5,190 Matching Annotations
  1. Aug 2018
    1. hydrolyzing

      To hydrolyze a molecule is to break it into two pieces by adding a water molecule to it. Some chemicals undergo this process spontaneously, but in biological systems enzymes often help hydrolyze large biological molecules.

    2. enzymatically degrade

      Enzymes are large biological molecules that help speed up the transformation of one molecule into another. Degrading a polymer generally involves breaking it down into smaller pieces. Enzymatic degradation uses natural or lab-made enzymes to break down polymers that could harm the environment into something smaller and more benign.

    3. gene homologs

      Sets of DNA in different organisms that encode similar traits in different organisms. Homologs are often used to show how certain traits, like the ability to digest PET, developed over the course of evolution.

    4. metabolism

      We often think of metabolism as the process by which humans break down food into energy; however, it can also be used to describe the process by which a cell breaks down a molecule, like PET in this case, for energy.

    5. Bootstrap values

      Used to show what percent of times a node, or a place where two different branches originate, shows up in a phylogenic tree. The tree is recreated many times using slightly different data samples. Higher bootstrap values suggest the node is more likely to be correct.

    6. phylogenetic tree

      A diagram that shows how different organisms or biological species, like enzymes in this case, are related to each other. A node, where there is a branch in the tree, represents when the two species have evolutionarily diverged from each other.

    7. liquid chromatography

      A technique for separating different compounds. The compounds are dissolved in some solvent and run through a thin tube called a column lined with a solid substance. Compounds that are attracted to the solid substance come out of the column after the compounds that are less attracted to the solid in the sample.

    8. SEM

      Stands for Scanning Electron Microscope. The microscope uses an electron beam that produces signals about the sample's surface and then converts that information into a picture. SEM allows us to see things too small to visualize with a more common light microscope.

    9. protozoa

      A type of single-celled organism. There is a lot of diversity among the different types of protozoa. Although they are single-celled like bacteria, they have different forms and behaviors. They typically lack a cell wall, for example, and many will survive by eating other organisms rather than by photosynthesis.

    10. morphological

      The morphology of a PET fiber describes its shape and surface texture. For example, we might describe its morphology as being rough, smooth, or flat. If there are morphological changes, that implies something about the bacteria changed the shape of the PET film.

    11. Fusarium oxysporum and F. solani,

      These are types of fungi. Both fungi cause disease in some plants and F. solani also causes disease in humans. Previous research has shown that they can produce enzymes that can degrade PET to some extent.

    1. pathogens

      Any foreign organism that can cause disease. Common pathogens are viruses, bacteria, and fungi.

      Bumble bee pathogens are organisms that cause detrimental effects in bumble bees.

      Since the mountainous regions occupied by bumble bees lack pathogens, the pathogens do not influence the evolution of mountainous bumble bees.

    2. phenotypes

      The physical expression of an organisms genetic makeup. Everything we physically observe in an organism is due to the expression of their genes (their genetic information).

      The phenotype of tongue length in bumble bees is highlighted in this study. Bumble bees featuring different genes that express tongue length display a variation in tongue length.

    3. Optimal foraging theory

      A theoretical model used to indicate how an animal will look for food. Factors that influence how an animal will forage for food depend on the costs of energy or risk gathering the food compared to the energy gain benefit from the food.

    4. foraging breadth

      The range or obtainable food sources for an organism.

      For the alpine bumble bees, this includes sources of nectar and nest building materials.

      This paper highlights how the foraging breadth of native bees is decreasing due to increasing competition from immigrant species.

    5. subalpine congeners

      Species of bees from subalpine climates, that are within the same genus.

      Climate change has warmed the alpine climate, making it's temperature closer to a subalpine climate, and increasing the range of the subalpine bee species.

    6. host plants

      Plants that are in a mutualistic relationship with the pollinators.

      In this paper, host plants are involved in a mutualistic relationship between themselves and bumble bees.

    7. B. sylvicola

      A species of bumble bee known as the forest bumblebee. It is native to North America and is found in open alpine grasslands near mountains.

      Bombus sylvicola feeds on plants such as lupines, fireweeds, and groundsels, which are all plants found in alpine habitats.

    8. Bombus balteatus

      A species of bumble bee known as the golden belted bumblebee. It lives in high altitude alpine habitats and has a long tongue that is more than two-thirds of its body size.

    9. coevolution

      Evolution is the change in alleles (genetic information) in a population over time. Coevolution is when two species influence the evolution of each other.

      Coevolution is generally observed when a long lasting mutualistic relationship between two species exists.

      As plants and bumble bees evolved alongside each other, each acted as a selective pressure for the other, altering their evolutionary paths so that each is better suited to live alongside the other.

    10. morphology

      The study of an organism's physical characteristics and their function.

      In a mutualistic relationship between species, scientists are able to match the morphological traits that directly affect the symbiotic relationship (morphological matching).

      This paper highlights the morphological matching between the corolla length of flowers and the tongue length of bumble bees.

    11. generalist foraging,

      Foraging is the act of an organism searching for food. Generalist foraging is when an organism forages for a wide variety of food, or in other words is more adept at foraging for whatever is more convenient. Bees showing generalist foraging will eat from a wider range of flowers.

    12. climate

      The common weather patterns of a given area.

      As climate change occurs, the prevailing weather patterns of all areas are viable to change as well.

      Changing climate of bumble bee habitats are causing changes in pollination requirements of bumble bees to flowers.

    13. corolla tubes

      The cylindrical opening created by the petals of a flower that leads to the reproductive organs of a given plant. The tube also leads to rewards for pollinates, such as nectar.

      The corolla tube is what a bumble bee sticks its tongue down to acquire nectar. The longer the corolla tube, the longer the tongue of a bumble bee must be to access the nectar held within the tube.

    14. pollinators

      A living organism capable of spreading pollen from one flower to another.

      Generally pollinators are insects or birds. The pollinator highlighted in this paper is the bumble bee.

    15. biodiversity

      A measurement of the number of species in an ecosystem.

      The greater the number of different species in a given ecosystem, the greater the biodiversity measurement of said ecosystem.

    16. agriculture

      The practices used in farming to produce goods, such as crops and animals.

      Agriculturally based mutualisms consist of symbiotic relationships between organisms and cultivated organisms.

    17. mutualisms

      A relationship between two different organisms where both species benefit from that relationship.

      The symbiotic relationship highlighted in this paper is the one between long-tongued bumble bees and plants. The bumble bees benefit the plants by pollinating them as they move from plant to plant and the plants benefit the bumble bees by giving them nourishment.

    1. high performance liquid chromatography

      High performance liquid chromatography (HPLC) is a technique commonly used in analytical chemistry to help separate, identify and quantify components in an organic mixture.

    2. Lipid assays

      Lipid assays include utilizing synthetic lipids to construct a lipid bilayer similar to the cell membrane. Lipid assay kits may be used to measure concentrations of lipid mixtures in comparison to membrane proteins in a cell membrane.

    3. previtellogenic stage (PVGS), an ovarian resting stage (ORS) and a vitellogenic stage (VGS)

      One of the most significant stages of the reproductive cycle is vitellogenesis which involves massive production of yolk protein and their accumulation in developing oocytes. Vitellogenesis is dependent on the availability of a blood meal and, as a consequence, is linked to transmission of pathogens. Therefore, vitellogenesis and other aspects of mosquito reproductive physiology is critical for their management of disease. The ovarian resting stage in the reproductive cycle of female mosquitoes is a time when the eggs are not being produced. In addition, the ovaries will not develop beyond a resting stage until a blood meal of adequate size has been taken.

    4. RNA interference (RNAi)

      RNA Interference is a response to double-stranded RNA that is responsible for the resistance of pathogenic nucleic acids such as certain mutations in base pairs, and regulates how genes express a particular protein.

    5. signaling pathway

      A signaling pathway allows an activation process to occur for a cell to have a specific function. In this case, communication takes place between these two different hormones, juvenile and insulin. These hormones work with energy to develop an insect.

    1. Parafilm

      Primarily used in laboratories. It is commonly used for sealing or protecting vessels (such as flasks or cuvettes). It is a ductile, malleable, waterproof, odorless, translucent, and cohesive thermoplastic.

    2. cruising specialist

      A type of fish that swim around and look for their prey, which are widely dispersed. They also have a stiff body with minimal drag when they swim. Sharks and salmon are also cruise specialists.

    3. Billfishes are considered to be among the fastest swimmers in the oceans.

      Billfish have long bills (elongated upper jaw), which allows them to cut through water, and aerodynamic bodies so they can swim in speeds of up to 120 kilometers per hour. Billfish include sailfish, swordfish, and marlin.

    1. distance metric

      A mathematical expression that defines the distance between any two elements in a set. Finding the distance between each of the elements in two feature vectors (each representing an image) would let you determine how similar those two images are. That is, the smaller the distance between the elements, the more similar the images are.

    2. locality-sensitive

      A type of hashing that aims to reduce the size of a large data set by mapping it into a table with fewer entries than pieces of data. To do this, similar pieces of data are assigned to the same entry in the table.

    1. Alopex lagopus

      Binomial nomenclature for the arctic fox. They are native to the arctic regions in the northern hemisphere, and are commonly found in the arctic tundra biome. They are carnivorous with a common diet of birds, hares and insects in the Aleutian islands.

    1. Brownian motion model of evolution

      In Brownian motion model of evolution, traits change randomly in distance and direction.

      The model uses two parameters: the population mean trait and the evolutionary rate parameter.

      This model is used in biology to compare traits between individual species and create phylogenetic trees.

    1. X-linked nephrogenic diabetes insipidus

      Nephrogenic diabetes insipidus (NDI) is a congenital disease characterized by the body's inability to make concentrated urine. It can be caused by mutations in two different genes, including AVPR2.

    1. trilateration

      A survey technique used to determine the location of points. Distances along the sides of a triangle are measured and angles computed. By constructing a series of adjacent triangles, distances between points can be accurately determined.

    2. clods deriving from disarticulation of desiccation polygons

      Desiccation polygons are areas bordered by cracks in the mud found in sedimentary rocks and mud flats. Disarticulation suggests that the polygons separated from the mud and formed individual clods of earth or rock.

    3. stratigraphic

      Stratigraphy is the study of rock layers. An analysis of a stratigraphic sequence would be looking at the types of sedimentary deposits, their age, and distribution from one area to another.

    4. holotype

      The single specimen that is used by the author of an article to describe and name a new species. It could also refer to two or more specimens described by the author when a single holotype is not identified.

    5. metamorphic rocks

      Formed when preexisting rocks are subjected to intense heat and pressure. This results in the original rocks changing both physically and chemically. Common examples are marble, slate, and schist.

    6. sexual dimorphism

      Refers to differences in appearance and size between males and females of the same species. Modern humans show a low level of difference in size and appearance. Differences between the sexes is much more pronounced in early hominins and in primates such as gorillas and orangutans.

    1. malaria

      Malaria is a flu-like disease caused by a parasite. The parasite infects and kills blood cells while also releasing toxins. If left untreated, this infection can result in organ failure and death. It is transmitted by certain species of mosquitoes.<br>

    2. pupal stage

      The pupal stage is the time at which the mosquito transforms from a water-inhabiting larvae to a wing-bearing adult. Much like butterfly metamorphosis, the mosquito is encased in a hard but thin shell-like structure.

    3. pools

      A collective sample. In this case, mRNA samples from multiple female mosquito embryos of the same age were combined before being sequenced. The same was done across different time points and for male mosquitoes. Because mosquitoes are small organisms, there is not enough cells/RNA to perform a quality sequencing reaction. Thus, several or maybe even hundreds of organisms must be combined in order to have enough material. When looking at sequencing data from "pools", you are actually observing the "average", but since these are laboratory raised mosquitoes, it is assumed that they are genetically identical. So the "average" is likely true for all organisms in the population.

    4. maternal tra mRNA

      The female egg cell is a rather large cell compared to the fertilizing male sperm cell. This large egg cell has more mRNA in the cytoplasm (as well as things like mitochondria) than the sperm cell. When the zygote is formed, there is a large maternal contribution of cytoplasmic goodies.

    5. dosage compensation

      A process by which the expression of genes on the autosomes (all the other chromosomes that are not sex chromosomes) and sex chromosomes (in both sexes) are balanced through either inactivation of chromosomes or increased gene expression from a chromosome.

    6. loss-of-function mutations

      Any change in DNA that results in a non-functional protein. Many different types of mutations can accomplish this, nonsense mutation and large deletions are the first thing that come to mind. They can render a protein non-functional by it being completely absent. Even missense mutations that change a single amino acid can render a protein non-functional if it hits a functional domain, even if the protein itself is present.

    7. karyotype

      A visualization of the number and kinds of chromosomes present in an organism. This term is used loosely here, as XY males were determined through PCR, not the traditional means of visualizing chromosomes under a microscope.

    8. secondary structure

      This level of structure in a protein is when the amino acid chain begins to have three-dimensional shape. Side chains of the amino acids fold and interact through chemical forces like hydrogen bonds, van der Waals interactions and hydrophobic interactions. The most common secondary structures are helices, sheets, loops and turns.

    9. helix-loop-helix motif

      This type of secondary structure in an amino acid chain is comprised of two alpha helices connected by a loop. This type of structure is indicative of the protein's ability to bind DNA as a transcription factor.

    10. open reading frames (ORFs)

      A stretch of DNA sequence that has the ability to be translated into protein (exons only). An ORF usually begins with a start codon (ATG) and ends with a stop codon (TAA, TAG or TGA).

    11. Reverse transcription (RT)–PCR analysis

      Similar to PCR, RT-PCR is a method that first converts mRNA in to DNA by use of a RT polymerase (enzymes like this are used in viruses like HIV). Once the RNA is in DNA form, the traditional PCR method can be used to amplify transcripts of interest.

    12. in vivo

      in vivo inside of a living organism. In this case an experiment that was done in a cell line (in vitro) and worked, was then done in a living organism to see if it would also work in the context of the whole animal.

    13. cell line

      A population of cells derived from a single cell isolated from an organism. Thus, all cells in the culture are genetically identical. Often different cell lines have unique experimental qualities to them. In this case, this line lacks the Y chromosome, which may have been genetically engineered or may have occurred by chance.

    14. gel loading control

      A control that helps to ensure that the same amount of RNA is added from each sample, so that if lower or higher levels of RNA are seen in different samples you can ensure it's due to biological differences and not just human loading error.

    15. zygotic expression

      There is a maternal to zygotic transition (MZT) in the zygote after blastoderm formation but before gastrulation. During this process maternally deposited RNAs from the egg are degraded and the new genome of the zygote is activated and begins transcription and translation of genes. The zygote is now on its own, without the support of good old mom.

    16. scaffold

      A section of genomic DNA sequence. As genome sequences are assembled computationally, scientists first call long sections of sequence a scaffold. They can experimentally determine where this section comes from (in this case the Y chromosome) but know that it is not all the sequences on the Y chromosome. In the mosquito, the Y chromosome is approximately 150 kilobases (kb), but this scaffold only represents 1/3 of the sequence (48 kb).

    17. reads

      A small segment of DNA sequence, approximately 100 bp in length. Before being sequenced, DNA (in this case RNA is converted back to DNA before sequencing) is chopped up into small fragments. Each of those small fragments are "read" before being computationally aligned to a reference genome sequence to determine where it comes from in the genome.

    18. transcriptomes

      The entirety of a cell, organ, organism's gene expression profile. Just like genomics (looking at the whole genome, instead of one gene at a time), transcriptomics looks at all of the transcripts (mRNAs) at once instead of one molecule at a time.

    19. sex-specific morphologies

      In most animal species, biological males and females have different outward appearances in addition to the different reproductive organs. Birds are some of the most obvious examples. Male peacocks have long and brightly colored tail feathers while female are a dull brown/green.

    20. upstream genes

      If you think of genetic and signaling pathways like a river, the genes at the very beginning of the pathway are the originating headwaters, or upstream. Whereas genes involved at the end of the pathway are downstream. What is upstream or downstream of you is relative to where you are in the pathway.

    21. sex determination system

      Not all sex determination pathways are like humans using the X and Y chromosomes. Over the course of evolution, organisms have developed different ways of genetically indicating male and female.

    1. inert and heavy masses

      Inert mass (m) is conceptually different from heavy mass (M). Heavy mass is a value that determines the strength of gravitational attraction, whereas inert mass (or inertial mass) is a value that indicates how resistant a thing is to a change of motion.

      Modern physicists use the term "gravitational mass" instead of "heavy mass."

    2. physical laws

      Physical laws are mathematical expressions that generalize physical phenomena. Physical laws explain and predict experimental results. Conservation of energy (ΔE=0) is one example of a physical law.

    3. perpetual motion never occurs in ordinary experience

      This kind of motion is impossible because it would require an infinite energy source, which violates the first law of thermodynamics (the Law of Conservation of Energy: The total energy of an isolated system is constant).

    4. kinematics

      Kinematics is a branch of mechanics concerned with the geometry of motion.

      (Einstein clarifies what he means by "kinematics" throughout the paper. When Einstein says kinematics, he specifically refers to the physics that treats space and time as separable entities.)

    5. inertia-system

      An inertia system of coordinates is a coordinate system that we can approximate to be stationary.

      For instance, we can describe the displacement of a baseball (the object of interest) relative to the baseball field (an inertia system of the baseball). Since both the baseball and the field are subject to the same rotational motion of Earth, the movement of the baseball can be described relative to the seemingly stationary field.*

      Einstein gives us a way to determine if a system of coordinates is an inertia system:

      A system of coordinates moving in the same direction and at the same rate as a system of inertia is itself a system of inertia.

      *For the purposes of this example, we have ignored the (negligible) effect of Earth's rotation. An observer on the surface of Earth must be accelerating to follow a circular path, and the entire system is subject to the non-inertial effects of gravity.

    6. systems of coordinates

      Systems of coordinates indicate the location of a point in space in reference to some other point. In doing so, systems of coordinates form a mathematical map of physical space.

      In Einstein's example, the system of coordinates for the railway train is the ground.

    7. the analytic, not the synthetic method

      Einstein says the analytic method is used to form theories of principle, whereas the synthetic method is used to form constructive theories. We can understand the methods as contrasts.

      The synthetic method supposes premises that help explain natural phenomena, while the analytic method reduces all natural phenomena to their common denominator. The synthetic method is a bottom-up approach, whereas the analytic method is a top-down approach.

      Another way to think about the difference is that the analytical approach starts with observations, whereas the synthetic method starts with hypotheses.

      (For those who are philosophy-inclined, Immanuel Kant discusses this distinction between the analytic and the synthetic.)

    8. kinetic theory of gases

      The kinetic theory of gases describes the motion of atoms in the gas phase and makes a number of assumptions such as:

      1. The gas molecules have negligible volume compared to their container.
      2. The molecules are constantly moving.
      3. All collisions are perfectly elastic.
  2. Jul 2018
    1. "a warp in space."

      Euclidian geometry presumes a uniform and constant arrangement of space. However, Einstein proposed (and others demonstrated) that space is "warped" around objects depending on their mass. The larger the mass, the greater the degree of warping.

      Because time is connected to space, it is also warped around massive objects.

    2. theory of relativity

      Einstein's theory of relativity is a two-part theory. Together, the two parts explain the motion of subatomic particles and gargantuan masses and address some of the shortcomings of earlier theories of motion.

      The theory is well known for combining the concepts of space and time, revealing that they are inseparable.

    1. Weathering

      Weathering is when pieces of plastic are mechanically broken up into smaller pieces. This is a problem because marine organisms can eat the smaller pieces but are unable to digest them. See the annotation for reference 16 for more information.

    2. Arctic sea ice

      Ice covers the Arctic Ocean. Over the course of a year, ice increases during fall and winter and melts during spring and summer. All of the ice does not melt entirely during the spring and summer; some of the ice persists from one year to the next.

    3. waste management infrastructure

      Waste management infrastructure is the collection of processes and facilities that properly dispose of wastes and reduce pollution. A major goal of waste management is often to reduce the amount of waste deposited in landfills by reuse or recycling.

    4. market sector

      Market sector is an economics term that describes a part of the economy made up of multiple industries. Examples of market sectors include energy, health care, consumer goods, media, utilities, etc.

    1. multigenerational aging schemes

      After a chemical is emitted it undergoes reactions in the atmosphere. The products of the initial chemical reaction then undergo additional reactions in the atmosphere. Multigenerational aging accounts for the reactions that occur after the initial reaction.