebrates. So due to the nature of the paper it refers to a lot of invertebrates and focuses on their development. The GIGA project focuses on invertebrates

The name of this paper is called "Green Fluorescent Protein as a Marker for Gene Expression." The marine invertebrate mentioned is the Aequorea victoria. This will contribute to the papers database. Can help with focusing on proteins of jelly fish.

This article contains the genome of the nematode C. elegans. The main purpose of GIGA is to obtain and database the genomes and infomration of the genome for others to use so this paper is a perfect candidate that reach this criteria.

This article speaks on the ENCODE project. ENCODE is a mass collection of functional parts of DNA. It focuses on the do's and do not's of database creation. This can serve as a source of how the creators of GIGA can go about creating their database, and steps they should take to ensure its success.

"Schistosoma mansoni is responsible for the neglected tropical disease schistosomiasis that affects 210 million people in 76 countries." It contains the genome for this species and goes into depth the characteristics of the genetic code. for instance it says that it contains a large amount of introns. Also shows how the information gathered has led researchers to begin new ideas of possible treatments and regulations of the disease.

This paper proposes a project so it isn't necessarily a topic that many people have researched. Due to the nature of the paper, the resources and past works will consist of published works that describe the pros of creating a database and examples of the types of works that will contribute to the GIGA project.

This database will only be able to be completed with the participation and commitment from the scientific community around the world.

This is one of the limitations that will be placed on researchers that plan on conducting research to contribute to this database. They restrict a certain proposed sampling to the non-insect and non-nematode ecdysozoans.

They propose a certain focus for researchers that wish to dedicate time to contributing to the database by stating that they should focus more on neglected groups of arthropods, specifically crustaceans.

GIGA aims to set standards for data acquisition and the processing of that data as well as the input of that data into their system. These standards will be progressively revised as better methods are discovered. These standards are to be used for a large variety of invertebrates. This standardization will allow for a more easily accessible and usable bank of information.

The project coordinators will also join with other networks to work together on future projects of common interest. They also understand that different countries have limits on the use of biological samples and thus their governments will be consulted with so that the international program is protected from any government agencies in the countries where the samples come from.

Once the data has been submitted by researchers, it will go through a quality control process to make sure that it reaches the quality and accuracy which the project requires. As well as to avoid duplicate data being published.

The currently available genome sequences at the time were reviewed and the missing phyla were taken note of. These missing areas in the so called "tree of life" were added to the list of species to be researched so that the data could be used to further other research.

The information gathered from experimentation will be unified by being submitted to the GIGA website, thus allowing researchers from all over the world to have access to the information at a moments notice. The website will also be used to host cooperative research projects that scientists from around the world could participate in and contribute data towards.

Selecting which organisms genetic information is to be gathered and recorded first will be determined at a meeting among researchers in the field. The priority of these organisms will also be determined by their accessibility to researchers as well as their ease of retrieving genetic information.

The purpose of the experiment is to create a genetic database of 7000 invertebrate species.

Read more on New York Times, which illustrates the founding and main goal in regards to the Human Microbiome projects.

The main goal of the project is to build an international community whose goal is to perform invertebrate research. This community will be used to avoid duplicate research and wasting time on studies that have already been conducted. They will also set in place standards by which the data must be gathered and presented so that is can be universally understood by everyone around the world and so that the data is accurate enough.

Read more in The Pharmaletter's article, where Zeltia's president has begun second-phase testing with the ET-743 anti-cancer drug for breast cancer and sarcomas.

Read more in New York Times, where China's overfishing led to the inevitable diminishing of multiple species, which led to the collapse of fisheries whose livelihoods depended on the fish.

https://www.nytimes.com/2017/04/30/world/asia/chinas-appetite-pushes-fisheries-to-the-brink.html

Referencing Box 1, this study was reviewed by the author classified this study as looking at population/species and as qualitative or quantitative estimate of flower or fruit production. The big conclusion of this study is that a rare species is seed-limited while dispersal limitation may play a secondary role in determining its abundance.

Referencing Box 1; The author of this paper looks at how plant phenology changes across succession in a community. Peres is studying keystone resources over many different seasons and how phenology changes over time. This aids in answering this papers research question of how phenology can be used in conservation to help keystone species.

Referencing Box 1; Schmidt and his colleagues focused on sustainability in harvesting non-timber forest products. They did this by analyzing flowering and fruiting time, as well as, the abundance and size of the fruits produced. This conservation effort was done using a large scale population control effort.

Referencing Box 1; Rossi and his colleagues focused their studies and conservations efforts on estimating carbon stocks and developing growth models in order to track and plan for future phenological changes and their effects on different tree species. Their models were developed by looking at tree growth rings within the trunks of various trees in order to look at the relative amounts of carbon dioxide intake and atmospheric carbon stocks at the time of the ring growth.

Garwood focused on seed germination in tropical environments in Panama. He was looking to help determine primary selective factors that controlled the timing of germination, the significance of seed dormancy, and to identify any major seed germination syndromes. These are all related to the success of a plant population and help scientists better understand and map out conservation efforts for species diversity.

Galetti and Dirzo reviewed the anthropogenic drivers of defaunation. They determined that direct drivers include hunting, poaching, and the presence of invasive species. Indirect drivers of defaunation include deforestation and fragmentation as a result of human activities. Some of the many consequences of defaunation are reduced ecosystem services and evolutionary changes in populations.

Bond and his colleagues reviewed previous research in order to draw parallels between the effects of fire and herbivory on ecosystems. They concluded that, like herbivores, fires select for particular plant traits. For example, small herbaceous plants that require a lot of light for growth and seed establishment are more likely to be wiped out by fires. They also suggested that species that thrive under conditions of repeated defoliation would dominate communities where fires are likely to occur.

Alvarado and colleagues analyzed the reproductive success of Madagascar sclerophyllous tapia woodlands in relation to fire frequency. They determined that more frequent fires resulted in increased latency of reproductive phenological events (flowering and fruit production in particular). Additionally, frequent fires reduced the overall number of individuals producing flower and fruits. It should be noted that the fires mentioned in this study were related to human activities.

Referencing Box 1; Ali and his colleagues established a calendar for the collection of seeds and other plant resources in order to properly manage the conservation of genetic resources in natural plant populations. This was done throughout population and species scale conservation. They made direct ground observations of plant phenophases (leafing, flowering, fruiting) and the environmental factors that effected these actions. Advancements in this conservation can be seen in efforts such as seed banks.

Ali and his colleagues focused their studies on the species diversity and conservation of various bird communities in Pakistan. This is important in understanding the relationship between the animal organisms within an ecosystem and their neighboring plants in order to obtain an optimal amount of species diversity within the ecosystem. This helps answer the question: what are the influences of climate change on phenology and what are the implications of those influences within a tropical environment?

Alberton and colleagues tested whether or not digital cameras (used as a near-surface monitoring system) can be used effectively for measuring phenological changes in plants (specifically leaf color change). They determined that digital cameras are a reliable tool to monitor change in regional leafing patterns. This means that on-the-ground phenological observations of individual plants may no longer need to be used. However, the authors suggest that both methods, on-ground and near-surface monitoring through photographs, should be used to collect the most accurate picture of phenological change.

The application of Land Surface Phenology may become increasingly important as technology advances. As scientists continue to better understand the drivers of phenological changes in the past, it can help us to plan for future changes within complex ecosystems such as tropical ecosystems.

The authors analyzed how phenology can aid in conservation science. With understanding the importance of this knowledge, scientists have laid out goals for future phenology studies, which includes creating a global model for monitoring changes in phenology to improve biodiversity. The key finding of this paper is understanding the importance of phenology and how it can help in future management discussions.

Although there is a lot of focus on what an ecosystem can offer us within society, in terms of a tropical ecosystem, managers of the specific services need to take into account the relative abundance of the various resources within the ecosystem. This is important in order to healthily sustain the diversity within the ecosystem while at the same time maximizing the productivity within the ecosystem for human use.

The causes for latent reproductive phenology in plants have yet to be determined. However, scientists can now use digital technologies (like digital cameras and remote sensing) to capture phenological events as they occur. This gives them the opportunity to examine changes without having to worry about the amount of time they have to analyze those changes.

Using three or more dimensional spaces in imaging techniques.

Imaging used to collect and process information across different wavelengths in the electromagnetic spectrum. The goal of hyperspectral imaging is to locate objects, identify materials, or detect processes. For example, this type of imaging has been used to detect early warning signs of disease in agricultural settings. This aids phenology in how individual species are identified and analyzed.

In plants, the layer of actively dividing cells that is responsible for secondary growth of stems and roots.

A keystone species is one that plays a particularly important role in an ecosystem; a species in which other species in a shared ecosystem depend on for survival.

The ability of an organism to withstand extreme weather conditions (such as drought).

The inability of an organism to withstand extreme weather conditions (such as drought).

Understanding the life cycle of plants helps us understand part of the world's plant diversity. This shows how phenology can make contributions to conservation biology.

Conspecific: individuals belonging to the same species.

Coexisting conspecifics: two species living together in the same habitat.

Extreme changes in climate decreases organisms' (of the same species) abilities to live together in the same habitat. This could be due to competition for resources.

Barriers that prevent different species from interbreeding. These could include isolation between habitats (physical barriers), behavioral isolation (differences in mating rituals), or mechanical isolation (incompatible reproductive structures).

Variation within a species group or between individuals of the same species.

A large naturally occurring community of plants and animals in a specific climate. Some examples of biomes include the tundra, forests, grasslands, and deserts.

A group of organisms that evolved from a common ancestor.

The complete mass of a living organism or the collective mass of entire community of living organisms. Biomass can be measured in total weight (with water) or dry weight.

The interbreeding between two individuals of a different species or variety of species.

Phenology can be used as a tool to aid in management decisions for plant restoration. This is a great example of how phenology can help make contributions to conservation biology. This study looked at a forest that developed under the selective pressure of fire which allowed scientist to study the forests reproductive phenology and how it was effected by the fire. They found that fire effects the timing of plant reproduction at community and landscape levels. This is a great example of how plant phenology can be used as a tool to aid in management decisions for plant restoration. This is a great example of how phenology can help make contributions to conservation biology.

The assessment of an organism's functions based on the outer appearance of the organism.

Relating to the classification of organisms based on their shared characteristics.

Two organisms of different species depend on each other for survival.

The loss of organisms from ecological communities.

Scientists are trying to gain an understanding on how relationships between plants and insects are affected by the changing climate. This helps us to understand how phenology can be used to study the effects of climate change.

A forested ecosystem that receives heavy rainfall and contains primarily deciduous and some trees.

A folivore is an herbivore that primarily consumes leaves (foliage).

Biocontrol measures or biological control is a method of controlling pests using natural enemy organisms. For example, mites, insects, and pathogens have all been used to eliminate invasive species.

Insects that feed on green plants.

This study looks at how climate change alters the rate of leaf senescence in which drought advances it and warming decreases it. This change affects the flow of nutrients within an ecosystem. This information helps us to understand how shifts in climate activity influences plant phenology, such as losing leaves sooner and disrupting the nutrient cycle.

The process by which autotrophic organisms use the suns energy to make its own food. An autotroph is an organism that does not rely on anything but itself for ways of gathering essential nutrients. Phenology can change the rates at which photosynthesis in tropical plants.

The process by which CO2 is removed from the atmosphere and stored in a physical structure (e.g. oceans, terrestrial ecosystems, geologic formations). This process can occur naturally or artificially.

The rate at which organic matter is produced in an ecosystem through photosynthetic and chemosynthetic organisms. For example the amount of carbon that is stored within a tree as a result of photosynthesis. Phenology can determine this rate.

The deterioration or aging of the functional characteristics of an organism. Leaf senescence is the last stage in leaf development. During leaf senescence, nutrients are eventually reused by the plant in other areas. For example, nitrogen from lost leaves is later used for the creation of stem proteins. This is key for understanding how plants grow and how plants cycle energy and matter.

The appearance of a large number of new leaves in a relatively short period of time. New leaves are produced simultaneously on all branches of a bare plant.

As concern for extinction rates rises, the need for conservation efforts to counteract these rates grows as well. Areas are being mapped out throughout Earth that are ranked by their ecological and economic significance for sustaining life on our planet. For more information about applications of conservation science, follow this link to see research and applications done by Groves and his colleagues. (https://academic.oup.com/bioscience/article/52/6/499/240341)

The process of managing an ecosystem to achieve maximum diversity in plant species in order to have a healthy fitness level within the ecosystem. Understanding changes in plant phenology will be necessary in order to develop the most effective conservation practices.

Fig. 2. (A)

The abiotic and biotic effects of human activities on plant life cycles. Abiotic influences as a result of human activities include climate change, modifications of geochemical cycles, and frequency of fires. Biotic influences as a result of human activities include habitat loss and fragmentation, hunting, and species invasion. These factors collectively influence plant phenology, including leafing, flowering and fruiting, and seed germination and establishment.

The collection and analysis of ecological data by the public alongside scientists.

A scientific method of dating historical events using the growth pattern of tree rings. These rings can be used to analyze the atmospheric conditions that would've existed during a specific time period.

A collection of dried plants.

Changes in community structures that occur at the outermost boundaries of a habitat. The edges of a habitat are its first defense against extreme weather conditions and other harmful disturbances. Phenology can help determine how edges in an ecosystem change over time.

Habitat fragmentation is a direct cause for the extinction of many plant and animal species. However, a recent study found that timely actions could easily slow extinction rates and save species as we implement more effective conservation efforts.

Read more in Science Daily: https://www.sciencedaily.com/releases/2016/07/160725090002.htm

Habitat loss due to the division of large, continuous habitats, into smaller isolated patches of habitats.

Hierarchal levels within a food chain. Bottom-up trophic organization is ordered as 1.) producer, 2.) primary consumer, 3.) secondary consumer, and 4.) tertiary consumer.

The role that an individual organism has in its respective ecosystem. An individual's niche includes its methods of survival (acquiring food, shelter, etc), how it reproduces, and all other interactions it has with the abiotic and biotic factors in its environment. Changes in plant phenology can affect the ability of organisms in a community to live and survive amongst each other.

The coexistence between two competing species in a community results from stabilizing (different niches) and equalizing forces (similar fitness). Equalizing forces reduce differences in fitness between two or more species, which makes competition relatively equal between them. Stabilizing forces promote greater competition between individuals of the same species as opposed to competition between two or more separate species.

Contributions from the natural environment that benefit human populations. In this case, the medicinal value that may be present in the plants within the tropical environment.

An organism that feeds on plant material.

Organisms that break down organic matter, primarily detritus. Detritus includes dead organisms and fecal materials.

Organisms that break down organic material, primarily the remains of other dead organisms. An example is the denitrification done by bacteria in order for plants to obtain natural nitrogen.

Whether or not plant reproductive processes (e.g. flowering) occur at the same time in a particular population. Synchrony of reproduction can either be advantageous or disadvantageous for a plant. For example, plants that reproduce within the same time period increase the number of potential plants with which an individual can exchange genes. However, if a large proportion of plants in a population are reproducing at the same time, seedling death could increase as a result of density-dependent processes.

The amount of time within a 24-hour period in which an organism is exposed to light; generally the length of a day.

Van der Sleen and colleagues determined that higher concentrations of atmospheric CO2 (as a result of human activities) increase plant photosynthetic rates and improve plants' water use efficiency. Increased CO2 increases the rate at which carbon can be used by plants as carbohydrates in light-independent reactions. However, photosynthesis rates eventually plateau as a result of another limiting factor (light intensity, temperature, etc).

Biological, geological, and chemical processes in which elements and other substances are moved through living systems and the surrounding environment.

Chuine and Beaubien used a process-based model (PHENOFIT) to predict species distribution. This model focuses on survival and reproductive success in relation to climatic variations. They determined that the phenology of plant species as it relates to variations in climate is a major determinant for species distribution. This model could potentially be used to predict the future distribution of plant species and make adjustments to our current practices accordingly.

The gradual increase in the overall temperature of Earth's atmosphere as a result of the greenhouse effect (trapping of the sun's warmth in the atmosphere), increased atmospheric CO2 and other greenhouse gasses, and pollution.

Living and non-living factors control what physical attributes are expressed in a plant species, due to changing environmental stresses.

Rosenzweig and colleagues noted that some major changes in phenology can be attributed to climate change. For example, rising oceanic temperatures are known to impact marine and freshwater biological systems in terms of phenology, migration, and community composition in algae, plankton, and fish.

"Construct an argument supported by evidence for how plants and animals (including humans) can change the environment to meet their needs"<br> This paper constructs an argument on how plants phenology changes due to the warming climate and how they adapt to these changes. Link: https://www.nextgenscience.org/pe/k-ess2-2-earths-systems

Relating to time. Temporal ecology focuses on the timing of ecological processes; for example, the timing of flowering events.

Relating to space. Spatial ecology focuses on the distribution of species. By understanding how the distribution of species changes overtime, scientists can better understand the ecological influences of climate change.

Invasive and exotic species are organisms that are either native or non-native to a particular ecosystem and could potentially cause harm to systems within that ecosystem.

Disturbances (in this case, ecological) as a result of human activities (e.g., agricultural practices, technology, and urbanizations).

A relationship between two organisms of different species in which each benefit from the other. For examples, yucca moths lays their eggs in the flowers they pollinate; the eventual yucca larvae consume the flowers' seeds.

The number and abundance of the various species living in an ecological community. Species abundance is the number of a specific species relative to surrounding species within that community.

Research question:

How can phenology be used to further our knowledge and success in conservation biology? What are the influences of climate change on phenology and what are the implications of those influences within a tropical environment?

A subfield of biology that focuses on the evolutionary processes (mutation, gene flow, genetic drift, and natural selection) that eventually resulted in the diversity of life on Earth, originating from a common ancestor.

The study of the relationships between all of the organisms within an ecosystem and their surrounding environment. Like in this paper looks at how plants interact with their environment and the changing climate.

The study of the interactions between living organisms and their surrounding atmospheric conditions. Some examples include, the relationship between agricultural yields and weather, plant tolerance to extreme weather conditions, and the impacts of pollution on plant species.

Changes in system processes within Earth's biosphere. The system includes land, oceans, the atmosphere, biodiversity, and the impact of human activities on key processes. An example is the effect of rising atmospheric carbon dioxide on sea levels and permafrost melting.

The study of life cycle events in living things; more specifically, the timing of these life cycle events. For example, a phenologist might study migratory patterns, hibernation cycles, seed dispersal, and dormancy. In this study, phenology is used to help scientists understand the effects of a changing climate.

A paper published in 2009, concluding that different exposure histories results in different levels of methylation.

A study in which the effect of the marine toxin Okadaic acid (OA) on certain genes that are related to cancer. In the study it was seen that there are alterations to the genes that could explain the relationship of OA to cancer.

Sunda has previously concluded that exposure to brevetoxins limit growth

Murell and Gibsons reviewed the effect of Red Tides on human health, particularly on the effect it has with DNA strands. It further supported their reasoning into investigate on Histone 2 dynamics during the toxic experiment.

Flewelling published a paper pinpointing areas in which saxitoxin (HABs) were found in food around the world. The Southeastern U.S was one of these areas in which saxitoxins were found. (DZ)

Also the paper talks about the effect of Karenia brevis's brevetoxins on food webs and the effects.

Dame's paper studies the interactions between the grazing of bivalves and their role in their respective environments (specifically, carrying capacity).

Cardozo focuses on the effects of the biotoxins released by the algae. From these effects the experiment is conducted upon what the toxins do on marine life organism in which the toxic effect is a natural defense mechanism.

A paper describing the dinoflagellate, karenia brevis. The paper explains the biotoxins released by it, how the biotoxins build up in shellfish, and what damage it does to other marine organisms.

The author further determined that due to the cause of the toxins released by the bacteria from the Red Tide it can influence methylation patterns of DNA. By influencing methylation , there exists a relationship in environmental stress and epigenetics. As the amount of time increases with the concentration of toxins remaining stable within the sample, the less there are accounts of genome wide DNA methylation.

Ultimately, the authors have observed a positive correlation between H2A.X and Oxidative DNA damage, in such that H2A.X increases in the presence of Oxidative DNA damage (due to the presence of brevotoxins). Based on these results, they have concluded that H2A.X is a good indicator of oxidative stress.

Reactive oxygen species inhabit the cell and can result in harm and lead to irregular protein and RNA transcription. By being unable to remove and detoxify the reactive oxygen species, then an imbalance between the cell and body is created as a source of stress which can lead to further detrimental effects.

The fixed position of a chromosomal unit which can carry a specific gene or origin of a phenotype trait.The position is usually used in order to determine what other factors attribute to a characteristic change.

Previously, a link has been discovered between the methylation of genes undergoing stress, and the ability of one genotype to produce more than one phenotype in order to adapt to its environment.

The authors found that the histone varaints that were derived from the major histones such as H2A.X, were also passed down as an evolutionary trait. The authors also determined that the antibodies could detect the histones in the oysters, and is signified as a possible method to detect further damage done by the toxic.

Associated.

The phosphorylation of H2A.X appeared to be positively correlated to the exposure of K. brevis to the Easter Oysters.

An analytical technique to precisely measure and observe the certain behaviors of an factor or subject. The results is typically an intensive property of the target of the assay in numerical terms.

The end of an amino acid chain signified by a carboxylic group.They are usually the end of protein synthesis , and has signals in the shape of sequences to retain and sort certain protein.

A method to detect and analyze specific amino acids sequences in certain proteins. The proteins are extracted which is then used with this analytical tool to determine the antibodies they bind to.The sample is then put under electrophoresis and transferred onto a membrane.

The scientists further studied the relationship between histone proteins and stress levels after acknowledging that a possible cause and effect exists.

By discovering that antibodies connected to the histones were valid, it also proved the oyster to be the best model to test on.

Because of lack of change over the course in the experiment, it is concluded that there is no response from the oyster in K. brevis in terms of gene modification in H2A.X, H2A.Z, and macroH2A transcription.

As described by past research of Talbert and Heinkoff, they're are a variety of epigentic mechanisms that are influenced by different amounts of stress drawn by the environment. One of these are the now testing of the recently discovered histone variants and and how each histone respond to environmental stress such as toxins.

The results showed that the simulation was an accurate representation of what happens during HAB.

The authors recorded and purified DNA from the gill tissue of the oysters in order to measure DNA methylation.

Later, the DNA sequences were amplified.

By using PCR methods, the samples were digested in order to asses the patterns of methylation and used to identify loci using Gowers Coefficient of Similarity.

The purpose in the experiment was conducted in the extraction of histone proteins. By using classic centrifuging and electrophoresis techniques, the histone proteins were separated in order to retrieve the different types of anti-proteins. The antibodies were then analyzed with the Western Blot using the antibodies.

The collection of the the oysters were at different time intervals in order to monitor and view different relationships between the algae concentrations and oyster infection number.The gills were the main focus of the time intervals to indicate how much of the algae was found in the oysters system.

The state of being repelled from water due to the lack of attraction. This is normally caused by shifting polarities of cells and molecules.

A 24h simulation using a culture of K. brevis and the eastern oyster specimens.

They were fed less prior so that during the simulation they would actively feed.

There were 4 time points where data was collected: 0hr, 3hr, 5hr, and 24hr.

The oysters were opened and the gills were flash frozen for later examination. This is because the brevetoxins contact the gills first and thus would experience DNA damage first.

Explains how oysters were collected and kept.

Collected: Rookery Bay National Estuarine Research Reserve, Naples FL

Kept: In lab tanks with controlled conditions. Fed twice a day.

Multiple research studies previously conducted show that brevetoxins are produced during FRT's.

Gavery and Roberts view the oyster as one of the best ways to speculate and monitor the progress of DNA methylation. They used this oyster model to view how the toxins can influence the rate of methylation and how stress affects epigentics factors.

In one experiment, one of the authors (Suarez-Ulloa) had previously studied the cause-effect relationship between environmental factors and subsequent epigenetic modifications triggering adaptive responses in marine invertebrates.

Large scale death.

Sentinel organisms are defined as organisms used to detect risks for humans through advanced warnings. In this case, for the Eastern Oysters. Ex: Canaries in coal mines.

In previous experiments conducted on Eastern Oysters, the author has successfully used bivalve mollusks as sentinel organisms.

The worst of a specifed thing (HABs).

Toxins are known to disrupt cell actions. The scientists expand on this idea by using the experimental model of an oyster because oysters can be used to determine epigenetic modifications passed down through generations, ultimately showing red tide effects.

Suspended in air.

Another way of saying a model or figure.

a substance produced by an organism. An example is when there is an accumulation in shellfish. If the shellfish is ingested by a human it can cause paralytic shellfish poisoning (PSP) which can cause damage to the nervous system and can paralyze muscles.

When aquatic animals and plants are raised and grown for food.

As one of the consequences in the bloom of red algal in the Southern East coat waters, will lead to changes in the marine ecosystems that inhabit the waters by releasing toxicity as Harmful Algal Blooms.

Read more at: https://oceanservice.noaa.gov/hazards/hab/

Another news story about possible epigenetic effects on marine life. This news story focuses on the current effects of the 1989 oil spill in Alaska on current herring populations.

https://www.newsdeeply.com/oceans/articles/2017/10/13/boom-and-busted-lessons-from-alaskas-mysterious-herring-collapse

When a phosphate group is added to a compound. Many times the addition of a phosphate results in a conformational change which can activate or deactivate the compound.

Yimizu, Chou, and Bando initially studied the structure of brevetoxin, and deemed it the most potent toxin found in Florida Red Tide.

González-Romero has previously conducted research on the stability and function of the H2A protein, concluding that it participates in the unfolding of chromatin fibers and therefore modifying enzymes and polymerases that facilitate gene expression.

Proteins found in chromatin.

The physical outward expression of a gene due to an organism's genotype.

Genotype is based off of the coded alleles of an organism.

DNA is not changed. Instead its the genes that are expressed or inactivated change in an organism.

Read more in NBC News:

https://www.nbcnews.com/science/environment/massive-red-tide-threatens-florida-beaches-n178661

Brevetoxins are neurotoxins produced by Karenia brevis.

These neurotoxins accumulate in shellfish and is the cause of neurotoxic shellfish poisoning (NSP).

NSP will cause disruption of neurological processes in humans.

Proliferation is the rapid increase in cell growth or organism reproduction.

Algal proliferation, in this paper, is the rapid growth of a the dinoflagellate Karenia brevis.

In DNA Methylation, a methyl group is added to the DNA in order to change the activity of the DNA segment. (For example: turning an "off" gene "on").

In this study, it was found that a small amount (17%) of the caterpillar (aka Lepidoptera) were found to be feeding on the Ficus in both the highlands and lowlands.

The study was done on the different species of caterpillar that fed in the highlands, in the lowlands and those that didn't feed on ficus as well. The results showed them which caterpillar species was dominant on the species on ficus in the lowlands and which were dominant on the species of ficus in the montane habitats/ highlands. The ones that were found to be dominant in the lowlands, typically did not feed on the highlands and vise versa.

A Comparison of Caterpillar (Lepidoptera) Assemblages on Ficus Trees in Papua New Guinea

A variable similar to the independent variable, that is observed and can help increase the results of the experiment.

This paper is a different version of the same type of research. This study provided backup information to further prove what was being stated and identified in this research.

These express results for another question posed that clarifies variables that pertain to the specialization of the main topic. What is important is to grasp that this variable was accounted for in the process of understanding how specialization works in P. subserratum.

This information clarifies a question posed in the introduction. This knowledge fills the gaps of different variables that could affect the main goal of specialization.

It stands for Two-dimensional non-metric multidimensional scaling ordination and is used to visualize how similar individual cases of a dataset are on a small axes.

Example:

Chlorophyll is a green pigment that is found in the chloroplasts of algae and plant cells. It works well to absorb sunlight which is then used to make carbohydrates, through a process called photosynthesis.

Invertebrates that are grouped together because of their unsegmented bodies, preferences for aquatic or damp-marshy habitat and usually the presence of an outer shell. Some examples are snails, octopuses, and mussels. In this experiment, they used the marsh slug (Deroceras laeve).

A perching bird, as classified by certain criteria pertaining to body morphology and positioning of toes. Passerines makes up half of all bird species.

The results show that there are much higher numbers of breeding seabirds on fox-free islands than on infested ones. This makes sense because foxes are predators of many types of birds which would lower the abundance of mating birds. This decrease in birds also had effects on the amount of guano being distributed across the land. This number decreased and in turn affected different nutrients that are derived in the soil from the bird guano such as phosphorous. Fox-free islands saw three times more soil phosphorus than fox infested islands. In this experiment, there is a chain effect of sorts going on where the presence or absence of foxes affects sea bird populations, which then affects guano inputs to the island and the soil nutrients derived from this are dependent again on sea bird populations that distribute the guano.

In this experiment, grids were designated over the island and 30 x 30 meter plots were established to sample within. In these plots the total soil nitrogen, phosphorous, amount of stable nitrogen isotope, and percentage nitrogen were sampled across grasses, forbs, dipterans, arachnids, passerines, and mollusks to determine how much of these nutrients were derived from the ocean. Organisms and soil that derive their nitrogen from a local source will have fewer amounts of nitrogen isotopes than those that get their nitrogen from higher trophic levels as is shown in Figure 3.

A general term to describe any herbaceous flowering plant that isn't a grass. In this experiment, they observed the species Achillea borealis, commonly known as boreal yarrow.

The paper by N. G. Hairston, F. .E. Smith, and L. B. Slobodkin, "Community structure, Population Control, and Competition," observed what and how organisms are limited by their respective resources. Producers may be limited by an array of variables: light, water, and nutrients. These limiting resources can cause a change in competition throughout the trophic levels. In this paper, the limiting resources are the nutrients from guano. As the foxes prey and decrease the number of seabirds visiting the island, the dispersal of guano also decreases on the island.

The phenomenon of a species or organism dying off or not being found in a specific area at all while it is still found elsewhere. If the foxes were allowed to persist uncontrolled, the sea birds may die off in the Aleutian Islands.

Overall, the study found that the introduction of foxes turned the once-grassland into a tundra with less productive plants in its place because of the nutrient deprivation caused by fox predation on the birds, who are the main nutrient distributors on the archipelago.

This shows the indirect effects that predation can have on ecosystems that rely so heavily on nutrient distribution from other living organisms, such as the seabirds. This also provides further evidence that trophic cascades do not only have to be top down; predators do effect herbivory, but there can be indirect effects from predators to plant communities through nutrient deprivation from predation on nutrient source organisms.

Tundras are flat and treeless swaths of land that have soil that is permanently frozen; in this example, it is bordered by the sea.

In this experiment, nutrients were added to a community that represented the fox-infested islands which increased the grass biomass and also created a more grass dominated environment overall.

The nutrient additions were meant to represent the spread of guano by the seabirds. In the fox-infested islands the seabird populations were scarce, which decreased guano accumulation. Therefore, the added nutrients represented the guano production by seabirds in the absence of seabird on the island that is fox-infested.

These nutrient additions are similar to the nutrient states of fox-free islands and show what the changes in ecosystem could have been like during the introduction of foxes.

In another experiment, they tried to mimic the disturbance in soil of seabirds burrowing, this negatively impacted the grass biomass and it was shown that fertilization by itself had the greatest positive effect on grass biomass and distribution. This helps explain the higher incidence of grasses in the fox-free islands.

A computer system that is designed to show geographical areas in different ways and can be manipulated for the collection of data. An example is the map of fox-free vs. fox-infested islands in Fig. 1 and the map of concentrated species in Fig. 3.

This figure shows the islands that were studied and their relative position on Earth. There are 9 fox-infested areas shown in red and 9 fox-free areas shown in blue, the sample size of islands is the same so the results cannot be attributed to the sample size difference. The yellow dot is the location of fertilization experiments.

This is very broadly what the experiment seeks to discover through looking at fox-infested and fox-free islands. This experiment is designed to assess effects of sea bird densities on soil nutrients and composition, plant abundance, primary productivity, and the flow of nutrients from lower organisms to higher ones (i.e. from plants to herbivores to carnivores.)

A geographic region of suitable habitat for a specific organism/organisms that is surrounded by unsuitable habitat. Therefore it is isolated via environmental conditions; in this case, the habitat of both the birds and foxes are the islands on which they reside that are surrounded by the ocean.

Both the bird species and Alopex lagopus are bound to their corresponding landscape. The foxes are trapped on their respective island because they lack the ability to swim to a new location. The birds are unable to use the same islands as Alopex lagopus because of the predation of Alopex lagopus. Therefore, both species belong to an insular ecosystem because of the unsuitable landscape around them.

Plant species on the archipelago are dependent on the nutrients from guano. Guano, bird poop, is rich with minerals and nutrients, like Nitrogen and Phosphorus. The plant species richness has been found to increase as the nutrient availability increases.

In the paper by J. Halaj et al. food webs are studied using the ratio of an isotope of nitrogen and carbon to see how much of it exists in different trophic levels and how the food web interacts both above and below ground. This study shows more of the direct effects of top down tropic cascades which are shown by the predation of sea birds by foxes in the study by Croll which also elaborates on the indirect effects of predators on the environment through the predation of sea birds decreasing nutrients to the system and changing the plant community structure. There is also isotope testing being used in this study to see its distribution across different species and soils between the fox infested and fox free islands.

According to Hairston et al. the populations of producers, consumers, and decomposers are limited by the resources they depend upon which are subject to limitation by the tropic levels both above through predation and below through low abundance. These limitations of herbivores by predation is helpful to the plant communities below as well. The Hairston et al. study provided the basis for the study of direct effects on top predators to terrestrial systems but this study further looks into the indirect effects of predation on plant communities. Providing evidence for indirect effects of nutrient deprivation due to predation using a large scale system that has room for replication.

Different genetic sequences melt at slightly different rates. Therefore, they can be analyzed using these melting point curves, where fluorescence is plotted on the y-axis and temperature on the x-axis.

If the DNA strand is composed of many guanine and cytosine bases, it will take a higher temperature to break the hydrogen bonds apart as opposed to adenine and thymine bases. This is why the E2 clade fluoresced at a higher temperature than the other clades.

A technique used in laboratories used to separate macromolecules based on size.The term refers to movement of charged particles in a fluid or gel under the influence of an electric field.

An instrument used to test for single nucleotide polymorphisms (SNP's) (common genetic variations among individuals) between DNA fragments.

Denaturing High-Performance Liquid Chromatography (dHPLC) is a technique that is used to separate chemicals in a mixture. dHPLC has been used on 19 patients with auto-inflammatory syndrome suspicion to spot polymorphism in the gene MVK. This technique is a quick and low cost process in order to obtain accurate screening of the mutations.

The processes used to create copies of DNA fragments.

PCR is a technique in the laboratory in which short sequences of DNA are amplified. Real-time PCR has been used to rapidly detect Salmonella from cloves. It has also been used to compare three different methods to extract DNA.