A model-based measurement utilized in data sets of phylogenetic comparative analysis made up of qualitative traits observed of species related to the same phylogenetic tree.

Hereditary information that offsprings receive from their parents which makes them unique.

The evolutionary track an organism has taken that sets it apart from the rest.

Unable to be stopped; unpreventable.

The new development of something of high value and/or importance.

Links that appear within a given post.

An Application Programming Interface (API) is a set of clearly defined methods of communication between various software components.

A community of interacting agents and their environment. In the context of this paper, the ecosystem has interacting agents (aggregates and followers), an environment (the Internet), and even predatory entities (police cybergroups, individual hackers, and website moderators).

Records of the same variables, which in the case of this paper are hashtags that may suggest ISIS-related activity, observed over a given period of time.

Remove or dissipate such as by melting, vaporization, erosion, etc.

The tendency for the substance to evaporate.

An un-selective approach to the cell membrane function. DEET has a selective effect on the cell membrane function.

Lasting only for a short time.

Olfactory receptors are neurons that are responsible for the detection of odorants which allow the sense of smell. Olfactory receptors are one of three types of receptors used by mosquitos, the others include ionotropic receptors and gustatory receptors.

The response to an antennal stimulation in which an insect stick out their proboscis, or tongue.

A substance in certain that adversely affects insects or other animals that eat them.

Properties dependent on the chemical composition or structure of the material.

A measurable/numerical method to gather data.

RNA interference is a gene silencing mechanism that is triggered by the injection by introducing double stranded RNA into the cells.

Cues related to eating and the sense of taste.

An organic compound with a distinct earthy flavor and aroma produced by a type of Actinobacteria.

A type of genetic engineering in which DNA is inserted, deleted or replaced in the genome.

Macromolecular pores in the cell membrane that form an aqueous pathway. Allows rapid flow of cations based on their electrochemical driving force.

A molecule that binds to a central metal atom to form a complex.

Derived from a different organism.

Tiny openings in the membrane that allow specific ions to pass through.

An arthropod sensory organ that consists of a modified cell or small group of cells of the cuticle, typically hair- or rod-shaped cuticle.

A chemical substance emitted by an organism and detected by another of a different species that gains advantage from this.

A field of study that uses genetic methods to investigate nature and origins of behavior.

Early in the discovery/ knowledge of the DEET modulation of multiple olfactory receptors

determined

Melanin

THIS IS ME ANNOTATING.

This is me looking at my annotation as I annotate.

A tough outer protective layer.

DNA synthesized from single-stranded RNA.

.

A genetic disease affecting the growth of hair, teeth, nails, and sweat glands.

Caudal: pertaining to the tail

Spinal: pertaining to the spine

Cervical: pertaining to the neck

Ventral: pertaining to the underside or abdominal part of the body

Humeral: pertaining to the humerus (a bone in the arm)

Femoral: pertaining to the femur (a bone in the leg)

Because an RNA sequence is read three bases at a time, if the number of bases deleted is a multiple of three, it will not change the reading frame.

A thick, platelike structure in the ectoderm that is a site of development in early embryos.

Members of the order squamata, or scaled reptiles. They are the largest and most recent order of reptiles and comprise all lizards and snakes.

A thickening of the ectoderm marking a site of future development of hair follicles, feathers, or teeth in the early embryo.

A transitional fossil that shows a transitional form between one species and another.

A cell that secretes sebum, an oily substance that waterproofs and lubricates skin.

To change to a form that contains keratine, a fibrous protein found in hair, nails, and hooves.

Sections of tissue that are made in a cryostat, a device that keeps samples at a very low temperature to preserve them.

A group of signaling molecules responsible for coordinating development in many different parts of the body.

Exists today.

A study is referred to as experimental if it contains random allocation of participants to experimental conditions or treatments in which a variable of interest is manipulated. Such experiments can allow claims that the manipulation has caused changes in outcomes.

For example, if we wanted to study the influence of rewards during class on students’ biology exam scores in an experimental study, we would randomly assign students to two conditions: In condition 1, students would receive candy bars for active participation in class, whereas in condition 2, students would not receive any candy bars.

Then we would observe the exam scores for each group of students, to judge if our candy-bar treatment improved the scores compared to the no-candy-bar control condition. We could then conclude if rewards cause better exam scores in this context.

A technique that allows a gene to be shut down and made nonfunctional. Researchers knock out genes to see what happens when they aren't active.

Plastic debris is plastic waste that has accidentally or deliberately been released into the marine or terrestrial environment.

Waste management is the set of systems required to manage waste from when it is created to when it is finally disposed of. Steps of waste management include collection, transport, treatment, and disposal.

Plastic resin beads are the raw materials from which items such as plastic water bottles are made.

In this context, persistence means that the plastic materials are very stable and resistant to degradation.

Mitigation is an action that reduces the severity or seriousness of a problem.

Extrapolation is the process of extending a graph or range of values by predicting unknown values from trends in the known data.

Who or what should be blamed when something happens?

Protect the driver at all costs

A temperate biome that is slightly warmer than the global average, marked by distinct seasons, sometimes with dry or rainy seasons. The forests are, as the name implies, of mixed composition. In this particular biome the predominant trees are broadleaf (ex: maple or oak) and conifers (ex: pine).

A biome found in temperate regions with warm summers, cool winters, and enough precipitation to support coniferous trees ("evergreens").

Shrubs and plants that have adapted to survive in locations with very low amounts of liquid water, including deserts as well as regions with ice and snow.

People receive a wide range of benefits from the environment, and these benefits are sometimes referred to as "ecosystem services."

The lowercase of the Greek letter sigma is used to indicate standard deviation. Here's a short video explanation: https://www.youtube.com/embed/MRqtXL2WX2M

These scenarios are different models of atmospheric greenhouse gas concentrations. Descriptions of each model can be found in a special issue of Climate Change from November 2011: https://link.springer.com/journal/10584/109/1/page/1

An agreement under the UNFCCC framework addressing three main aims:

• lessening greenhouse gas emissions,
• preparing for and negating the effects of climate change, and
• financing dedicated to accomplish the previous two aims.

Under the agreement, countries set targets to lessen global warming, develop plans to meet those targets, and report on their progress.

The agreement was negotiated in Paris at the 21st Conference of the Parties of the UNFCCC in December 2015 and adopted in 2016.

Pollen grains are made of materials that are highly resistant to breaking down in the environment, so they can be found in sediments going back thousands of years (and even further in the fossil record). The grains are diverse and researchers can identify the plant types they come from by examining them under a microscope. This allows researchers to see which seed-baring plants were in a given location in the past by taking sediment core samples and examining the pollen grains in each layer. The deeper the layer, the older the layer.

The geographic area surrounding the Mediterranean Sea. There are many different sets of boundaries for this region used by researchers, historians, and others. For this paper, the authors use the region between longitudes 10°W to 45°E and latitudes 28°N to 48°N. The region can be seen in Figure 3, and an approximate map of the region is included here.

Tooth fused to the inner edge of the jaw. They are loosely attached and can regenerate if lost.

Part of the limb farthest from the body, such as the hand or foot.

The scaleless bearded dragons have two copies of the same alleles (Sca). This gene is codominant, meaning both alleles are expressed even in heterozygotes.

Placed on top of one another.

The use of antibodies to detect specific proteins in a tissue (using the principle that antibodies will selectively bind to certain antigens).

A subset of a larger population.

Analysis of the structure of a tissue.

The "typical" phenotype that is seen in nature.

The tumor necrosis factor (TNF) superfamily is a group of proteins involved in programmed cell death.

A type of dominance where two alleles of a gene in a heterozygote are fully expressed.

Placodes are very short-lived during development and do not form in the same place.

Bumps in the layer that joins the epidermis (outer layer of the skin) and the dermis (middle layer of the skin).

Small, spherical groups of cells that contain a cavity from which hair, teeth, feathers, etc. can grow.

Covered by bony or horny plates or scales.

Related to birds.

Similarity of structure, physiology, or development of different species that is a result of a common evolutionary ancestor.

Refers to evolutionary lineage (species linked by a common ancestor).

Specific molecules that, when present, indicate the presence of a structure or a particular stage of development.

Cells shaped like columns.

A protein involved in cell signaling between two layers of skin (ectoderm and mesoderm). It is especially important in embryo formation and promotes the formation of hair follicles, sweat glands, and teeth.

Related to the study of tissues.

The process by which a structure or pathway that evolved for one function gains additional functions.

The idea that two species share an ancestor somewhere in their lineage. Common ancestry is visualized in a phylogenetic tree.

Pronounced "neo-NICK-uh-tin-oid." A large family of pesticides that is currently the most widely used type of pesticide in the world, for both commercial and home use. The "nicotin" refers to the biochemical similarities between these pesticides and nicotine, which itself evolved in plants as an herbivore repellent. Both chemicals work by affecting the nervous system and, in toxic doses, cause paralysis and death.

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

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

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

All of the mRNA transcripts in a cell.

Biologically produced light.

The process of how a single stranded DNA form hydrogen bonds with other complementary DNA strands to make double stranded DNA.Often used in the PCR steps of creating or mass producing certain DNA sequences. (EM)

Heterospecific is used to classify organisms. "Hetero" means differ, and "specific" pertains to a particular subject/concept. Heterospecific means organisms that aren't the same species. ~J.D.A.

Conspecific is also like heterospecific as it pertains to classifying species. In the sentence it seems to be an opposing word to heterospecific. If heterospecific means organisms of differ species, then conspecfics must mean the opposite--must mean organisms of same species. ~J.D.A.

Parsimony analysis deals with simplicity. In regards to science, there will be various explanations to certain phenomenon. According to parsimony analysis, the simplest explanation is the best one. ~J.D.A.

Tenable is defined as something that can be "holdable". It could mean that something must have enough support for it to be upheld. In other words, if someone has an argument against an idea, the explanation should be enough to defend the concept. ~J.D.A.

Concordant means to agree. A variation of this word would be "concor", which has the same meaning. For this paper, the word may be used to describe how data collected seem to show the same variation or consistency. ~J.D.A.

The word shoal describes a shallow body of water. This is synonymous to sandbars or elevated sand in beaches. Therefore, something that "shoals" means that it doesn't have much depth. ~J.D.A.

Strombinid refers to the taxa Strombidae. It's a family of medium-sized conch sea snails. Gastropods is also another term used to describe the Mollusca phylum. ~J.D.A.

"Intra" means within. Divergence is when something separates. Thus, this word could mean how species diverge from each other from within the same oceanic community. ~J.D.A.

The classic allopatric model is also known as geographic speciation or the dumbbell model. Classic allopatric model is a kind of speciation that occurs when biological populations of the same species become isolated from each other. This isolation is what will prevent genetic exchange between the separated populations. ~S.Z.

Foraminifera are single-celled planktonic animals. They have an external shell and a granular ectoplasm for catching their food. When they die their shell becomes part of seafloor matter. ~J.D.A.

Allozyme is an enzyme. They are coded by differ alleles found at the same locus of the gene. They were studied in this experiment via taxonomic branching to map out closely related pairs. ~J.D.A.

A gene coding for the cytochrome oxidase enzyme. This enzyme is found in the mitochondrial membrane. It is responsible for catalyzing transfer of electrons to the oxygen atom. This is for the electron transport chain to make ATP as a product. ~J.D.A.

straightforward, clear. (SZ)

Sporadic production is referring to production that occurs in an irregular manner. the fertile clutches will occur in at an inconsistent interval. ~S.Z

Transisthmian refers to the opposite sides of an isthmus. The authors utilize this term to portray that the shrimps that were measured were from opposite sides (Pacific side and Caribbean side) of the Isthmus of Panama. ~J.D.A. (DV)

Speciation is an evolutionary process where populations become distinct from each other over a long period of time and develop into a new species. (JP)

Phylogeny refers to the study of evolutionary history among groups of organisms or individuals. The phylogenetic tree is a diagram that illustrates the relationships among species; this diagram is based on similarities and differences in the physical or genetic characteristics of different organisms. This diagram shows that all organisms originate from a single ancestor but have diverged due to speciation over a long period of time. (JP)

Taxonomy deals with naming and classifying organisms. A taxonomic group of any rank, such as a species, family, or class is a taxa. ~S.Z.

The mutation rate of biomolecules is calculated and used narrow down the time in prehistory when two or more organisms diverged. (SZ)

Staggered suggests that the occurrence or arrangement of events did not happen at the same time. Staggered isolation is the thought of organisms become genetically isolated at different events or moments in time, therefore leading to speciation of these organisms. (DV)

Isthmus is a stretch of narrow land that connects two large landmasses and separates two bodies of water.

The Isthmus of Panama formed 3 million years ago connecting North America and South America, while separating the Pacific Ocean and the Caribbean. (DV)

Taxa refers to taxonomical groups like species, family, or class. Taxa are used in classifying organisms based on relatedness of characteristics.

Sister taxa refers to two groups in which the organisms derived from a common ancestral organism, therefore these two groups are very closely related. (DV)

Divergence is the differentiation of something (like an organism's genetic information) from its common state.

Molecular divergence is the differentiation between the nucleotide sequence in DNA or amino acid sequences in proteins of organisms. (DV)

The snapping shrimp (Alpheus) is a species of shrimp well known for their asymmetrical claws which when closed produce a loud snapping noise. They borrow in the sand and attack their prey by quickly reaching out with their larger claw to capture it. (DV)

A process by which a species evolves into two or more descendant or different forms (SZ)

This explains the process of gene transfer. Usually this is observed from shifts in genes between different populations. So lets say a blue bird from one population migrates out of its territory and mates with a brown bird from the new population, the allele frequency shifts. ~J.D.A.

Offspring that have different alleles than their parents as a result of genetic recombination (such as crossing over and random assortment of chromosomes which causes each sex cell to be different from the parents' sex cells). These offspring are then crossed with each other so that resulting generations have nearly identical genes.

The genetic makeup of an individual inherited from one's parents. Genotypes are particularly important in determining which variant of an allele or trait that individual has. When the author says that 14 genotypes were sowed, they mean that 14 different combinations of the same genes were planted in the populations. The plants each had their own variety of these genes. This is an important distinction because a genotype does not mean that the plants had different genes. They simply had different varieties of them.

Random processes, events occurring with no apparent relationship or meaning. Stochastic models are necessary for ecological studies because environmental systems are often impacted by random events such as natural catastrophes or human interference. In order to account for this randomness, multiple trials are done in studies to ensure that the results were not simply a result of randomness. The more trials that affirm a result, the less likely it is that result is due to chance.

The random selection of organisms to survive and reproduce. Unlike other selection devices, genetic drift is completely due to random chance. An example of genetic drift could be something like a volcano erupting and randomly taking out half of the population just due to chance. Genetic drift is typically more pronounced in smaller populations because changes in allele frequencies are more observable when even just a few members of a population are removed. If those members had a unique trait, their removal can be very influential on the traits of that population.

Factors outside the strand of DNA that impact how the genes are expressed. The most common examples of this are DNA methylation and histone modifications. Both essentially make the DNA harder to access by the enzymes that convert it into proteins. These epigenetic regulators are mostly caused by environmental factors such as nutrition or exposure to certain chemicals. These epigenetic changes are heritable, meaning the modifications can be passed on to offspring.

a molecular technique that purifies proteins and finds binding partners by using antibodies that can bind specifically to the protein. Can help find protein complexes.

a test used to confirm the presence of a protein species or to identify natural binding partners for the RNA

computer run simulations

The coelom is the body cavity in which the intestines and digestive organs lay in. -Sindy

An empirical research is a research that uses observations that are verifiable rather than theories. The level of significance in an empirical research is the probability of rejecting the null hypothesis.

The HIF pathway is one of the molecular pathways used to regulate angiogenesis. The Hypoxia inducible factor (HIF) proteins act as transcription factors by inducing the vascular endothelial growth factor (VEGF) promoter. HIF proteins are activated as a result of low oxygen concentration. In normal conditions, the HIF protein is rapidly degraded by the actions of Von Hippel–Lindau (VHL) tumor suppressor proteins. VHL proteins bind to hydroxylated HIF and targets HIF for proteasomal degradation. However, under hypoxia, HIF is no longer bounded to oxygen and VHL can’t bind to HIF, resulting in the activation of HIF. HIF can then induce angiogenesis by activating VEGF genes.

Gene Ontology is an initiative that aims to address different concepts and vocabularies aimed to describe the functions of a gene and its products. Gene ontology studies genes based in three major categories: biological component, molecular functions and cellular compartments.

In genetics, candidate genes are genes that are likely to cause a disease due to their location or their protein products. Candidate genes are studies based on a priori knowledge. A priori knowledge is gained based on detective and derivative reasoning. Hence, a priori candidates are genes that cause disease and have been studied and analyzed.

Normally, under hypoxic conditions, the blood vessels constrict. In Tibetans this physiologic reaction does not occur.

The levels of oxygen in the blood have fallen below normal

Perennial plants grow and bloom over the spring and summer, but die back every autumn and winter, This seasonal process involves the annual gain and loss of the biomass required for blooming.

These tests involved cars driving on actual roads, instead of test (or "simulated") roads used for experiments.

Autonomous vehicles can navigate an environment without input from humans. One example of an autonomous vehicle is a self-driving car.

Nonsynonymous substitutions are a nucleotide mutations that alters the amino acid sequence of a protein. These differ from silent mutations, because they alter the amino acid sequences. - Jake Barbee

Splicing refers to RNA gene splicing which is, the editing of new messenger RNA transcript into a mature messenger RNA. Splicing removes introns, joining together only the exons to create a mature mRNA. - Jake Barbee

time elapsed between start and completion of the morris water maze

Amyloid beta precursor protein (APP); The protein is found in many tissues and concentrated at the synapses of neurons.The protein itself is not dangerous, it is found in many tissues and concentrated at the synapses of neurons. Truncated forms of APP can form plaques that cause AB toxicity.

Receptor and ion channel protein found in neurons, which controls the ability of synapses to weaken or strengthen due to brain activity level and memory function.

A kinase that helps transfer a phosphate group to a specific site on the tau protein. Each isoform of the p38 kinase phosphorylates tau at a different site. A kinase is a protein that catalyzes the transfer of a phosphate group to a specific site on a specific protein.

Alzheimer’s disease is a brain disorder that worsens with age and has no known cure. The disease affects different aspects of cognition and memory, and can eventually lead to shutdown of the body. https://www.youtube.com/watch?v=fT7UovfLl8c

Amyloid beta is a short chain amino acid and is a main component of amyloid plaques that are associated with Alzheimer’s. Amyloid beta plaques are located outside of neurons. Amyloid beta plaques are composed of amyloid precursor protein (APP) that is truncated into a shorter form. Amyloid beta toxicity occurs when the build of of amyloid beta plaques becomes toxic to neural cells.

A mutant variant of T205 with the mutation in the phosphorylation site

A mutant variant of T205 that changes the site to act like a constitutively active phosphorylation site

Mice are placed in a circular pool of water. In one of the quadrants, a hidden platform is present. The platform allows the mice to stand instead of swim.The mice are shown where the platform is and how to get to it multiple times. After showing the mice, the researchers put the mice somewhere in the four quadrants and track their movement as the mice attempt to find the platform. Time to escape can also be quantified. (https://www.jove.com/video/2920/morris-water-maze-test-for-learning-memory-deficits-alzheimers)

Tau is a protein that stabilizes microtubular cytoplasmic components in neurons.

A technique to find protein-protein complexes by precipitating an antigen protein from a solution using an antibody that binds to a particular antigen from a sample.

response of a neuron to a stimulus

electrical signals recorded from individual neurons

after the initial step

the time between seizures

change or variation

to add an inorganic phosphate group to a substance, usually to affect the activity of the substance

completely; throughout

death

to move up and down on a scale

A protein that phosphorylates Tau and is involved in neuronal growth.

A wave on an EEG that is a sharp wave or spike that is a marker for patients with epilepsy or a focus of seizure studies.

Electroencephalography (EEG), measures electrical activity of the brain Epileptiform: A wave on an EEG that is a sharp wave or spike that is a marker for patients with epilepsy or a focus of seizure studies.

to aggravate, make a situation worse

to amplify, make greater in size or value

Pentylenetetrazole, a central nervous system (CNS) stimulant used to assess the excitability of the CNS. The drug is administered and 30 minutes after, seizure profiles are examined.

The death or damage of nerve cells by over stimulation by neurotransmitters.

A deviation from the normal type behavior

The Human Genome Project was an effort to map and understand all of the genes that make up the human genome. Although it was announced complete in 2003, we still have much to learn about the genome.

Genome-scale CRISPR knockout.

"Bootstrapping" is a process that allows scientists to ensure that their statistical data sets are correct by doing hundreds of random samplings.

RW

Vertical lines in these graphs represent error bars, which represent the level of uncertainty in results. The larger the variation in data, the longer the error bars will be. These graphs have been created with 95% certainty.

RW

This p value is considered "significant", meaning that the results did not happen by chance.

RW

P values greater than .001 are generally considered insignificant in statistics

RW

marriage between close relatives

enzyme that produces fluorescent colors when activated and is often used to study gene expression

bacterial DNA sequences that contain snippets of viral DNA, allowing scientists to modify genes within an organism (by removing or adding DNA)

The observable characteristics/traits of organisms

An idea that is credible and reasonable

Is a drug that targets peroxisome proliferator-activated receptor. Peroxisome proliferator-activated receptor are nuclear receptors, which also act as transcription factors.

drugs used by diabetic patients to regulate blood glucose levels.

Normal oxygen levels.

Able to be passed on to the next generation

Data was arranged on a table or chart

Are genes that are not on sex chromosomes

Localization signals are amino acid sequences that aid in nuclear transport by tagging proteins destined into the nucleus.

A measurement unit: 200 kilobytes

Calcium found on the inside of the cell, typically found in the mitochondria.

CAMK2D gene encodes for calcium dependent protein kinase type 2 delta, which is a serine/threonine protein kinase family.

Heme oxygenase 2 (HMOX2) is an enzyme that catalyzes the breakdown of heme.

Family of genes that regulate lipid synthesis and drug metabolism.

Is one of the member of the cytochrome P450 superfamily, and regulates metabolism of xenobiotics in the body. Xenobiotics are chemical compounds found in the body, but are not synthesized within the body.

Cytochrome P450 17A1 is a gene encoding for enzymes of the cytochrome P450 superfamily, which regulate the synthesis of various lipids and drug metabolism.

The breakdown or storage of fats that occurs within cells, primary in the liver.

Peroxisome proliferator activated receptors are receptors found on the nuclear membrane that can act as transcription factors that induce certain genes.

Following a certain phenomenon

Structures that do not extend over one another

A continuous uninterrupted sequence