5,190 Matching Annotations
  1. Dec 2018
    1. biomass

      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.

    2. biocontrol measures

      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.

    3. photosynthesis

      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.

    4. carbon sequestration

      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.

    5. primary productivity

      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.

    6. senescence

      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.

    7. conservation practices

      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.

    8. dendrochronology

      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.

    9. edge effects

      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.

    10. bottom-up trophic organization

      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.

    11. species niche concept

      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.

    12. community-level coexistence theory

      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.

    13. ecosystem services

      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.

    14. decomposers

      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.

    15. synchrony of plant reproduction

      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.

    16. biogeochemical processes

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

    17. global warming

      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.

    18. spatial

      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.

    19. exotic and invasive species

      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.

    20. mutualistic interactions

      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.

    21. species diversity

      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.

    22. evolutionary biology

      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.

    23. ecology

      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.

    24. biometeorology

      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.

    25. global change

      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.

    26. Phenology

      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.

    1. reciprocal transplant experiment

      The reciprocal transplant experiment is an experiment where organisms from two or more environments are introduced to each other.

      The experiment is commonly used to test how well the organisms adapt, and sources of growth variation (genetic or environmental).

    2. two-dimensional NMDS ordination

      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:

    3. chlorophyll

      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.

    4. regression

      Regression analysis is a statistical model made up up of a series of processes used to understand how the dependent variable changes when any of the independent variables are modified.

    5. parapatric distribution

      Parapatric distribution refers to a distributional pattern where pairs of taxa are partially overlapping or have separate but adjacent distributions, typically along common boundaries.

    6. herbivore to circumvent or detoxify defenses

      An example of this defense is how a monarch butterfly caterpillar holds on to a milkweed's toxins to then use it for their own protection and survival.

    7. Environmental gradients

      A progressive change over time of the nonliving factors that make up an environment examples of nonliving factors in an environment would be altitude, temperature, depth, humidity etc.

    8. habitat-mediated speciation

      Habitat-mediated speciation is the emergence of different species throughout evolution, brought about by the natural environment and its effects.

    9. chlorophyll

      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.

    10. plant defense allocation

      Allocation refers to the distribution of something for a specific purpose.

      Plant defense allocation is one of the ways a plant can protect itself, its resources and reduce the impact of herbivores.

    1. Markov Chain Monte Carlo methods

      MCMC methods are a class of algorithms for sampling from a probability distribution. By constructing a Markov chain, a sample of the desired distribution by observing the chain after a number of steps.

    1. spatial abundance pattern.

      Spatial and temporal abundance patterns relate to the study. Temporal abundance pattern has to do with quantity over a period of time and spatial abundance patterns have to do with quantity over a particular area of space.

    2. site-fidelity

      Side-fidelity, also known as philanthropy, is the likelihood of a particular organism to stay in a set habitat, or to return to it. There are many reasons to this, such as breeding and food abundance.

    1. Pacific bluefin tuna (Thunnus orientalis)

      The Pacific bluefin tuna are smaller than the Atlantic bluefin tuna. It reaches the maximum length of 3m and a maximum weight of 540kg.

    1. teleomorphic

      The sexual life stage of the fungi where cells become polarized, or have two obvious ends, and through cell division form long structures called hyphae. In some fungi, the individual cells are multinucleate. Only some fungi are capable of this form of reproduction; for example, baker’s yeasts used in beer fermentation are not able to grow this way.

    2. radiations

      Genetic or molecular diversification. As genetic changes occur over time (evolution), diversity will increase within a group, illustrated by branching on a phylogenetic tree.

    3. single nucleotide polymorphisms (SNPs)

      A variation in a single base pair (A, T, C, G) in a DNA sequence. Some sites in a gene are more likely to mutate than others. Phylogenetic information is based on genetic differences between organisms, and single nucleotide polymorphisms (SNPs) provide the most information.

    4. lichen thalli

      Generally, lichen thallus (singular form of thalli) types fall into four basic growth forms: crustose, squamulose, foliose, and fruticose.

      Lichen thalli can develop into a diverse range of structures: multiple-branched tufts; flat, leaf-like structures; filamentous structures; and aggregates of tiny plates.

    5. nomenclatural synonyms

      The naming of all living species is governed by rule books called codes of nomenclature. According to these rules, if it is discovered that the same organism has been named twice, for instance by different people who didn’t know each other at different times, then the older name is given priority and the second name becomes a “synonym."

      In this case, studies of the main fungal partner in Bryoria fremontii and B. tortuosa showed that they are genetically identical, and thus the two names technically should become nomenclatural synonyms. If this rule would be followed through here, the older name (Bryoria fremontii) must be used because it is older. However, the authors chose not to follow the rule so that they would still have names to use to discuss the two different lichen phenotypes

    6. molecular clock

      The molecular clock theory posits that changes (mutations) occur at a constant rate, and that we can use the number of changes between any two sequences to find out approximately when the sequences diverged from one another. To apply a molecular clock to a phylogeny one must use a rooted tree (see Figure 2A).

    7. lichen symbiosis

      Watch a video from the Havard Museum of Natural History about what defines a lichen. This video describes lichens, symbiosis, and the lichen life cycle. Notice that the video makes no reference to basidiomycete yeasts.

    1. cis-vaccenyl acetate (cVA)

      Since flies do not have verbal language, they communicate with one another by releasing and responding to chemicals known as chemosensory cues. Different cues can have different meanings. For instance, some cues released by the female can signal to the male that she is ready to mate. Other cues, like the one described here (cVA), can signal that the female is no longer looking to mate, thus driving away any unwanted males.

    2. conditioning assays

      An experimental method used to determine if and how much an animal enjoys one thing over another. The concept behind this is similar to a two-choice preference assay (described earlier). In this particular experiment, the researchers used a Y maze.

      As shown in the diagram, the animal starts in one prong of the maze (the picture here depicts a rat, but the researchers in the current study used flies). The other two prongs of the maze are each loaded with one of the two options being presented to the animal. This could be a food reward, a physical object, an odor, etc. Whichever of the two prongs the animal opts to spend the most time in is considered its preferred choice.

    3. down-regulation

      A genetic manipulation wherein the expression of a gene is reduced. In this case, the authors want to experimentally reduce the amount of NPF or NPF receptors (NPFR) that the flies are producing in order to inhibit the function of the NPF molecule. This is accomplished by down-regulating the genes that cause NPF or NPFR to be made.

      Think of a gene as a radio with a volume knob. The cell is always making the molecules that the gene dictates (aka playing music on the radio), but a scientist can turn the knob to reduce the amount of the molecule that is produced (turn down the volume).

    4. immunohistochemistry

      A technique for detecting the presence of particular substance in cells. Typically, this is done by taking the cells of interest and pouring a specialized, colored dye over them. This dye is selectively attracted to the substance that you are interested in—wherever the substance is present, the dye will stick. If the molecule you are searching for is not present, the dye will simply wash off. This technique can therefore be used to detect where in a group of cells a molecule might be present, as well as how much of that molecule is present in that location. In this experiment, the researchers poured a dye that sticks to NPF over sections of the flies' brains in order to detect how much NPF was present.

    5. restraint stress

      An experimental method for causing rodents to experience stress. Specifically, restraint stress involves placing a mouse in a small plastic tube. This tube is tight enough to prevent the mouse from moving too much. This inability to move causes the mice to experience intense discomfort and stress.

    6. Caenorhabditis elegans

      A species of worm that is often used to study the effects of various genes. C. elegans are used because all of their genes are known, they are relatively easy to genetically manipulate, and they have a number of genetic similarities to human beings and other mammals.

    7. homolog

      Researchers have found a number of genes in Drosophila flies that are remarkably similar in composition to genes that are found in people. Often, these highly similar genes between the two species serve overlapping functions as well. Such similar (but not completely identical) genes that exist across species are referred to as homologs of one another. As an analogy, if you think of an iPhone as a gene, then an iPhone 6 and an iPhone 8 might be considered homologs of one another in that they are extremely similar in a number of ways, but not quite identical.

    8. receptive virgin females

      Female flies, who have never mated before, that accept the sexual advances of males, and will often mate with them. For this reason, they are considered "receptive" to the act of mating.

    9. courtship conditioning

      Refers to a type of commonly employed behavioral model in Drosophila research. In this model, a male is exposed to a female who has already mated with a different fly. The male Drosophila will attempt to court the female by carrying out a series of behaviors such as tapping her with his forelegs, or singing her a song. However, since the female has already mated, she will not be receptive to these attempts, and the male fly will experience sexual rejection. This leads to an overall reduction in the male's courtship attempts.

    10. a cue

      In behavioral neuroscience, cues refer to elements in one's environment that predict an upcoming event. For example, the ringing of the school bell at noon might be considered a cue for lunch. Cues are important because they often take on the ability to motivate organisms to do things, even though cues themselves have no inherent value.

    11. genetically tractable

      Something that is tractable is easy to control or influence. The genetics of the Drosophila fruit fly are considered tractable because we are aware of every single gene in this species, and it is easy to engineer flies that possess or lack specific genes. This ability to insert or remove specific genes from a fly's DNA allows scientists to understand the roles that these genes play.

    12. addictive behavior

      In neuropsychology, addictive behaviors are a specific class of behaviors that one might exhibit while suffering from addiction. An example of an addictive behavior would be compulsive pursuit of a specific substance/activity, in spite of negative consequences associated with doing so.

    13. ethanol

      The common chemical name for alcohol. In a beverage such as wine, for instance, the sugar in the grapes gets converted into ethanol during the fermentation process. This is what makes wine alcoholic.

    14. neural pathways

      Refers to a set of neurons in the brain that work together towards some common goal. This goal can be very tangible, such as regulating a certain behavior. Often, these cells are connected to one another in a way that allows them to communicate, somewhat similar to a circuit of wires that one may expect to find in an electronic appliance.

    1. basal breeds

      A group of 16 dogs breeds, which are distinct from modern dogs because their DNA is less mixed. Basal breeds include: Afghan hound, Akita, Alaskan Malamute, American Eskimo, Basenji, Canaan, Chow Chow, Dingo, Eurasier, Finnish Spitz, New Guinea singing dog, Saluki, Samoyed, Shar-Pei, Shiba Inu, and the Siberian Husky.

  2. Nov 2018
    1. secondary gene flow

      Genetic variation is transferred from one population to another, two times over. That is, after the first transfer, there is a period of separation between the two populations and then genetic variation is transferred again.

    1. multiprobe

      This refers to a specific type of indexing (listing) strategy that is used in LSH to limit the number of hash tables and reduce computational time. Multiprobe also means that instead of only checking a single bin for similar items, it will look at nearby bins, as well, just in case.

    2. deep learning

      This is a type of machine learning. Machine learning is the process of getting computers to run without being directly programmed. To do this, a computer scientist will use a sample data set to "train" a computer how to respond to a particular problem. The goal is that the computer could then learn certain rules so it can also solve the same or similar problems, even with data it's never seen before.

      Deep learning extends this process to multiple layers, creating artificial networks of problem solving so that computers can solve more complicated problems without human input.

    3. Euclidean distance

      The straight-line distance between two points in Euclidean space. Euclidean space is the traditional, three dimensional x,y,z space that is commonly used in geometry.

    4. brute force linear search

      This is a general problem-solving technique that involves listing all possible candidates for a problem and checking one by one to see which one(s) provide a solution.

      In this example, it would be like taking your picture of an elephant and manually comparing it to every other image on the internet to find the 100 that are most similar. In problems where there are many possible candidates for a solution (like this example), brute force linear search is an extremely slow way of trying to solve the problem!

    5. binary random connection matrix

      A connection matrix is a table of rows and columns, each consisting of positions on a graph. In each entry, the matrix has a 1 or 0 depending on whether the row positions and column positions are adjacent (1) or not (0).

      It is random because the connections (representing connections between PNs and KCs) are random, and it is binary because it uses only ones and zeros.

    6. Kenyon cells

      One of the types of cells found in the "mushroom bodies" of the olfactory system. Mushroom bodies are important for olfactory learning and memory and—you guessed it—look like mushrooms.

    7. stimuli

      Any thing or event that causes a neuron or set of neurons to become active.

      When a nerve cell is activated, it triggers an action potential, which is a temporary change in the electric charge of the cell relative to its surroundings. This depolarization causes nearby locations to similarly depolarize (think about a line of dominoes falling down) and an electrical signal travels through the brain.

      On a graph, this action potential looks like a brief spike, which is why scientists sometimes refer to this process of neurons releasing action potentials as "spiking."

    1. zygotic

      A zygote is the cell that is formed by the male sex cell (sperm) and the female sex cell (egg). Zygotic refers to the characteristics of these early cells involved in replication.

    2. annotation

      Designation of where genes or genetic elements are in genomic sequences. This is by far the most difficult task for scientists and is constantly changing as we learn more about important features of the genome. Often, uncommon model organisms (like the mosquito) suffer from lack of annotation because scientists are more focused on other organisms like the human, mouse, or fruit fly.

    3. sex-specifically spliced genes

      Most genes have several coding regions (exons) interrupted by noncoding regions (introns). When a gene is translated into pre-mRNA, the molecule will go through processing to remove the introns and create a mature mRNA molecule for translation. During this process, exons or parts of exons can be removed as well, leading to several possible mRNA versions (also called isoforms) of the same gene. In this case, males will express one version of the gene and females will express a different version of the same gene.

    4. sex determination

      The process by which and organism becomes male or female, in both appearance and reproductive capabilities. In most species this is genetic, as discussed here. However, in other species, sex can be determined by external environmental factors and can sometimes switch during the organism's life.

    1. Deep brain stimulation (DBS)

      A therapy option for Parkinson's disease, epilepsy, and depression patients where metal electrodes are inserted into deep brain regions. A stimulator placed near the collarbone then sends an electrical impulse through wires connected to the electrodes targeting neurons in the implanted area.

    1. executive impairments in the control task

      Executive impairments refers to reduced function of processes such as memory, controlled response to stimuli, capacity to shift between different topics and tasks, and focus—which regulate and control cognitive functions.